query
stringlengths 5
1.23k
| positive
stringlengths 53
15.2k
| id_
int64 0
252k
| task_name
stringlengths 87
242
| negative
sequencelengths 20
553
|
---|---|---|---|---|
Return either the full or truncated version of a QIIME - formatted taxonomy string . | def split_phylogeny ( p , level = "s" ) : level = level + "__" result = p . split ( level ) return result [ 0 ] + level + result [ 1 ] . split ( ";" ) [ 0 ] | 0 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L159-L177 | [
"def",
"listen_user_events",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"_user_id",
":",
"raise",
"AmigoCloudError",
"(",
"self",
".",
"error_msg",
"[",
"'logged_in_websockets'",
"]",
")",
"response",
"=",
"self",
".",
"get",
"(",
"'/me/start_websocket_session'",
")",
"websocket_session",
"=",
"response",
"[",
"'websocket_session'",
"]",
"auth_data",
"=",
"{",
"'userid'",
":",
"self",
".",
"_user_id",
",",
"'websocket_session'",
":",
"websocket_session",
"}",
"self",
".",
"amigosocket",
".",
"emit",
"(",
"'authenticate'",
",",
"auth_data",
")"
] |
Check to make sure the supplied directory path does not exist if so create it . The method catches OSError exceptions and returns a descriptive message instead of re - raising the error . | def ensure_dir ( d ) : if not os . path . exists ( d ) : try : os . makedirs ( d ) except OSError as oe : # should not happen with os.makedirs # ENOENT: No such file or directory if os . errno == errno . ENOENT : msg = twdd ( """One or more directories in the path ({}) do not exist. If
you are specifying a new directory for output, please ensure
all other directories in the path currently exist.""" ) return msg . format ( d ) else : msg = twdd ( """An error occurred trying to create the output directory
({}) with message: {}""" ) return msg . format ( d , oe . strerror ) | 1 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L180-L206 | [
"def",
"getTotalAssociations",
"(",
"self",
",",
"wifiInterfaceId",
"=",
"1",
",",
"timeout",
"=",
"1",
")",
":",
"namespace",
"=",
"Wifi",
".",
"getServiceType",
"(",
"\"getTotalAssociations\"",
")",
"+",
"str",
"(",
"wifiInterfaceId",
")",
"uri",
"=",
"self",
".",
"getControlURL",
"(",
"namespace",
")",
"results",
"=",
"self",
".",
"execute",
"(",
"uri",
",",
"namespace",
",",
"\"GetTotalAssociations\"",
",",
"timeout",
"=",
"timeout",
")",
"return",
"int",
"(",
"results",
"[",
"\"NewTotalAssociations\"",
"]",
")"
] |
Takes either a file path or an open file handle checks validity and returns an open file handle or raises an appropriate Exception . | def file_handle ( fnh , mode = "rU" ) : handle = None if isinstance ( fnh , file ) : if fnh . closed : raise ValueError ( "Input file is closed." ) handle = fnh elif isinstance ( fnh , str ) : handle = open ( fnh , mode ) return handle | 2 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L209-L231 | [
"def",
"get_batch_size",
"(",
"batch",
":",
"Union",
"[",
"Dict",
",",
"torch",
".",
"Tensor",
"]",
")",
"->",
"int",
":",
"if",
"isinstance",
"(",
"batch",
",",
"torch",
".",
"Tensor",
")",
":",
"return",
"batch",
".",
"size",
"(",
"0",
")",
"# type: ignore",
"elif",
"isinstance",
"(",
"batch",
",",
"Dict",
")",
":",
"return",
"get_batch_size",
"(",
"next",
"(",
"iter",
"(",
"batch",
".",
"values",
"(",
")",
")",
")",
")",
"else",
":",
"return",
"0"
] |
Find the user specified categories in the map and create a dictionary to contain the relevant data for each type within the categories . Multiple categories will have their types combined such that each possible combination will have its own entry in the dictionary . | def gather_categories ( imap , header , categories = None ) : # If no categories provided, return all SampleIDs if categories is None : return { "default" : DataCategory ( set ( imap . keys ( ) ) , { } ) } cat_ids = [ header . index ( cat ) for cat in categories if cat in header and "=" not in cat ] table = OrderedDict ( ) conditions = defaultdict ( set ) for i , cat in enumerate ( categories ) : if "=" in cat and cat . split ( "=" ) [ 0 ] in header : cat_name = header [ header . index ( cat . split ( "=" ) [ 0 ] ) ] conditions [ cat_name ] . add ( cat . split ( "=" ) [ 1 ] ) # If invalid categories or conditions identified, return all SampleIDs if not cat_ids and not conditions : return { "default" : DataCategory ( set ( imap . keys ( ) ) , { } ) } #If only category column given, return column-wise SampleIDs if cat_ids and not conditions : for sid , row in imap . items ( ) : cat_name = "_" . join ( [ row [ cid ] for cid in cat_ids ] ) if cat_name not in table : table [ cat_name ] = DataCategory ( set ( ) , { } ) table [ cat_name ] . sids . add ( sid ) return table # Collect all condition names cond_ids = set ( ) for k in conditions : try : cond_ids . add ( header . index ( k ) ) except ValueError : continue idx_to_test = set ( cat_ids ) . union ( cond_ids ) # If column name and condition given, return overlapping SampleIDs of column and # condition combinations for sid , row in imap . items ( ) : if all ( [ row [ header . index ( c ) ] in conditions [ c ] for c in conditions ] ) : key = "_" . join ( [ row [ idx ] for idx in idx_to_test ] ) try : assert key in table . keys ( ) except AssertionError : table [ key ] = DataCategory ( set ( ) , { } ) table [ key ] . sids . add ( sid ) try : assert len ( table ) > 0 except AssertionError : return { "default" : DataCategory ( set ( imap . keys ( ) ) , { } ) } else : return table | 3 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L238-L309 | [
"def",
"_getLPA",
"(",
"self",
")",
":",
"return",
"str",
"(",
"self",
".",
"line",
")",
"+",
"\":\"",
"+",
"str",
"(",
"self",
".",
"pos",
")",
"+",
"\":\"",
"+",
"str",
"(",
"self",
".",
"absPosition",
")"
] |
Parses the unifrac results file into a dictionary | def parse_unifrac ( unifracFN ) : with open ( unifracFN , "rU" ) as uF : first = uF . next ( ) . split ( "\t" ) lines = [ line . strip ( ) for line in uF ] unifrac = { "pcd" : OrderedDict ( ) , "eigvals" : [ ] , "varexp" : [ ] } if first [ 0 ] == "pc vector number" : return parse_unifrac_v1_8 ( unifrac , lines ) elif first [ 0 ] == "Eigvals" : return parse_unifrac_v1_9 ( unifrac , lines ) else : raise ValueError ( "File format not supported/recognized. Please check input " "unifrac file." ) | 4 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L311-L334 | [
"def",
"_get_port_speed_price_id",
"(",
"items",
",",
"port_speed",
",",
"no_public",
",",
"location",
")",
":",
"for",
"item",
"in",
"items",
":",
"if",
"utils",
".",
"lookup",
"(",
"item",
",",
"'itemCategory'",
",",
"'categoryCode'",
")",
"!=",
"'port_speed'",
":",
"continue",
"# Check for correct capacity and if the item matches private only",
"if",
"any",
"(",
"[",
"int",
"(",
"utils",
".",
"lookup",
"(",
"item",
",",
"'capacity'",
")",
")",
"!=",
"port_speed",
",",
"_is_private_port_speed_item",
"(",
"item",
")",
"!=",
"no_public",
",",
"not",
"_is_bonded",
"(",
"item",
")",
"]",
")",
":",
"continue",
"for",
"price",
"in",
"item",
"[",
"'prices'",
"]",
":",
"if",
"not",
"_matches_location",
"(",
"price",
",",
"location",
")",
":",
"continue",
"return",
"price",
"[",
"'id'",
"]",
"raise",
"SoftLayer",
".",
"SoftLayerError",
"(",
"\"Could not find valid price for port speed: '%s'\"",
"%",
"port_speed",
")"
] |
Function to parse data from older version of unifrac file obtained from Qiime version 1 . 8 and earlier . | def parse_unifrac_v1_8 ( unifrac , file_data ) : for line in file_data : if line == "" : break line = line . split ( "\t" ) unifrac [ "pcd" ] [ line [ 0 ] ] = [ float ( e ) for e in line [ 1 : ] ] unifrac [ "eigvals" ] = [ float ( entry ) for entry in file_data [ - 2 ] . split ( "\t" ) [ 1 : ] ] unifrac [ "varexp" ] = [ float ( entry ) for entry in file_data [ - 1 ] . split ( "\t" ) [ 1 : ] ] return unifrac | 5 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L337-L356 | [
"def",
"working_directory",
"(",
"self",
")",
":",
"if",
"self",
".",
"chroot_directory",
"and",
"not",
"self",
".",
"_working_directory",
".",
"startswith",
"(",
"self",
".",
"chroot_directory",
")",
":",
"return",
"self",
".",
"chroot_directory",
"+",
"self",
".",
"_working_directory",
"else",
":",
"return",
"self",
".",
"_working_directory"
] |
Function to parse data from newer version of unifrac file obtained from Qiime version 1 . 9 and later . | def parse_unifrac_v1_9 ( unifrac , file_data ) : unifrac [ "eigvals" ] = [ float ( entry ) for entry in file_data [ 0 ] . split ( "\t" ) ] unifrac [ "varexp" ] = [ float ( entry ) * 100 for entry in file_data [ 3 ] . split ( "\t" ) ] for line in file_data [ 8 : ] : if line == "" : break line = line . split ( "\t" ) unifrac [ "pcd" ] [ line [ 0 ] ] = [ float ( e ) for e in line [ 1 : ] ] return unifrac | 6 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L359-L378 | [
"def",
"stop",
"(",
"self",
")",
":",
"self",
".",
"_stopped",
"=",
"True",
"for",
"result",
"in",
"self",
".",
"_results",
":",
"result",
".",
"_set_result",
"(",
"Failure",
"(",
"ReactorStopped",
"(",
")",
")",
")"
] |
Determine color - category mapping . If color_column was specified then map the category names to color values . Otherwise use the palettable colors to automatically generate a set of colors for the group values . | def color_mapping ( sample_map , header , group_column , color_column = None ) : group_colors = OrderedDict ( ) group_gather = gather_categories ( sample_map , header , [ group_column ] ) if color_column is not None : color_gather = gather_categories ( sample_map , header , [ color_column ] ) # match sample IDs between color_gather and group_gather for group in group_gather : for color in color_gather : # allow incomplete assignment of colors, if group sids overlap at # all with the color sids, consider it a match if group_gather [ group ] . sids . intersection ( color_gather [ color ] . sids ) : group_colors [ group ] = color else : bcolors = itertools . cycle ( Set3_12 . hex_colors ) for group in group_gather : group_colors [ group ] = bcolors . next ( ) return group_colors | 7 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/util.py#L380-L419 | [
"def",
"update_topology",
"(",
")",
":",
"for",
"topology",
"in",
"Topology",
".",
"objects",
".",
"all",
"(",
")",
":",
"try",
":",
"topology",
".",
"update",
"(",
")",
"except",
"Exception",
"as",
"e",
":",
"msg",
"=",
"'Failed to update {}'",
".",
"format",
"(",
"topology",
".",
"__repr__",
"(",
")",
")",
"logger",
".",
"exception",
"(",
"msg",
")",
"print",
"(",
"'{0}: {1}\\n'",
"'see networking.log for more information\\n'",
".",
"format",
"(",
"msg",
",",
"e",
".",
"__class__",
")",
")"
] |
return reverse completment of read | def rev_c ( read ) : rc = [ ] rc_nucs = { 'A' : 'T' , 'T' : 'A' , 'G' : 'C' , 'C' : 'G' , 'N' : 'N' } for base in read : rc . extend ( rc_nucs [ base . upper ( ) ] ) return rc [ : : - 1 ] | 8 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/shuffle_genome.py#L27-L35 | [
"def",
"get_site_url",
"(",
")",
":",
"site_url",
"=",
"getattr",
"(",
"_THREAD_LOCAL",
",",
"_THREAD_SITE_URL",
",",
"None",
")",
"if",
"site_url",
"is",
"None",
":",
"site_url",
"=",
"SITE_URL",
"or",
"get_site_url_",
"(",
")",
"setattr",
"(",
"_THREAD_LOCAL",
",",
"_THREAD_SITE_URL",
",",
"site_url",
")",
"return",
"site_url"
] |
randomly shuffle genome | def shuffle_genome ( genome , cat , fraction = float ( 100 ) , plot = True , alpha = 0.1 , beta = 100000 , min_length = 1000 , max_length = 200000 ) : header = '>randomized_%s' % ( genome . name ) sequence = list ( '' . join ( [ i [ 1 ] for i in parse_fasta ( genome ) ] ) ) length = len ( sequence ) shuffled = [ ] # break genome into pieces while sequence is not False : s = int ( random . gammavariate ( alpha , beta ) ) if s <= min_length or s >= max_length : continue if len ( sequence ) < s : seq = sequence [ 0 : ] else : seq = sequence [ 0 : s ] sequence = sequence [ s : ] # if bool(random.getrandbits(1)) is True: # seq = rev_c(seq) # print('fragment length: %s reverse complement: True' % ('{:,}'.format(s)), file=sys.stderr) # else: # print('fragment length: %s reverse complement: False' % ('{:,}'.format(s)), file=sys.stderr) shuffled . append ( '' . join ( seq ) ) if sequence == [ ] : break # shuffle pieces random . shuffle ( shuffled ) # subset fragments if fraction == float ( 100 ) : subset = shuffled else : max_pieces = int ( length * fraction / 100 ) subset , total = [ ] , 0 for fragment in shuffled : length = len ( fragment ) if total + length <= max_pieces : subset . append ( fragment ) total += length else : diff = max_pieces - total subset . append ( fragment [ 0 : diff ] ) break # combine sequences, if requested if cat is True : yield [ header , '' . join ( subset ) ] else : for i , seq in enumerate ( subset ) : yield [ '%s fragment:%s' % ( header , i ) , seq ] | 9 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/shuffle_genome.py#L37-L87 | [
"def",
"process_new_issues",
"(",
"self",
",",
"volumes",
",",
"existing_issues",
")",
":",
"new_issues",
"=",
"{",
"}",
"for",
"issue_id",
",",
"volume",
"in",
"volumes",
".",
"items",
"(",
")",
":",
"state",
"=",
"EBSIssueState",
".",
"DETECTED",
".",
"value",
"if",
"issue_id",
"in",
"existing_issues",
":",
"issue",
"=",
"existing_issues",
"[",
"issue_id",
"]",
"data",
"=",
"{",
"'state'",
":",
"state",
",",
"'notes'",
":",
"issue",
".",
"notes",
",",
"'last_notice'",
":",
"issue",
".",
"last_notice",
"}",
"if",
"issue",
".",
"update",
"(",
"data",
")",
":",
"new_issues",
".",
"setdefault",
"(",
"issue",
".",
"volume",
".",
"account",
",",
"[",
"]",
")",
".",
"append",
"(",
"issue",
")",
"self",
".",
"log",
".",
"debug",
"(",
"'Updated EBSVolumeAuditIssue {}'",
".",
"format",
"(",
"issue_id",
")",
")",
"else",
":",
"properties",
"=",
"{",
"'volume_id'",
":",
"volume",
".",
"id",
",",
"'account_id'",
":",
"volume",
".",
"account_id",
",",
"'location'",
":",
"volume",
".",
"location",
",",
"'state'",
":",
"state",
",",
"'last_change'",
":",
"datetime",
".",
"now",
"(",
")",
",",
"'last_notice'",
":",
"None",
",",
"'notes'",
":",
"[",
"]",
"}",
"issue",
"=",
"EBSVolumeAuditIssue",
".",
"create",
"(",
"issue_id",
",",
"properties",
"=",
"properties",
")",
"new_issues",
".",
"setdefault",
"(",
"issue",
".",
"volume",
".",
"account",
",",
"[",
"]",
")",
".",
"append",
"(",
"issue",
")",
"return",
"new_issues"
] |
If the fit contains statistically insignificant parameters remove them . Returns a pruned fit where all parameters have p - values of the t - statistic below p_max | def _prune ( self , fit , p_max ) : def remove_from_model_desc ( x , model_desc ) : """
Return a model_desc without x
""" rhs_termlist = [ ] for t in model_desc . rhs_termlist : if not t . factors : # intercept, add anyway rhs_termlist . append ( t ) elif not x == t . factors [ 0 ] . _varname : # this is not the term with x rhs_termlist . append ( t ) md = ModelDesc ( model_desc . lhs_termlist , rhs_termlist ) return md corrected_model_desc = ModelDesc ( fit . model . formula . lhs_termlist [ : ] , fit . model . formula . rhs_termlist [ : ] ) pars_to_prune = fit . pvalues . where ( fit . pvalues > p_max ) . dropna ( ) . index . tolist ( ) try : pars_to_prune . remove ( 'Intercept' ) except : pass while pars_to_prune : corrected_model_desc = remove_from_model_desc ( pars_to_prune [ 0 ] , corrected_model_desc ) fit = fm . ols ( corrected_model_desc , data = self . df ) . fit ( ) pars_to_prune = fit . pvalues . where ( fit . pvalues > p_max ) . dropna ( ) . index . tolist ( ) try : pars_to_prune . remove ( 'Intercept' ) except : pass return fit | 10 | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/regression.py#L222-L272 | [
"def",
"write_asc_file",
"(",
"filename",
",",
"data",
",",
"xsize",
",",
"ysize",
",",
"geotransform",
",",
"nodata_value",
")",
":",
"UtilClass",
".",
"mkdir",
"(",
"os",
".",
"path",
".",
"dirname",
"(",
"FileClass",
".",
"get_file_fullpath",
"(",
"filename",
")",
")",
")",
"header",
"=",
"'NCOLS %d\\n'",
"'NROWS %d\\n'",
"'XLLCENTER %f\\n'",
"'YLLCENTER %f\\n'",
"'CELLSIZE %f\\n'",
"'NODATA_VALUE %f'",
"%",
"(",
"xsize",
",",
"ysize",
",",
"geotransform",
"[",
"0",
"]",
"+",
"0.5",
"*",
"geotransform",
"[",
"1",
"]",
",",
"geotransform",
"[",
"3",
"]",
"-",
"(",
"ysize",
"-",
"0.5",
")",
"*",
"geotransform",
"[",
"1",
"]",
",",
"geotransform",
"[",
"1",
"]",
",",
"nodata_value",
")",
"with",
"open",
"(",
"filename",
",",
"'w'",
",",
"encoding",
"=",
"'utf-8'",
")",
"as",
"f",
":",
"f",
".",
"write",
"(",
"header",
")",
"for",
"i",
"in",
"range",
"(",
"0",
",",
"ysize",
")",
":",
"for",
"j",
"in",
"range",
"(",
"0",
",",
"xsize",
")",
":",
"f",
".",
"write",
"(",
"'%s\\t'",
"%",
"repr",
"(",
"data",
"[",
"i",
"]",
"[",
"j",
"]",
")",
")",
"f",
".",
"write",
"(",
"'\\n'",
")",
"f",
".",
"close",
"(",
")"
] |
Return the best fit based on rsquared | def find_best_rsquared ( list_of_fits ) : res = sorted ( list_of_fits , key = lambda x : x . rsquared ) return res [ - 1 ] | 11 | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/regression.py#L275-L278 | [
"def",
"message",
"(",
"self",
",",
"assistant_id",
",",
"session_id",
",",
"input",
"=",
"None",
",",
"context",
"=",
"None",
",",
"*",
"*",
"kwargs",
")",
":",
"if",
"assistant_id",
"is",
"None",
":",
"raise",
"ValueError",
"(",
"'assistant_id must be provided'",
")",
"if",
"session_id",
"is",
"None",
":",
"raise",
"ValueError",
"(",
"'session_id must be provided'",
")",
"if",
"input",
"is",
"not",
"None",
":",
"input",
"=",
"self",
".",
"_convert_model",
"(",
"input",
",",
"MessageInput",
")",
"if",
"context",
"is",
"not",
"None",
":",
"context",
"=",
"self",
".",
"_convert_model",
"(",
"context",
",",
"MessageContext",
")",
"headers",
"=",
"{",
"}",
"if",
"'headers'",
"in",
"kwargs",
":",
"headers",
".",
"update",
"(",
"kwargs",
".",
"get",
"(",
"'headers'",
")",
")",
"sdk_headers",
"=",
"get_sdk_headers",
"(",
"'conversation'",
",",
"'V2'",
",",
"'message'",
")",
"headers",
".",
"update",
"(",
"sdk_headers",
")",
"params",
"=",
"{",
"'version'",
":",
"self",
".",
"version",
"}",
"data",
"=",
"{",
"'input'",
":",
"input",
",",
"'context'",
":",
"context",
"}",
"url",
"=",
"'/v2/assistants/{0}/sessions/{1}/message'",
".",
"format",
"(",
"*",
"self",
".",
"_encode_path_vars",
"(",
"assistant_id",
",",
"session_id",
")",
")",
"response",
"=",
"self",
".",
"request",
"(",
"method",
"=",
"'POST'",
",",
"url",
"=",
"url",
",",
"headers",
"=",
"headers",
",",
"params",
"=",
"params",
",",
"json",
"=",
"data",
",",
"accept_json",
"=",
"True",
")",
"return",
"response"
] |
Return a df with predictions and confidence interval | def _predict ( self , fit , df ) : # Add model results to data as column 'predictions' df_res = df . copy ( ) if 'Intercept' in fit . model . exog_names : df_res [ 'Intercept' ] = 1.0 df_res [ 'predicted' ] = fit . predict ( df_res ) if not self . allow_negative_predictions : df_res . loc [ df_res [ 'predicted' ] < 0 , 'predicted' ] = 0 prstd , interval_l , interval_u = wls_prediction_std ( fit , df_res [ fit . model . exog_names ] , alpha = 1 - self . confint ) df_res [ 'interval_l' ] = interval_l df_res [ 'interval_u' ] = interval_u if 'Intercept' in df_res : df_res . drop ( labels = [ 'Intercept' ] , axis = 1 , inplace = True ) return df_res | 12 | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/regression.py#L292-L338 | [
"def",
"user_deleted_from_site_event",
"(",
"event",
")",
":",
"userid",
"=",
"event",
".",
"principal",
"catalog",
"=",
"api",
".",
"portal",
".",
"get_tool",
"(",
"'portal_catalog'",
")",
"query",
"=",
"{",
"'object_provides'",
":",
"WORKSPACE_INTERFACE",
"}",
"query",
"[",
"'workspace_members'",
"]",
"=",
"userid",
"workspaces",
"=",
"[",
"IWorkspace",
"(",
"b",
".",
"_unrestrictedGetObject",
"(",
")",
")",
"for",
"b",
"in",
"catalog",
".",
"unrestrictedSearchResults",
"(",
"query",
")",
"]",
"for",
"workspace",
"in",
"workspaces",
":",
"workspace",
".",
"remove_from_team",
"(",
"userid",
")"
] |
Calculate the relative abundance of each OTUID in a Sample . | def relative_abundance ( biomf , sampleIDs = None ) : if sampleIDs is None : sampleIDs = biomf . ids ( ) else : try : for sid in sampleIDs : assert sid in biomf . ids ( ) except AssertionError : raise ValueError ( "\nError while calculating relative abundances: The sampleIDs provided do" " not match the sampleIDs in biom file. Please double check the sampleIDs" " provided.\n" ) otuIDs = biomf . ids ( axis = "observation" ) norm_biomf = biomf . norm ( inplace = False ) return { sample : { otuID : norm_biomf . get_value_by_ids ( otuID , sample ) for otuID in otuIDs } for sample in sampleIDs } | 13 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L11-L41 | [
"def",
"getNewQuery",
"(",
"connection",
"=",
"None",
",",
"commitOnEnd",
"=",
"False",
",",
"*",
"args",
",",
"*",
"*",
"kargs",
")",
":",
"if",
"connection",
"is",
"None",
":",
"return",
"query",
".",
"PySQLQuery",
"(",
"getNewConnection",
"(",
"*",
"args",
",",
"*",
"*",
"kargs",
")",
",",
"commitOnEnd",
"=",
"commitOnEnd",
")",
"else",
":",
"#Updated 7/24/08 to include commitOnEnd here",
"#-Chandler Prall",
"return",
"query",
".",
"PySQLQuery",
"(",
"connection",
",",
"commitOnEnd",
"=",
"commitOnEnd",
")"
] |
Calculate the mean OTU abundance percentage . | def mean_otu_pct_abundance ( ra , otuIDs ) : sids = ra . keys ( ) otumeans = defaultdict ( int ) for oid in otuIDs : otumeans [ oid ] = sum ( [ ra [ sid ] [ oid ] for sid in sids if oid in ra [ sid ] ] ) / len ( sids ) * 100 return otumeans | 14 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L44-L67 | [
"def",
"format_log_context",
"(",
"msg",
",",
"connection",
"=",
"None",
",",
"keyspace",
"=",
"None",
")",
":",
"connection_info",
"=",
"connection",
"or",
"'DEFAULT_CONNECTION'",
"if",
"keyspace",
":",
"msg",
"=",
"'[Connection: {0}, Keyspace: {1}] {2}'",
".",
"format",
"(",
"connection_info",
",",
"keyspace",
",",
"msg",
")",
"else",
":",
"msg",
"=",
"'[Connection: {0}] {1}'",
".",
"format",
"(",
"connection_info",
",",
"msg",
")",
"return",
"msg"
] |
Calculate the mean relative abundance percentage . | def MRA ( biomf , sampleIDs = None , transform = None ) : ra = relative_abundance ( biomf , sampleIDs ) if transform is not None : ra = { sample : { otuID : transform ( abd ) for otuID , abd in ra [ sample ] . items ( ) } for sample in ra . keys ( ) } otuIDs = biomf . ids ( axis = "observation" ) return mean_otu_pct_abundance ( ra , otuIDs ) | 15 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L70-L92 | [
"def",
"unpack_rsp",
"(",
"cls",
",",
"rsp_pb",
")",
":",
"ret_type",
"=",
"rsp_pb",
".",
"retType",
"ret_msg",
"=",
"rsp_pb",
".",
"retMsg",
"if",
"ret_type",
"!=",
"RET_OK",
":",
"return",
"RET_ERROR",
",",
"ret_msg",
",",
"None",
"res",
"=",
"{",
"}",
"if",
"rsp_pb",
".",
"HasField",
"(",
"'s2c'",
")",
":",
"res",
"[",
"'server_version'",
"]",
"=",
"rsp_pb",
".",
"s2c",
".",
"serverVer",
"res",
"[",
"'login_user_id'",
"]",
"=",
"rsp_pb",
".",
"s2c",
".",
"loginUserID",
"res",
"[",
"'conn_id'",
"]",
"=",
"rsp_pb",
".",
"s2c",
".",
"connID",
"res",
"[",
"'conn_key'",
"]",
"=",
"rsp_pb",
".",
"s2c",
".",
"connAESKey",
"res",
"[",
"'keep_alive_interval'",
"]",
"=",
"rsp_pb",
".",
"s2c",
".",
"keepAliveInterval",
"else",
":",
"return",
"RET_ERROR",
",",
"\"rsp_pb error\"",
",",
"None",
"return",
"RET_OK",
",",
"\"\"",
",",
"res"
] |
Calculate the total number of sequences in each OTU or SampleID . | def raw_abundance ( biomf , sampleIDs = None , sample_abd = True ) : results = defaultdict ( int ) if sampleIDs is None : sampleIDs = biomf . ids ( ) else : try : for sid in sampleIDs : assert sid in biomf . ids ( ) except AssertionError : raise ValueError ( "\nError while calculating raw total abundances: The sampleIDs provided " "do not match the sampleIDs in biom file. Please double check the " "sampleIDs provided.\n" ) otuIDs = biomf . ids ( axis = "observation" ) for sampleID in sampleIDs : for otuID in otuIDs : abd = biomf . get_value_by_ids ( otuID , sampleID ) if sample_abd : results [ sampleID ] += abd else : results [ otuID ] += abd return results | 16 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L95-L135 | [
"def",
"internal2external_grad",
"(",
"xi",
",",
"bounds",
")",
":",
"ge",
"=",
"np",
".",
"empty_like",
"(",
"xi",
")",
"for",
"i",
",",
"(",
"v",
",",
"bound",
")",
"in",
"enumerate",
"(",
"zip",
"(",
"xi",
",",
"bounds",
")",
")",
":",
"a",
"=",
"bound",
"[",
"0",
"]",
"# minimum",
"b",
"=",
"bound",
"[",
"1",
"]",
"# maximum",
"if",
"a",
"==",
"None",
"and",
"b",
"==",
"None",
":",
"# No constraints",
"ge",
"[",
"i",
"]",
"=",
"1.0",
"elif",
"b",
"==",
"None",
":",
"# only min",
"ge",
"[",
"i",
"]",
"=",
"v",
"/",
"np",
".",
"sqrt",
"(",
"v",
"**",
"2",
"+",
"1",
")",
"elif",
"a",
"==",
"None",
":",
"# only max",
"ge",
"[",
"i",
"]",
"=",
"-",
"v",
"/",
"np",
".",
"sqrt",
"(",
"v",
"**",
"2",
"+",
"1",
")",
"else",
":",
"# both min and max",
"ge",
"[",
"i",
"]",
"=",
"(",
"b",
"-",
"a",
")",
"*",
"np",
".",
"cos",
"(",
"v",
")",
"/",
"2.",
"return",
"ge"
] |
Function to transform the total abundance calculation for each sample ID to another format based on user given transformation function . | def transform_raw_abundance ( biomf , fn = math . log10 , sampleIDs = None , sample_abd = True ) : totals = raw_abundance ( biomf , sampleIDs , sample_abd ) return { sid : fn ( abd ) for sid , abd in totals . items ( ) } | 17 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/phylotoast/biom_calc.py#L138-L155 | [
"def",
"parse_instance",
"(",
"self",
",",
"global_params",
",",
"region",
",",
"reservation",
")",
":",
"for",
"i",
"in",
"reservation",
"[",
"'Instances'",
"]",
":",
"instance",
"=",
"{",
"}",
"vpc_id",
"=",
"i",
"[",
"'VpcId'",
"]",
"if",
"'VpcId'",
"in",
"i",
"and",
"i",
"[",
"'VpcId'",
"]",
"else",
"ec2_classic",
"manage_dictionary",
"(",
"self",
".",
"vpcs",
",",
"vpc_id",
",",
"VPCConfig",
"(",
"self",
".",
"vpc_resource_types",
")",
")",
"instance",
"[",
"'reservation_id'",
"]",
"=",
"reservation",
"[",
"'ReservationId'",
"]",
"instance",
"[",
"'id'",
"]",
"=",
"i",
"[",
"'InstanceId'",
"]",
"get_name",
"(",
"i",
",",
"instance",
",",
"'InstanceId'",
")",
"get_keys",
"(",
"i",
",",
"instance",
",",
"[",
"'KeyName'",
",",
"'LaunchTime'",
",",
"'InstanceType'",
",",
"'State'",
",",
"'IamInstanceProfile'",
",",
"'SubnetId'",
"]",
")",
"# Network interfaces & security groups",
"manage_dictionary",
"(",
"instance",
",",
"'network_interfaces'",
",",
"{",
"}",
")",
"for",
"eni",
"in",
"i",
"[",
"'NetworkInterfaces'",
"]",
":",
"nic",
"=",
"{",
"}",
"get_keys",
"(",
"eni",
",",
"nic",
",",
"[",
"'Association'",
",",
"'Groups'",
",",
"'PrivateIpAddresses'",
",",
"'SubnetId'",
",",
"'Ipv6Addresses'",
"]",
")",
"instance",
"[",
"'network_interfaces'",
"]",
"[",
"eni",
"[",
"'NetworkInterfaceId'",
"]",
"]",
"=",
"nic",
"self",
".",
"vpcs",
"[",
"vpc_id",
"]",
".",
"instances",
"[",
"i",
"[",
"'InstanceId'",
"]",
"]",
"=",
"instance"
] |
Compute the Mann - Whitney U test for unequal group sample sizes . | def print_MannWhitneyU ( div_calc ) : try : x = div_calc . values ( ) [ 0 ] . values ( ) y = div_calc . values ( ) [ 1 ] . values ( ) except : return "Error setting up input arrays for Mann-Whitney U Test. Skipping " "significance testing." T , p = stats . mannwhitneyu ( x , y ) print "\nMann-Whitney U test statistic:" , T print "Two-tailed p-value: {}" . format ( 2 * p ) | 18 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/diversity.py#L54-L66 | [
"def",
"_extract_ocsp_certs",
"(",
"self",
",",
"ocsp_response",
")",
":",
"status",
"=",
"ocsp_response",
"[",
"'response_status'",
"]",
".",
"native",
"if",
"status",
"==",
"'successful'",
":",
"response_bytes",
"=",
"ocsp_response",
"[",
"'response_bytes'",
"]",
"if",
"response_bytes",
"[",
"'response_type'",
"]",
".",
"native",
"==",
"'basic_ocsp_response'",
":",
"response",
"=",
"response_bytes",
"[",
"'response'",
"]",
".",
"parsed",
"if",
"response",
"[",
"'certs'",
"]",
":",
"for",
"other_cert",
"in",
"response",
"[",
"'certs'",
"]",
":",
"if",
"self",
".",
"certificate_registry",
".",
"add_other_cert",
"(",
"other_cert",
")",
":",
"self",
".",
"_revocation_certs",
"[",
"other_cert",
".",
"issuer_serial",
"]",
"=",
"other_cert"
] |
Compute the Kruskal - Wallis H - test for independent samples . A typical rule is that each group must have at least 5 measurements . | def print_KruskalWallisH ( div_calc ) : calc = defaultdict ( list ) try : for k1 , v1 in div_calc . iteritems ( ) : for k2 , v2 in v1 . iteritems ( ) : calc [ k1 ] . append ( v2 ) except : return "Error setting up input arrays for Kruskal-Wallis H-Test. Skipping " "significance testing." h , p = stats . kruskal ( * calc . values ( ) ) print "\nKruskal-Wallis H-test statistic for {} groups: {}" . format ( str ( len ( div_calc ) ) , h ) print "p-value: {}" . format ( p ) | 19 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/diversity.py#L69-L84 | [
"def",
"_record_offset",
"(",
"self",
")",
":",
"offset",
"=",
"self",
".",
"blob_file",
".",
"tell",
"(",
")",
"self",
".",
"event_offsets",
".",
"append",
"(",
"offset",
")"
] |
Parses the given options passed in at the command line . | def handle_program_options ( ) : parser = argparse . ArgumentParser ( description = "Calculate the alpha diversity\
of a set of samples using one or more \
metrics and output a kernal density \
estimator-smoothed histogram of the \
results." ) parser . add_argument ( "-m" , "--map_file" , help = "QIIME mapping file." ) parser . add_argument ( "-i" , "--biom_fp" , help = "Path to the BIOM table" ) parser . add_argument ( "-c" , "--category" , help = "Specific category from the mapping file." ) parser . add_argument ( "-d" , "--diversity" , default = [ "shannon" ] , nargs = "+" , help = "The alpha diversity metric. Default \
value is 'shannon', which will calculate the Shannon\
entropy. Multiple metrics can be specified (space separated).\
The full list of metrics is available at:\
http://scikit-bio.org/docs/latest/generated/skbio.diversity.alpha.html.\
Beta diversity metrics will be supported in the future." ) parser . add_argument ( "--x_label" , default = [ None ] , nargs = "+" , help = "The name of the diversity metric to be displayed on the\
plot as the X-axis label. If multiple metrics are specified,\
then multiple entries for the X-axis label should be given." ) parser . add_argument ( "--color_by" , help = "A column name in the mapping file containing\
hexadecimal (#FF0000) color values that will\
be used to color the groups. Each sample ID must\
have a color entry." ) parser . add_argument ( "--plot_title" , default = "" , help = "A descriptive title that will appear at the top \
of the output plot. Surround with quotes if there are\
spaces in the title." ) parser . add_argument ( "-o" , "--output_dir" , default = "." , help = "The directory plots will be saved to." ) parser . add_argument ( "--image_type" , default = "png" , help = "The type of image to save: png, svg, pdf, eps, etc..." ) parser . add_argument ( "--save_calculations" , help = "Path and name of text file to store the calculated " "diversity metrics." ) parser . add_argument ( "--suppress_stats" , action = "store_true" , help = "Do not display " "significance testing results which are shown by default." ) parser . add_argument ( "--show_available_metrics" , action = "store_true" , help = "Supply this parameter to see which alpha diversity metrics " " are available for usage. No calculations will be performed" " if this parameter is provided." ) return parser . parse_args ( ) | 20 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/diversity.py#L122-L168 | [
"def",
"identical",
"(",
"self",
",",
"other",
")",
":",
"try",
":",
"return",
"(",
"self",
".",
"name",
"==",
"other",
".",
"name",
"and",
"self",
".",
"_all_compat",
"(",
"other",
",",
"'identical'",
")",
")",
"except",
"(",
"TypeError",
",",
"AttributeError",
")",
":",
"return",
"False"
] |
make blast db | def blastdb ( fasta , maxfile = 10000000 ) : db = fasta . rsplit ( '.' , 1 ) [ 0 ] type = check_type ( fasta ) if type == 'nucl' : type = [ 'nhr' , type ] else : type = [ 'phr' , type ] if os . path . exists ( '%s.%s' % ( db , type [ 0 ] ) ) is False and os . path . exists ( '%s.00.%s' % ( db , type [ 0 ] ) ) is False : print ( '# ... making blastdb for: %s' % ( fasta ) , file = sys . stderr ) os . system ( 'makeblastdb \
-in %s -out %s -dbtype %s -max_file_sz %s >> log.txt' % ( fasta , db , type [ 1 ] , maxfile ) ) else : print ( '# ... database found for: %s' % ( fasta ) , file = sys . stderr ) return db | 21 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/search.py#L28-L46 | [
"def",
"access_required",
"(",
"config",
"=",
"None",
")",
":",
"def",
"_access_required",
"(",
"http_method_handler",
")",
":",
"def",
"secure_http_method_handler",
"(",
"self",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"# authentication context must be set",
"if",
"not",
"self",
".",
"__provider_config__",
".",
"authentication",
":",
"_message",
"=",
"\"Service available to authenticated users only, no auth context provider set in handler\"",
"authentication_error",
"=",
"prestans",
".",
"exception",
".",
"AuthenticationError",
"(",
"_message",
")",
"authentication_error",
".",
"request",
"=",
"self",
".",
"request",
"raise",
"authentication_error",
"# check for access by calling is_authorized_user",
"if",
"not",
"self",
".",
"__provider_config__",
".",
"authentication",
".",
"is_authorized_user",
"(",
"config",
")",
":",
"_message",
"=",
"\"Service available to authorized users only\"",
"authorization_error",
"=",
"prestans",
".",
"exception",
".",
"AuthorizationError",
"(",
"_message",
")",
"authorization_error",
".",
"request",
"=",
"self",
".",
"request",
"raise",
"authorization_error",
"http_method_handler",
"(",
"self",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
"return",
"wraps",
"(",
"http_method_handler",
")",
"(",
"secure_http_method_handler",
")",
"return",
"_access_required"
] |
make usearch db | def usearchdb ( fasta , alignment = 'local' , usearch_loc = 'usearch' ) : if '.udb' in fasta : print ( '# ... database found: %s' % ( fasta ) , file = sys . stderr ) return fasta type = check_type ( fasta ) db = '%s.%s.udb' % ( fasta . rsplit ( '.' , 1 ) [ 0 ] , type ) if os . path . exists ( db ) is False : print ( '# ... making usearch db for: %s' % ( fasta ) , file = sys . stderr ) if alignment == 'local' : os . system ( '%s -makeudb_ublast %s -output %s >> log.txt' % ( usearch_loc , fasta , db ) ) elif alignment == 'global' : os . system ( '%s -makeudb_usearch %s -output %s >> log.txt' % ( usearch_loc , fasta , db ) ) else : print ( '# ... database found for: %s' % ( fasta ) , file = sys . stderr ) return db | 22 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/search.py#L68-L85 | [
"def",
"noise",
"(",
"mesh",
",",
"magnitude",
"=",
"None",
")",
":",
"if",
"magnitude",
"is",
"None",
":",
"magnitude",
"=",
"mesh",
".",
"scale",
"/",
"100.0",
"random",
"=",
"(",
"np",
".",
"random",
".",
"random",
"(",
"mesh",
".",
"vertices",
".",
"shape",
")",
"-",
".5",
")",
"*",
"magnitude",
"vertices_noise",
"=",
"mesh",
".",
"vertices",
".",
"copy",
"(",
")",
"+",
"random",
"# make sure we've re- ordered faces randomly",
"triangles",
"=",
"np",
".",
"random",
".",
"permutation",
"(",
"vertices_noise",
"[",
"mesh",
".",
"faces",
"]",
")",
"mesh_type",
"=",
"util",
".",
"type_named",
"(",
"mesh",
",",
"'Trimesh'",
")",
"permutated",
"=",
"mesh_type",
"(",
"*",
"*",
"triangles_module",
".",
"to_kwargs",
"(",
"triangles",
")",
")",
"return",
"permutated"
] |
Pretty print . | def _pp ( dict_data ) : for key , val in dict_data . items ( ) : # pylint: disable=superfluous-parens print ( '{0:<11}: {1}' . format ( key , val ) ) | 23 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/control.py#L11-L15 | [
"def",
"_add_dependency",
"(",
"self",
",",
"dependency",
",",
"var_name",
"=",
"None",
")",
":",
"if",
"var_name",
"is",
"None",
":",
"var_name",
"=",
"next",
"(",
"self",
".",
"temp_var_names",
")",
"# Don't add duplicate dependencies",
"if",
"(",
"dependency",
",",
"var_name",
")",
"not",
"in",
"self",
".",
"dependencies",
":",
"self",
".",
"dependencies",
".",
"append",
"(",
"(",
"dependency",
",",
"var_name",
")",
")",
"return",
"var_name"
] |
Print licenses . | def print_licences ( params , metadata ) : if hasattr ( params , 'licenses' ) : if params . licenses : _pp ( metadata . licenses_desc ( ) ) sys . exit ( 0 ) | 24 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/control.py#L27-L36 | [
"def",
"on_response",
"(",
"self",
",",
"ch",
",",
"method_frame",
",",
"props",
",",
"body",
")",
":",
"LOGGER",
".",
"debug",
"(",
"\"rabbitmq.Requester.on_response\"",
")",
"if",
"self",
".",
"corr_id",
"==",
"props",
".",
"correlation_id",
":",
"self",
".",
"response",
"=",
"{",
"'props'",
":",
"props",
",",
"'body'",
":",
"body",
"}",
"else",
":",
"LOGGER",
".",
"warn",
"(",
"\"rabbitmq.Requester.on_response - discarded response : \"",
"+",
"str",
"(",
"props",
".",
"correlation_id",
")",
")",
"LOGGER",
".",
"debug",
"(",
"\"natsd.Requester.on_response - discarded response : \"",
"+",
"str",
"(",
"{",
"'properties'",
":",
"props",
",",
"'body'",
":",
"body",
"}",
")",
")"
] |
Check repository existence . | def check_repository_existence ( params ) : repodir = os . path . join ( params . outdir , params . name ) if os . path . isdir ( repodir ) : raise Conflict ( 'Package repository "{0}" has already exists.' . format ( repodir ) ) | 25 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/control.py#L39-L47 | [
"def",
"OnAdjustVolume",
"(",
"self",
",",
"event",
")",
":",
"self",
".",
"volume",
"=",
"self",
".",
"player",
".",
"audio_get_volume",
"(",
")",
"if",
"event",
".",
"GetWheelRotation",
"(",
")",
"<",
"0",
":",
"self",
".",
"volume",
"=",
"max",
"(",
"0",
",",
"self",
".",
"volume",
"-",
"10",
")",
"elif",
"event",
".",
"GetWheelRotation",
"(",
")",
">",
"0",
":",
"self",
".",
"volume",
"=",
"min",
"(",
"200",
",",
"self",
".",
"volume",
"+",
"10",
")",
"self",
".",
"player",
".",
"audio_set_volume",
"(",
"self",
".",
"volume",
")"
] |
Generate package repository . | def generate_package ( params ) : pkg_data = package . PackageData ( params ) pkg_tree = package . PackageTree ( pkg_data ) pkg_tree . generate ( ) pkg_tree . move ( ) VCS ( os . path . join ( pkg_tree . outdir , pkg_tree . name ) , pkg_tree . pkg_data ) | 26 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/control.py#L59-L68 | [
"def",
"main",
"(",
")",
":",
"alarm",
"=",
"XBeeAlarm",
"(",
"'/dev/ttyUSB0'",
",",
"'\\x56\\x78'",
")",
"routine",
"=",
"SimpleWakeupRoutine",
"(",
"alarm",
")",
"from",
"time",
"import",
"sleep",
"while",
"True",
":",
"\"\"\"\n Run the routine with 10 second delays\n \"\"\"",
"try",
":",
"print",
"\"Waiting 5 seconds...\"",
"sleep",
"(",
"5",
")",
"print",
"\"Firing\"",
"routine",
".",
"trigger",
"(",
")",
"except",
"KeyboardInterrupt",
":",
"break"
] |
print single reads to stderr | def print_single ( line , rev ) : if rev is True : seq = rc ( [ '' , line [ 9 ] ] ) [ 1 ] qual = line [ 10 ] [ : : - 1 ] else : seq = line [ 9 ] qual = line [ 10 ] fq = [ '@%s' % line [ 0 ] , seq , '+%s' % line [ 0 ] , qual ] print ( '\n' . join ( fq ) , file = sys . stderr ) | 27 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/sam2fastq.py#L13-L24 | [
"def",
"set_cache_dir",
"(",
"directory",
")",
":",
"global",
"cache_dir",
"if",
"directory",
"is",
"None",
":",
"cache_dir",
"=",
"None",
"return",
"if",
"not",
"os",
".",
"path",
".",
"exists",
"(",
"directory",
")",
":",
"os",
".",
"makedirs",
"(",
"directory",
")",
"if",
"not",
"os",
".",
"path",
".",
"isdir",
"(",
"directory",
")",
":",
"raise",
"ValueError",
"(",
"\"not a directory\"",
")",
"cache_dir",
"=",
"directory"
] |
convert sam to fastq | def sam2fastq ( sam , singles = False , force = False ) : L , R = None , None for line in sam : if line . startswith ( '@' ) is True : continue line = line . strip ( ) . split ( ) bit = [ True if i == '1' else False for i in bin ( int ( line [ 1 ] ) ) . split ( 'b' ) [ 1 ] [ : : - 1 ] ] while len ( bit ) < 8 : bit . append ( False ) pair , proper , na , nap , rev , mrev , left , right = bit # make sure read is paired if pair is False : if singles is True : print_single ( line , rev ) continue # check if sequence is reverse-complemented if rev is True : seq = rc ( [ '' , line [ 9 ] ] ) [ 1 ] qual = line [ 10 ] [ : : - 1 ] else : seq = line [ 9 ] qual = line [ 10 ] # check if read is forward or reverse, return when both have been found if left is True : if L is not None and force is False : print ( 'sam file is not sorted' , file = sys . stderr ) print ( '\te.g.: %s' % ( line [ 0 ] ) , file = sys . stderr ) exit ( ) if L is not None : L = None continue L = [ '@%s' % line [ 0 ] , seq , '+%s' % line [ 0 ] , qual ] if R is not None : yield L yield R L , R = None , None if right is True : if R is not None and force is False : print ( 'sam file is not sorted' , file = sys . stderr ) print ( '\te.g.: %s' % ( line [ 0 ] ) , file = sys . stderr ) exit ( ) if R is not None : R = None continue R = [ '@%s' % line [ 0 ] , seq , '+%s' % line [ 0 ] , qual ] if L is not None : yield L yield R L , R = None , None | 28 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/sam2fastq.py#L26-L78 | [
"def",
"get_changed_devices",
"(",
"self",
",",
"timestamp",
")",
":",
"if",
"timestamp",
"is",
"None",
":",
"payload",
"=",
"{",
"}",
"else",
":",
"payload",
"=",
"{",
"'timeout'",
":",
"SUBSCRIPTION_WAIT",
",",
"'minimumdelay'",
":",
"SUBSCRIPTION_MIN_WAIT",
"}",
"payload",
".",
"update",
"(",
"timestamp",
")",
"# double the timeout here so requests doesn't timeout before vera",
"payload",
".",
"update",
"(",
"{",
"'id'",
":",
"'lu_sdata'",
",",
"}",
")",
"logger",
".",
"debug",
"(",
"\"get_changed_devices() requesting payload %s\"",
",",
"str",
"(",
"payload",
")",
")",
"r",
"=",
"self",
".",
"data_request",
"(",
"payload",
",",
"TIMEOUT",
"*",
"2",
")",
"r",
".",
"raise_for_status",
"(",
")",
"# If the Vera disconnects before writing a full response (as lu_sdata",
"# will do when interrupted by a Luup reload), the requests module will",
"# happily return 200 with an empty string. So, test for empty response,",
"# so we don't rely on the JSON parser to throw an exception.",
"if",
"r",
".",
"text",
"==",
"\"\"",
":",
"raise",
"PyveraError",
"(",
"\"Empty response from Vera\"",
")",
"# Catch a wide swath of what the JSON parser might throw, within",
"# reason. Unfortunately, some parsers don't specifically return",
"# json.decode.JSONDecodeError, but so far most seem to derive what",
"# they do throw from ValueError, so that's helpful.",
"try",
":",
"result",
"=",
"r",
".",
"json",
"(",
")",
"except",
"ValueError",
"as",
"ex",
":",
"raise",
"PyveraError",
"(",
"\"JSON decode error: \"",
"+",
"str",
"(",
"ex",
")",
")",
"if",
"not",
"(",
"type",
"(",
"result",
")",
"is",
"dict",
"and",
"'loadtime'",
"in",
"result",
"and",
"'dataversion'",
"in",
"result",
")",
":",
"raise",
"PyveraError",
"(",
"\"Unexpected/garbled response from Vera\"",
")",
"# At this point, all good. Update timestamp and return change data.",
"device_data",
"=",
"result",
".",
"get",
"(",
"'devices'",
")",
"timestamp",
"=",
"{",
"'loadtime'",
":",
"result",
".",
"get",
"(",
"'loadtime'",
")",
",",
"'dataversion'",
":",
"result",
".",
"get",
"(",
"'dataversion'",
")",
"}",
"return",
"[",
"device_data",
",",
"timestamp",
"]"
] |
sort sam file | def sort_sam ( sam , sort ) : tempdir = '%s/' % ( os . path . abspath ( sam ) . rsplit ( '/' , 1 ) [ 0 ] ) if sort is True : mapping = '%s.sorted.sam' % ( sam . rsplit ( '.' , 1 ) [ 0 ] ) if sam != '-' : if os . path . exists ( mapping ) is False : os . system ( "\
sort -k1 --buffer-size=%sG -T %s -o %s %s\
" % ( sbuffer , tempdir , mapping , sam ) ) else : mapping = 'stdin-sam.sorted.sam' p = Popen ( "sort -k1 --buffer-size=%sG -T %s -o %s" % ( sbuffer , tempdir , mapping ) , stdin = sys . stdin , shell = True ) p . communicate ( ) mapping = open ( mapping ) else : if sam == '-' : mapping = sys . stdin else : mapping = open ( sam ) return mapping | 29 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/subset_sam.py#L14-L37 | [
"def",
"cmd_oreoled",
"(",
"self",
",",
"args",
")",
":",
"if",
"len",
"(",
"args",
")",
"<",
"4",
":",
"print",
"(",
"\"Usage: oreoled LEDNUM RED GREEN BLUE <RATE>\"",
")",
"return",
"lednum",
"=",
"int",
"(",
"args",
"[",
"0",
"]",
")",
"pattern",
"=",
"[",
"0",
"]",
"*",
"24",
"pattern",
"[",
"0",
"]",
"=",
"ord",
"(",
"'R'",
")",
"pattern",
"[",
"1",
"]",
"=",
"ord",
"(",
"'G'",
")",
"pattern",
"[",
"2",
"]",
"=",
"ord",
"(",
"'B'",
")",
"pattern",
"[",
"3",
"]",
"=",
"ord",
"(",
"'0'",
")",
"pattern",
"[",
"4",
"]",
"=",
"0",
"pattern",
"[",
"5",
"]",
"=",
"int",
"(",
"args",
"[",
"1",
"]",
")",
"pattern",
"[",
"6",
"]",
"=",
"int",
"(",
"args",
"[",
"2",
"]",
")",
"pattern",
"[",
"7",
"]",
"=",
"int",
"(",
"args",
"[",
"3",
"]",
")",
"self",
".",
"master",
".",
"mav",
".",
"led_control_send",
"(",
"self",
".",
"settings",
".",
"target_system",
",",
"self",
".",
"settings",
".",
"target_component",
",",
"lednum",
",",
"255",
",",
"8",
",",
"pattern",
")"
] |
randomly subset sam file | def sub_sam ( sam , percent , sort = True , sbuffer = False ) : mapping = sort_sam ( sam , sort ) pool = [ 1 for i in range ( 0 , percent ) ] + [ 0 for i in range ( 0 , 100 - percent ) ] c = cycle ( [ 1 , 2 ] ) for line in mapping : line = line . strip ( ) . split ( ) if line [ 0 ] . startswith ( '@' ) : # get the sam header yield line continue if int ( line [ 1 ] ) <= 20 : # is this from a single read? if random . choice ( pool ) == 1 : yield line else : n = next ( c ) if n == 1 : prev = line if n == 2 and random . choice ( pool ) == 1 : yield prev yield line | 30 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/subset_sam.py#L39-L60 | [
"def",
"post",
"(",
"self",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"try",
":",
"resp",
"=",
"self",
".",
"session",
".",
"post",
"(",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
"if",
"resp",
".",
"status_code",
"in",
"_EXCEPTIONS_BY_CODE",
":",
"raise",
"_EXCEPTIONS_BY_CODE",
"[",
"resp",
".",
"status_code",
"]",
"(",
"resp",
".",
"reason",
")",
"if",
"resp",
".",
"status_code",
"!=",
"requests",
".",
"codes",
"[",
"'ok'",
"]",
":",
"raise",
"exceptions",
".",
"Etcd3Exception",
"(",
"resp",
".",
"reason",
")",
"except",
"requests",
".",
"exceptions",
".",
"Timeout",
"as",
"ex",
":",
"raise",
"exceptions",
".",
"ConnectionTimeoutError",
"(",
"six",
".",
"text_type",
"(",
"ex",
")",
")",
"except",
"requests",
".",
"exceptions",
".",
"ConnectionError",
"as",
"ex",
":",
"raise",
"exceptions",
".",
"ConnectionFailedError",
"(",
"six",
".",
"text_type",
"(",
"ex",
")",
")",
"return",
"resp",
".",
"json",
"(",
")"
] |
convert fq to fa | def fq2fa ( fq ) : c = cycle ( [ 1 , 2 , 3 , 4 ] ) for line in fq : n = next ( c ) if n == 1 : seq = [ '>%s' % ( line . strip ( ) . split ( '@' , 1 ) [ 1 ] ) ] if n == 2 : seq . append ( line . strip ( ) ) yield seq | 31 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/fastq2fasta.py#L11-L22 | [
"def",
"run_configurations",
"(",
"callback",
",",
"sections_reader",
")",
":",
"base",
"=",
"dict",
"(",
"OPTIONS",
")",
"sections",
"=",
"sections_reader",
"(",
")",
"if",
"sections",
"is",
"None",
":",
"logger",
".",
"info",
"(",
"\"Configuration not found in .ini files. \"",
"\"Running with default settings\"",
")",
"recompile",
"(",
")",
"elif",
"sections",
"==",
"[",
"]",
":",
"logger",
".",
"info",
"(",
"\"Configuration does not match current runtime. \"",
"\"Exiting\"",
")",
"results",
"=",
"[",
"]",
"for",
"section",
",",
"options",
"in",
"sections",
":",
"OPTIONS",
".",
"clear",
"(",
")",
"OPTIONS",
".",
"update",
"(",
"base",
")",
"OPTIONS",
".",
"update",
"(",
"options",
")",
"logger",
".",
"debug",
"(",
"\"Running configuration from section \\\"%s\\\". OPTIONS: %r\"",
",",
"section",
",",
"OPTIONS",
")",
"results",
".",
"append",
"(",
"callback",
"(",
")",
")",
"return",
"results"
] |
Converts the returned value of wrapped function to the type of the first arg or to the type specified by a kwarg key return_type s value . | def change_return_type ( f ) : @ wraps ( f ) def wrapper ( * args , * * kwargs ) : if kwargs . has_key ( 'return_type' ) : return_type = kwargs [ 'return_type' ] kwargs . pop ( 'return_type' ) return return_type ( f ( * args , * * kwargs ) ) elif len ( args ) > 0 : return_type = type ( args [ 0 ] ) return return_type ( f ( * args , * * kwargs ) ) else : return f ( * args , * * kwargs ) return wrapper | 32 | https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/decorators.py#L11-L27 | [
"def",
"is_running",
"(",
"self",
")",
":",
"self",
".",
"__update_status",
"(",
")",
"return",
"self",
".",
"status",
"==",
"Status",
".",
"UP",
"or",
"self",
".",
"status",
"==",
"Status",
".",
"DECOMMISSIONED"
] |
Converts all args to set type via self . setify function . | def convert_args_to_sets ( f ) : @ wraps ( f ) def wrapper ( * args , * * kwargs ) : args = ( setify ( x ) for x in args ) return f ( * args , * * kwargs ) return wrapper | 33 | https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/decorators.py#L30-L38 | [
"def",
"remove_pickle_problems",
"(",
"obj",
")",
":",
"if",
"hasattr",
"(",
"obj",
",",
"\"doc_loader\"",
")",
":",
"obj",
".",
"doc_loader",
"=",
"None",
"if",
"hasattr",
"(",
"obj",
",",
"\"embedded_tool\"",
")",
":",
"obj",
".",
"embedded_tool",
"=",
"remove_pickle_problems",
"(",
"obj",
".",
"embedded_tool",
")",
"if",
"hasattr",
"(",
"obj",
",",
"\"steps\"",
")",
":",
"obj",
".",
"steps",
"=",
"[",
"remove_pickle_problems",
"(",
"s",
")",
"for",
"s",
"in",
"obj",
".",
"steps",
"]",
"return",
"obj"
] |
Membuat objek - objek entri dari laman yang diambil . | def _init_entri ( self , laman ) : sup = BeautifulSoup ( laman . text , 'html.parser' ) estr = '' for label in sup . find ( 'hr' ) . next_siblings : if label . name == 'hr' : self . entri . append ( Entri ( estr ) ) break if label . name == 'h2' : if estr : self . entri . append ( Entri ( estr ) ) estr = '' estr += str ( label ) . strip ( ) | 34 | https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L46-L63 | [
"def",
"clone",
"(",
"self",
",",
"*",
"args",
",",
"*",
"*",
"kwargs",
")",
":",
"return",
"self",
".",
"_client",
".",
"clone_scope",
"(",
"*",
"args",
",",
"source_scope",
"=",
"self",
",",
"*",
"*",
"kwargs",
")"
] |
Memproses kata dasar yang ada dalam nama entri . | def _init_kata_dasar ( self , dasar ) : for tiap in dasar : kata = tiap . find ( 'a' ) dasar_no = kata . find ( 'sup' ) kata = ambil_teks_dalam_label ( kata ) self . kata_dasar . append ( kata + ' [{}]' . format ( dasar_no . text . strip ( ) ) if dasar_no else kata ) | 35 | https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L126-L139 | [
"def",
"fast_sync_snapshot_decompress",
"(",
"snapshot_path",
",",
"output_dir",
")",
":",
"if",
"not",
"tarfile",
".",
"is_tarfile",
"(",
"snapshot_path",
")",
":",
"return",
"{",
"'error'",
":",
"'Not a tarfile-compatible archive: {}'",
".",
"format",
"(",
"snapshot_path",
")",
"}",
"if",
"not",
"os",
".",
"path",
".",
"exists",
"(",
"output_dir",
")",
":",
"os",
".",
"makedirs",
"(",
"output_dir",
")",
"with",
"tarfile",
".",
"TarFile",
".",
"bz2open",
"(",
"snapshot_path",
",",
"'r'",
")",
"as",
"f",
":",
"tarfile",
".",
"TarFile",
".",
"extractall",
"(",
"f",
",",
"path",
"=",
"output_dir",
")",
"return",
"{",
"'status'",
":",
"True",
"}"
] |
Mengembalikan hasil serialisasi objek Entri ini . | def serialisasi ( self ) : return { "nama" : self . nama , "nomor" : self . nomor , "kata_dasar" : self . kata_dasar , "pelafalan" : self . pelafalan , "bentuk_tidak_baku" : self . bentuk_tidak_baku , "varian" : self . varian , "makna" : [ makna . serialisasi ( ) for makna in self . makna ] } | 36 | https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L141-L156 | [
"def",
"construct_ctcp",
"(",
"*",
"parts",
")",
":",
"message",
"=",
"' '",
".",
"join",
"(",
"parts",
")",
"message",
"=",
"message",
".",
"replace",
"(",
"'\\0'",
",",
"CTCP_ESCAPE_CHAR",
"+",
"'0'",
")",
"message",
"=",
"message",
".",
"replace",
"(",
"'\\n'",
",",
"CTCP_ESCAPE_CHAR",
"+",
"'n'",
")",
"message",
"=",
"message",
".",
"replace",
"(",
"'\\r'",
",",
"CTCP_ESCAPE_CHAR",
"+",
"'r'",
")",
"message",
"=",
"message",
".",
"replace",
"(",
"CTCP_ESCAPE_CHAR",
",",
"CTCP_ESCAPE_CHAR",
"+",
"CTCP_ESCAPE_CHAR",
")",
"return",
"CTCP_DELIMITER",
"+",
"message",
"+",
"CTCP_DELIMITER"
] |
Mengembalikan representasi string untuk semua makna entri ini . | def _makna ( self ) : if len ( self . makna ) > 1 : return '\n' . join ( str ( i ) + ". " + str ( makna ) for i , makna in enumerate ( self . makna , 1 ) ) return str ( self . makna [ 0 ] ) | 37 | https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L158-L170 | [
"def",
"as_of",
"(",
"self",
",",
"qtime",
"=",
"None",
")",
":",
"clone",
"=",
"self",
".",
"_clone",
"(",
")",
"clone",
".",
"querytime",
"=",
"QueryTime",
"(",
"time",
"=",
"qtime",
",",
"active",
"=",
"True",
")",
"return",
"clone"
] |
Mengembalikan representasi string untuk nama entri ini . | def _nama ( self ) : hasil = self . nama if self . nomor : hasil += " [{}]" . format ( self . nomor ) if self . kata_dasar : hasil = " » ". j oin( s elf. k ata_dasar) » " + h sil return hasil | 38 | https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L172-L184 | [
"def",
"as_of",
"(",
"self",
",",
"qtime",
"=",
"None",
")",
":",
"clone",
"=",
"self",
".",
"_clone",
"(",
")",
"clone",
".",
"querytime",
"=",
"QueryTime",
"(",
"time",
"=",
"qtime",
",",
"active",
"=",
"True",
")",
"return",
"clone"
] |
Mengembalikan representasi string untuk varian entri ini . Dapat digunakan untuk Varian maupun Bentuk tidak baku . | def _varian ( self , varian ) : if varian == self . bentuk_tidak_baku : nama = "Bentuk tidak baku" elif varian == self . varian : nama = "Varian" else : return '' return nama + ': ' + ', ' . join ( varian ) | 39 | https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L186-L202 | [
"def",
"as_of",
"(",
"self",
",",
"qtime",
"=",
"None",
")",
":",
"clone",
"=",
"self",
".",
"_clone",
"(",
")",
"clone",
".",
"querytime",
"=",
"QueryTime",
"(",
"time",
"=",
"qtime",
",",
"active",
"=",
"True",
")",
"return",
"clone"
] |
Memproses kelas kata yang ada dalam makna . | def _init_kelas ( self , makna_label ) : kelas = makna_label . find ( color = 'red' ) lain = makna_label . find ( color = 'darkgreen' ) info = makna_label . find ( color = 'green' ) if kelas : kelas = kelas . find_all ( 'span' ) if lain : self . kelas = { lain . text . strip ( ) : lain [ 'title' ] . strip ( ) } self . submakna = lain . next_sibling . strip ( ) self . submakna += ' ' + makna_label . find ( color = 'grey' ) . text . strip ( ) else : self . kelas = { k . text . strip ( ) : k [ 'title' ] . strip ( ) for k in kelas } if kelas else { } self . info = info . text . strip ( ) if info else '' | 40 | https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L239-L259 | [
"def",
"crc",
"(",
"self",
")",
":",
"# will make sure everything has been transferred",
"# to datastore that needs to be before returning crc",
"result",
"=",
"self",
".",
"_data",
".",
"fast_hash",
"(",
")",
"if",
"hasattr",
"(",
"self",
".",
"mesh",
",",
"'crc'",
")",
":",
"# bitwise xor combines hashes better than a sum",
"result",
"^=",
"self",
".",
"mesh",
".",
"crc",
"(",
")",
"return",
"result"
] |
Memproses contoh yang ada dalam makna . | def _init_contoh ( self , makna_label ) : indeks = makna_label . text . find ( ': ' ) if indeks != - 1 : contoh = makna_label . text [ indeks + 2 : ] . strip ( ) self . contoh = contoh . split ( '; ' ) else : self . contoh = [ ] | 41 | https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L261-L273 | [
"def",
"setHalfLife",
"(",
"self",
",",
"halfLife",
",",
"timeUnit",
")",
":",
"self",
".",
"_timeUnit",
"=",
"timeUnit",
"self",
".",
"_decayFactor",
"=",
"exp",
"(",
"log",
"(",
"0.5",
")",
"/",
"halfLife",
")",
"return",
"self"
] |
Mengembalikan hasil serialisasi objek Makna ini . | def serialisasi ( self ) : return { "kelas" : self . kelas , "submakna" : self . submakna , "info" : self . info , "contoh" : self . contoh } | 42 | https://github.com/laymonage/kbbi-python/blob/1a52ba8bcc6dc4c5c1215f9e00207aca264287d6/kbbi/kbbi.py#L275-L287 | [
"def",
"escape_latex",
"(",
"text",
")",
":",
"text",
"=",
"unicode",
"(",
"text",
".",
"decode",
"(",
"'utf-8'",
")",
")",
"CHARS",
"=",
"{",
"'&'",
":",
"r'\\&'",
",",
"'%'",
":",
"r'\\%'",
",",
"'$'",
":",
"r'\\$'",
",",
"'#'",
":",
"r'\\#'",
",",
"'_'",
":",
"r'\\_'",
",",
"'{'",
":",
"r'\\{'",
",",
"'}'",
":",
"r'\\}'",
",",
"'~'",
":",
"r'\\~{}'",
",",
"'^'",
":",
"r'\\^{}'",
",",
"'\\\\'",
":",
"r'\\textbackslash{}'",
",",
"}",
"escaped",
"=",
"\"\"",
".",
"join",
"(",
"[",
"CHARS",
".",
"get",
"(",
"char",
",",
"char",
")",
"for",
"char",
"in",
"text",
"]",
")",
"return",
"escaped",
".",
"encode",
"(",
"'utf-8'",
")"
] |
Build sphinx documentation . | def build_sphinx ( pkg_data , projectdir ) : try : version , _minor_version = pkg_data . version . rsplit ( '.' , 1 ) except ValueError : version = pkg_data . version args = ' ' . join ( ( 'sphinx-quickstart' , '--sep' , '-q' , '-p "{name}"' , '-a "{author}"' , '-v "{version}"' , '-r "{release}"' , '-l en' , '--suffix=.rst' , '--master=index' , '--ext-autodoc' , '--ext-viewcode' , '--makefile' , '{projectdir}' ) ) . format ( name = pkg_data . name , author = pkg_data . author , version = version , release = pkg_data . version , projectdir = projectdir ) if subprocess . call ( shlex . split ( args ) ) == 0 : _touch_gitkeep ( projectdir ) | 43 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/docs.py#L8-L40 | [
"def",
"relative_humidity_wet_psychrometric",
"(",
"dry_bulb_temperature",
",",
"web_bulb_temperature",
",",
"pressure",
",",
"*",
"*",
"kwargs",
")",
":",
"return",
"(",
"psychrometric_vapor_pressure_wet",
"(",
"dry_bulb_temperature",
",",
"web_bulb_temperature",
",",
"pressure",
",",
"*",
"*",
"kwargs",
")",
"/",
"saturation_vapor_pressure",
"(",
"dry_bulb_temperature",
")",
")"
] |
make bowtie db | def bowtiedb ( fa , keepDB ) : btdir = '%s/bt2' % ( os . getcwd ( ) ) # make directory for if not os . path . exists ( btdir ) : os . mkdir ( btdir ) btdb = '%s/%s' % ( btdir , fa . rsplit ( '/' , 1 ) [ - 1 ] ) if keepDB is True : if os . path . exists ( '%s.1.bt2' % ( btdb ) ) : return btdb p = subprocess . Popen ( 'bowtie2-build -q %s %s' % ( fa , btdb ) , shell = True ) p . communicate ( ) return btdb | 44 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/crossmap.py#L16-L31 | [
"def",
"parse",
"(",
"self",
",",
"content",
")",
":",
"raw",
"=",
"{",
"}",
"try",
":",
"root",
"=",
"etree",
".",
"fromstring",
"(",
"content",
")",
"except",
"SyntaxError",
"as",
"e",
":",
"raise",
"ValueError",
"(",
"*",
"e",
".",
"args",
")",
"for",
"child",
"in",
"root",
":",
"raw",
"[",
"child",
".",
"tag",
"]",
"=",
"child",
".",
"text",
"formatted",
"=",
"self",
".",
"format",
"(",
"raw",
")",
"msg_type",
"=",
"formatted",
"[",
"'type'",
"]",
"msg_parser",
"=",
"getattr",
"(",
"self",
",",
"'parse_%s'",
"%",
"msg_type",
",",
"None",
")",
"if",
"callable",
"(",
"msg_parser",
")",
":",
"parsed",
"=",
"msg_parser",
"(",
"raw",
")",
"else",
":",
"parsed",
"=",
"self",
".",
"parse_invalid_type",
"(",
"raw",
")",
"formatted",
".",
"update",
"(",
"parsed",
")",
"return",
"formatted"
] |
generate bowtie2 command | def bowtie ( sam , btd , f , r , u , opt , no_shrink , threads ) : bt2 = 'bowtie2 -x %s -p %s ' % ( btd , threads ) if f is not False : bt2 += '-1 %s -2 %s ' % ( f , r ) if u is not False : bt2 += '-U %s ' % ( u ) bt2 += opt if no_shrink is False : if f is False : bt2 += ' | shrinksam -u -k %s-shrunk.sam ' % ( sam ) else : bt2 += ' | shrinksam -k %s-shrunk.sam ' % ( sam ) else : bt2 += ' > %s.sam' % ( sam ) return bt2 | 45 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/crossmap.py#L33-L50 | [
"def",
"format_string",
"(",
"self",
",",
"s",
",",
"args",
",",
"kwargs",
")",
":",
"if",
"isinstance",
"(",
"s",
",",
"Markup",
")",
":",
"formatter",
"=",
"SandboxedEscapeFormatter",
"(",
"self",
",",
"s",
".",
"escape",
")",
"else",
":",
"formatter",
"=",
"SandboxedFormatter",
"(",
"self",
")",
"kwargs",
"=",
"_MagicFormatMapping",
"(",
"args",
",",
"kwargs",
")",
"rv",
"=",
"formatter",
".",
"vformat",
"(",
"s",
",",
"args",
",",
"kwargs",
")",
"return",
"type",
"(",
"s",
")",
"(",
"rv",
")"
] |
map all read sets against all fasta files | def crossmap ( fas , reads , options , no_shrink , keepDB , threads , cluster , nodes ) : if cluster is True : threads = '48' btc = [ ] for fa in fas : btd = bowtiedb ( fa , keepDB ) F , R , U = reads if F is not False : if U is False : u = False for i , f in enumerate ( F ) : r = R [ i ] if U is not False : u = U [ i ] sam = '%s/%s-vs-%s' % ( os . getcwd ( ) , fa . rsplit ( '/' , 1 ) [ - 1 ] , f . rsplit ( '/' , 1 ) [ - 1 ] . rsplit ( '.' , 3 ) [ 0 ] ) btc . append ( bowtie ( sam , btd , f , r , u , options , no_shrink , threads ) ) else : f = False r = False for u in U : sam = '%s/%s-vs-%s' % ( os . getcwd ( ) , fa . rsplit ( '/' , 1 ) [ - 1 ] , u . rsplit ( '/' , 1 ) [ - 1 ] . rsplit ( '.' , 3 ) [ 0 ] ) btc . append ( bowtie ( sam , btd , f , r , u , options , no_shrink , threads ) ) if cluster is False : for i in btc : p = subprocess . Popen ( i , shell = True ) p . communicate ( ) else : ID = '' . join ( random . choice ( [ str ( i ) for i in range ( 0 , 9 ) ] ) for _ in range ( 5 ) ) for node , commands in enumerate ( chunks ( btc , nodes ) , 1 ) : bs = open ( '%s/crossmap-qsub.%s.%s.sh' % ( os . getcwd ( ) , ID , node ) , 'w' ) print ( '\n' . join ( commands ) , file = bs ) bs . close ( ) p = subprocess . Popen ( 'qsub -V -N crossmap %s' % ( bs . name ) , shell = True ) p . communicate ( ) | 46 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/crossmap.py#L55-L96 | [
"async",
"def",
"socket_connection",
"(",
"self",
")",
":",
"if",
"not",
"self",
".",
"_registered",
":",
"_LOGGER",
".",
"error",
"(",
"'Client not registered, cannot start socket.'",
")",
"return",
"url",
"=",
"'{}?DeviceID={}&api_key={}'",
".",
"format",
"(",
"self",
".",
"construct_url",
"(",
"SOCKET_URL",
")",
",",
"self",
".",
"_api_id",
",",
"self",
".",
"_api_key",
")",
"fail_count",
"=",
"0",
"while",
"True",
":",
"_LOGGER",
".",
"debug",
"(",
"'Attempting Socket Connection.'",
")",
"try",
":",
"with",
"async_timeout",
".",
"timeout",
"(",
"DEFAULT_TIMEOUT",
",",
"loop",
"=",
"self",
".",
"_event_loop",
")",
":",
"self",
".",
"wsck",
"=",
"await",
"self",
".",
"_api_session",
".",
"ws_connect",
"(",
"url",
")",
"# Enable sever session updates:",
"try",
":",
"msg",
"=",
"await",
"self",
".",
"wsck",
".",
"send_str",
"(",
"'{\"MessageType\":\"SessionsStart\", \"Data\": \"0,1500\"}'",
")",
"except",
"Exception",
"as",
"err",
":",
"# Catch all for now",
"_LOGGER",
".",
"error",
"(",
"'Failure setting session updates: %s'",
",",
"err",
")",
"raise",
"ValueError",
"(",
"'Session updates error.'",
")",
"_LOGGER",
".",
"debug",
"(",
"'Socket Connected!'",
")",
"fail_count",
"=",
"0",
"while",
"True",
":",
"msg",
"=",
"await",
"self",
".",
"wsck",
".",
"receive",
"(",
")",
"if",
"msg",
".",
"type",
"==",
"aiohttp",
".",
"WSMsgType",
".",
"text",
":",
"# Process data",
"self",
".",
"process_msg",
"(",
"msg",
".",
"data",
")",
"elif",
"msg",
".",
"type",
"==",
"aiohttp",
".",
"WSMsgType",
".",
"closed",
":",
"raise",
"ValueError",
"(",
"'Websocket was closed.'",
")",
"elif",
"msg",
".",
"type",
"==",
"aiohttp",
".",
"WSMsgType",
".",
"error",
":",
"_LOGGER",
".",
"debug",
"(",
"'Websocket encountered an error: %s'",
",",
"msg",
")",
"raise",
"ValueError",
"(",
"'Websocket error.'",
")",
"except",
"(",
"aiohttp",
".",
"ClientError",
",",
"asyncio",
".",
"TimeoutError",
",",
"aiohttp",
".",
"WSServerHandshakeError",
",",
"ConnectionRefusedError",
",",
"OSError",
",",
"ValueError",
")",
"as",
"err",
":",
"if",
"not",
"self",
".",
"_shutdown",
":",
"fail_count",
"+=",
"1",
"_LOGGER",
".",
"debug",
"(",
"'Websocket unintentionally closed.'",
"' Trying reconnect in %ss. Error: %s'",
",",
"(",
"fail_count",
"*",
"5",
")",
"+",
"5",
",",
"err",
")",
"await",
"asyncio",
".",
"sleep",
"(",
"15",
",",
"self",
".",
"_event_loop",
")",
"continue",
"else",
":",
"break"
] |
Returns a connection object from the router given args . | def get_conn ( self , * args , * * kwargs ) : connections = self . __connections_for ( 'get_conn' , args = args , kwargs = kwargs ) if len ( connections ) is 1 : return connections [ 0 ] else : return connections | 47 | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/base.py#L100-L113 | [
"def",
"denormalize_volume",
"(",
"volume",
")",
":",
"id",
"=",
"volume",
".",
"get",
"(",
"'id'",
",",
"None",
")",
"res",
"=",
"dict",
"(",
")",
"res",
".",
"update",
"(",
"volume",
"[",
"'metadata'",
"]",
")",
"denorm_attachments",
"=",
"list",
"(",
")",
"for",
"a",
"in",
"volume",
"[",
"'attachments'",
"]",
":",
"denorm_attachments",
".",
"append",
"(",
"Archivant",
".",
"denormalize_attachment",
"(",
"a",
")",
")",
"res",
"[",
"'_attachments'",
"]",
"=",
"denorm_attachments",
"return",
"id",
",",
"res"
] |
return the non - direct init if the direct algorithm has been selected . | def __get_nondirect_init ( self , init ) : crc = init for i in range ( self . Width ) : bit = crc & 0x01 if bit : crc ^= self . Poly crc >>= 1 if bit : crc |= self . MSB_Mask return crc & self . Mask | 48 | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L98-L110 | [
"def",
"vocab_token_counts",
"(",
"text_filepattern",
",",
"max_lines",
")",
":",
"ret",
"=",
"{",
"}",
"for",
"i",
",",
"line",
"in",
"enumerate",
"(",
"_read_filepattern",
"(",
"text_filepattern",
",",
"max_lines",
"=",
"max_lines",
")",
")",
":",
"if",
"\",\"",
"not",
"in",
"line",
":",
"tf",
".",
"logging",
".",
"warning",
"(",
"\"Malformed vocab line #%d '%s'\"",
",",
"i",
",",
"line",
")",
"continue",
"token",
",",
"count",
"=",
"line",
".",
"rsplit",
"(",
"\",\"",
",",
"1",
")",
"ret",
"[",
"_native_to_unicode",
"(",
"token",
")",
"]",
"=",
"int",
"(",
"count",
")",
"return",
"ret"
] |
reflect a data word i . e . reverts the bit order . | def reflect ( self , data , width ) : x = data & 0x01 for i in range ( width - 1 ) : data >>= 1 x = ( x << 1 ) | ( data & 0x01 ) return x | 49 | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L115-L123 | [
"def",
"update",
"(",
"self",
",",
"friendly_name",
"=",
"values",
".",
"unset",
",",
"unique_name",
"=",
"values",
".",
"unset",
")",
":",
"return",
"self",
".",
"_proxy",
".",
"update",
"(",
"friendly_name",
"=",
"friendly_name",
",",
"unique_name",
"=",
"unique_name",
",",
")"
] |
Classic simple and slow CRC implementation . This function iterates bit by bit over the augmented input message and returns the calculated CRC value at the end . | def bit_by_bit ( self , in_data ) : # If the input data is a string, convert to bytes. if isinstance ( in_data , str ) : in_data = [ ord ( c ) for c in in_data ] register = self . NonDirectInit for octet in in_data : if self . ReflectIn : octet = self . reflect ( octet , 8 ) for i in range ( 8 ) : topbit = register & self . MSB_Mask register = ( ( register << 1 ) & self . Mask ) | ( ( octet >> ( 7 - i ) ) & 0x01 ) if topbit : register ^= self . Poly for i in range ( self . Width ) : topbit = register & self . MSB_Mask register = ( ( register << 1 ) & self . Mask ) if topbit : register ^= self . Poly if self . ReflectOut : register = self . reflect ( register , self . Width ) return register ^ self . XorOut | 50 | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L128-L156 | [
"def",
"get_default_storage_policy_of_datastore",
"(",
"profile_manager",
",",
"datastore",
")",
":",
"# Retrieve all datastores visible",
"hub",
"=",
"pbm",
".",
"placement",
".",
"PlacementHub",
"(",
"hubId",
"=",
"datastore",
".",
"_moId",
",",
"hubType",
"=",
"'Datastore'",
")",
"log",
".",
"trace",
"(",
"'placement_hub = %s'",
",",
"hub",
")",
"try",
":",
"policy_id",
"=",
"profile_manager",
".",
"QueryDefaultRequirementProfile",
"(",
"hub",
")",
"except",
"vim",
".",
"fault",
".",
"NoPermission",
"as",
"exc",
":",
"log",
".",
"exception",
"(",
"exc",
")",
"raise",
"VMwareApiError",
"(",
"'Not enough permissions. Required privilege: '",
"'{0}'",
".",
"format",
"(",
"exc",
".",
"privilegeId",
")",
")",
"except",
"vim",
".",
"fault",
".",
"VimFault",
"as",
"exc",
":",
"log",
".",
"exception",
"(",
"exc",
")",
"raise",
"VMwareApiError",
"(",
"exc",
".",
"msg",
")",
"except",
"vmodl",
".",
"RuntimeFault",
"as",
"exc",
":",
"log",
".",
"exception",
"(",
"exc",
")",
"raise",
"VMwareRuntimeError",
"(",
"exc",
".",
"msg",
")",
"policy_refs",
"=",
"get_policies_by_id",
"(",
"profile_manager",
",",
"[",
"policy_id",
"]",
")",
"if",
"not",
"policy_refs",
":",
"raise",
"VMwareObjectRetrievalError",
"(",
"'Storage policy with id \\'{0}\\' was '",
"'not found'",
".",
"format",
"(",
"policy_id",
")",
")",
"return",
"policy_refs",
"[",
"0",
"]"
] |
This function generates the CRC table used for the table_driven CRC algorithm . The Python version cannot handle tables of an index width other than 8 . See the generated C code for tables with different sizes instead . | def gen_table ( self ) : table_length = 1 << self . TableIdxWidth tbl = [ 0 ] * table_length for i in range ( table_length ) : register = i if self . ReflectIn : register = self . reflect ( register , self . TableIdxWidth ) register = register << ( self . Width - self . TableIdxWidth + self . CrcShift ) for j in range ( self . TableIdxWidth ) : if register & ( self . MSB_Mask << self . CrcShift ) != 0 : register = ( register << 1 ) ^ ( self . Poly << self . CrcShift ) else : register = ( register << 1 ) if self . ReflectIn : register = self . reflect ( register >> self . CrcShift , self . Width ) << self . CrcShift tbl [ i ] = register & ( self . Mask << self . CrcShift ) return tbl | 51 | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L190-L212 | [
"def",
"setGradingNotFinishedStateAction",
"(",
"self",
",",
"request",
",",
"queryset",
")",
":",
"for",
"subm",
"in",
"queryset",
":",
"subm",
".",
"state",
"=",
"Submission",
".",
"GRADING_IN_PROGRESS",
"subm",
".",
"save",
"(",
")"
] |
The Standard table_driven CRC algorithm . | def table_driven ( self , in_data ) : # If the input data is a string, convert to bytes. if isinstance ( in_data , str ) : in_data = [ ord ( c ) for c in in_data ] tbl = self . gen_table ( ) register = self . DirectInit << self . CrcShift if not self . ReflectIn : for octet in in_data : tblidx = ( ( register >> ( self . Width - self . TableIdxWidth + self . CrcShift ) ) ^ octet ) & 0xff register = ( ( register << ( self . TableIdxWidth - self . CrcShift ) ) ^ tbl [ tblidx ] ) & ( self . Mask << self . CrcShift ) register = register >> self . CrcShift else : register = self . reflect ( register , self . Width + self . CrcShift ) << self . CrcShift for octet in in_data : tblidx = ( ( register >> self . CrcShift ) ^ octet ) & 0xff register = ( ( register >> self . TableIdxWidth ) ^ tbl [ tblidx ] ) & ( self . Mask << self . CrcShift ) register = self . reflect ( register , self . Width + self . CrcShift ) & self . Mask if self . ReflectOut : register = self . reflect ( register , self . Width ) return register ^ self . XorOut | 52 | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/_crc_algorithms.py#L217-L242 | [
"def",
"remove",
"(",
"self",
",",
"membership_id",
")",
":",
"path",
"=",
"'{}/remove'",
".",
"format",
"(",
"membership_id",
")",
"url",
"=",
"utils",
".",
"urljoin",
"(",
"self",
".",
"url",
",",
"path",
")",
"payload",
"=",
"{",
"'membership_id'",
":",
"membership_id",
"}",
"response",
"=",
"self",
".",
"session",
".",
"post",
"(",
"url",
",",
"json",
"=",
"payload",
")",
"return",
"response",
".",
"ok"
] |
parse masked sequence into non - masked and masked regions | def parse_masked ( seq , min_len ) : nm , masked = [ ] , [ [ ] ] prev = None for base in seq [ 1 ] : if base . isupper ( ) : nm . append ( base ) if masked != [ [ ] ] and len ( masked [ - 1 ] ) < min_len : nm . extend ( masked [ - 1 ] ) del masked [ - 1 ] prev = False elif base . islower ( ) : if prev is False : masked . append ( [ ] ) masked [ - 1 ] . append ( base ) prev = True return nm , masked | 53 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/strip_masked.py#L13-L31 | [
"def",
"dl_cub",
"(",
"cub_url",
",",
"cub_archive_name",
")",
":",
"with",
"open",
"(",
"cub_archive_name",
",",
"'wb'",
")",
"as",
"f",
":",
"remote_file",
"=",
"urllib2",
".",
"urlopen",
"(",
"cub_url",
")",
"meta",
"=",
"remote_file",
".",
"info",
"(",
")",
"# The server may provide us with the size of the file.",
"cl_header",
"=",
"meta",
".",
"getheaders",
"(",
"\"Content-Length\"",
")",
"remote_file_size",
"=",
"int",
"(",
"cl_header",
"[",
"0",
"]",
")",
"if",
"len",
"(",
"cl_header",
")",
">",
"0",
"else",
"None",
"# Initialise variables",
"local_file_size",
"=",
"0",
"block_size",
"=",
"128",
"*",
"1024",
"# Do the download",
"while",
"True",
":",
"data",
"=",
"remote_file",
".",
"read",
"(",
"block_size",
")",
"if",
"not",
"data",
":",
"break",
"f",
".",
"write",
"(",
"data",
")",
"local_file_size",
"+=",
"len",
"(",
"data",
")",
"if",
"(",
"remote_file_size",
"is",
"not",
"None",
"and",
"not",
"local_file_size",
"==",
"remote_file_size",
")",
":",
"log",
".",
"warn",
"(",
"\"Local file size '{}' \"",
"\"does not match remote '{}'\"",
".",
"format",
"(",
"local_file_size",
",",
"remote_file_size",
")",
")",
"remote_file",
".",
"close",
"(",
")"
] |
remove masked regions from fasta file as long as they are longer than min_len | def strip_masked ( fasta , min_len , print_masked ) : for seq in parse_fasta ( fasta ) : nm , masked = parse_masked ( seq , min_len ) nm = [ '%s removed_masked >=%s' % ( seq [ 0 ] , min_len ) , '' . join ( nm ) ] yield [ 0 , nm ] if print_masked is True : for i , m in enumerate ( [ i for i in masked if i != [ ] ] , 1 ) : m = [ '%s insertion:%s' % ( seq [ 0 ] , i ) , '' . join ( m ) ] yield [ 1 , m ] | 54 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/strip_masked.py#L33-L45 | [
"def",
"__launchThreads",
"(",
"self",
",",
"numThreads",
")",
":",
"i",
"=",
"0",
"while",
"i",
"<",
"numThreads",
":",
"self",
".",
"__logger",
".",
"debug",
"(",
"\"Launching thread number \"",
"+",
"str",
"(",
"i",
")",
")",
"i",
"+=",
"1",
"newThr",
"=",
"Thread",
"(",
"target",
"=",
"self",
".",
"__processUsers",
")",
"newThr",
".",
"setDaemon",
"(",
"True",
")",
"self",
".",
"__threads",
".",
"add",
"(",
"newThr",
")",
"newThr",
".",
"start",
"(",
")"
] |
Return arcsine transformed relative abundance from a BIOM format file . | def get_relative_abundance ( biomfile ) : biomf = biom . load_table ( biomfile ) norm_biomf = biomf . norm ( inplace = False ) rel_abd = { } for sid in norm_biomf . ids ( ) : rel_abd [ sid ] = { } for otuid in norm_biomf . ids ( "observation" ) : otuname = oc . otu_name ( norm_biomf . metadata ( otuid , axis = "observation" ) [ "taxonomy" ] ) otuname = " " . join ( otuname . split ( "_" ) ) abd = norm_biomf . get_value_by_ids ( otuid , sid ) rel_abd [ sid ] [ otuname ] = abd ast_rel_abd = bc . arcsine_sqrt_transform ( rel_abd ) return ast_rel_abd | 55 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/network_plots_gephi.py#L33-L57 | [
"def",
"is_expired",
"(",
"self",
",",
"max_idle_seconds",
")",
":",
"now",
"=",
"current_time",
"(",
")",
"return",
"(",
"self",
".",
"expiration_time",
"is",
"not",
"None",
"and",
"self",
".",
"expiration_time",
"<",
"now",
")",
"or",
"(",
"max_idle_seconds",
"is",
"not",
"None",
"and",
"self",
".",
"last_access_time",
"+",
"max_idle_seconds",
"<",
"now",
")"
] |
Find an OTU ID in a Newick - format tree . Return the starting position of the ID or None if not found . | def find_otu ( otuid , tree ) : for m in re . finditer ( otuid , tree ) : before , after = tree [ m . start ( ) - 1 ] , tree [ m . start ( ) + len ( otuid ) ] if before in [ "(" , "," , ")" ] and after in [ ":" , ";" ] : return m . start ( ) return None | 56 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/iTol.py#L17-L26 | [
"async",
"def",
"_wait_exponentially",
"(",
"self",
",",
"exception",
",",
"max_wait_time",
"=",
"300",
")",
":",
"wait_time",
"=",
"min",
"(",
"(",
"2",
"**",
"self",
".",
"_connection_attempts",
")",
"+",
"random",
".",
"random",
"(",
")",
",",
"max_wait_time",
")",
"try",
":",
"wait_time",
"=",
"exception",
".",
"response",
"[",
"\"headers\"",
"]",
"[",
"\"Retry-After\"",
"]",
"except",
"(",
"KeyError",
",",
"AttributeError",
")",
":",
"pass",
"self",
".",
"_logger",
".",
"debug",
"(",
"\"Waiting %s seconds before reconnecting.\"",
",",
"wait_time",
")",
"await",
"asyncio",
".",
"sleep",
"(",
"float",
"(",
"wait_time",
")",
")"
] |
Replace the OTU ids in the Newick phylogenetic tree format with truncated OTU names | def newick_replace_otuids ( tree , biomf ) : for val , id_ , md in biomf . iter ( axis = "observation" ) : otu_loc = find_otu ( id_ , tree ) if otu_loc is not None : tree = tree [ : otu_loc ] + oc . otu_name ( md [ "taxonomy" ] ) + tree [ otu_loc + len ( id_ ) : ] return tree | 57 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/iTol.py#L29-L40 | [
"def",
"_eval_progress",
"(",
"self",
",",
"match",
")",
":",
"_locals",
"=",
"{",
"k",
":",
"safe_float",
"(",
"v",
")",
"for",
"k",
",",
"v",
"in",
"match",
".",
"groupdict",
"(",
")",
".",
"items",
"(",
")",
"}",
"if",
"\"x\"",
"not",
"in",
"_locals",
":",
"_locals",
"[",
"\"x\"",
"]",
"=",
"[",
"safe_float",
"(",
"x",
")",
"for",
"x",
"in",
"match",
".",
"groups",
"(",
")",
"]",
"try",
":",
"return",
"int",
"(",
"eval",
"(",
"self",
".",
"progress_expr",
",",
"{",
"}",
",",
"_locals",
")",
")",
"except",
":",
"return",
"None"
] |
return genome info for choosing representative | def genome_info ( genome , info ) : try : scg = info [ '#SCGs' ] dups = info [ '#SCG duplicates' ] length = info [ 'genome size (bp)' ] return [ scg - dups , length , genome ] except : return [ False , False , info [ 'genome size (bp)' ] , genome ] | 58 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L97-L112 | [
"def",
"_send_and_wait",
"(",
"self",
",",
"*",
"*",
"kwargs",
")",
":",
"frame_id",
"=",
"self",
".",
"next_frame_id",
"kwargs",
".",
"update",
"(",
"dict",
"(",
"frame_id",
"=",
"frame_id",
")",
")",
"self",
".",
"_send",
"(",
"*",
"*",
"kwargs",
")",
"timeout",
"=",
"datetime",
".",
"now",
"(",
")",
"+",
"const",
".",
"RX_TIMEOUT",
"while",
"datetime",
".",
"now",
"(",
")",
"<",
"timeout",
":",
"try",
":",
"frame",
"=",
"self",
".",
"_rx_frames",
".",
"pop",
"(",
"frame_id",
")",
"raise_if_error",
"(",
"frame",
")",
"return",
"frame",
"except",
"KeyError",
":",
"sleep",
"(",
"0.1",
")",
"continue",
"_LOGGER",
".",
"exception",
"(",
"\"Did not receive response within configured timeout period.\"",
")",
"raise",
"exceptions",
".",
"ZigBeeResponseTimeout",
"(",
")"
] |
choose represenative genome and print cluster information | def print_clusters ( fastas , info , ANI ) : header = [ '#cluster' , 'num. genomes' , 'rep.' , 'genome' , '#SCGs' , '#SCG duplicates' , 'genome size (bp)' , 'fragments' , 'list' ] yield header in_cluster = [ ] for cluster_num , cluster in enumerate ( connected_components ( ANI ) ) : cluster = sorted ( [ genome_info ( genome , info [ genome ] ) for genome in cluster ] , key = lambda x : x [ 0 : ] , reverse = True ) rep = cluster [ 0 ] [ - 1 ] cluster = [ i [ - 1 ] for i in cluster ] size = len ( cluster ) for genome in cluster : in_cluster . append ( genome ) try : stats = [ size , rep , genome , info [ genome ] [ '#SCGs' ] , info [ genome ] [ '#SCG duplicates' ] , info [ genome ] [ 'genome size (bp)' ] , info [ genome ] [ '# contigs' ] , cluster ] except : stats = [ size , rep , genome , 'n/a' , 'n/a' , info [ genome ] [ 'genome size (bp)' ] , info [ genome ] [ '# contigs' ] , cluster ] if rep == genome : stats = [ '*%s' % ( cluster_num ) ] + stats else : stats = [ cluster_num ] + stats yield stats # print singletons try : start = cluster_num + 1 except : start = 0 fastas = set ( [ i . rsplit ( '.' , 1 ) [ 0 ] . rsplit ( '/' , 1 ) [ - 1 ] . rsplit ( '.contigs' ) [ 0 ] for i in fastas ] ) for cluster_num , genome in enumerate ( fastas . difference ( set ( in_cluster ) ) , start ) : try : stats = [ '*%s' % ( cluster_num ) , 1 , genome , genome , info [ genome ] [ '#SCGs' ] , info [ genome ] [ '#SCG duplicates' ] , info [ genome ] [ 'genome size (bp)' ] , info [ genome ] [ '# contigs' ] , [ genome ] ] except : stats = [ '*%s' % ( cluster_num ) , 1 , genome , genome , 'n/a' , 'n/a' , info [ genome ] [ 'genome size (bp)' ] , info [ genome ] [ '# contigs' ] , [ genome ] ] yield stats | 59 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L114-L163 | [
"def",
"delete",
"(",
"self",
",",
"data_src",
")",
":",
"items",
"=",
"self",
".",
"objects",
"[",
"data_src",
"]",
".",
"data",
".",
"keys",
"(",
")",
"# items to edit",
"self",
".",
"reg",
".",
"unregister",
"(",
"items",
")",
"# remove items from Registry",
"self",
".",
"layer",
".",
"pop",
"(",
"data_src",
")",
"# remove data source from layer",
"self",
".",
"objects",
".",
"pop",
"(",
"data_src",
")",
"# remove data_source object",
"self",
".",
"sources",
".",
"pop",
"(",
"data_src",
")"
] |
convert ggKbase genome info tables to dictionary | def parse_ggKbase_tables ( tables , id_type ) : g2info = { } for table in tables : for line in open ( table ) : line = line . strip ( ) . split ( '\t' ) if line [ 0 ] . startswith ( 'name' ) : header = line header [ 4 ] = 'genome size (bp)' header [ 12 ] = '#SCGs' header [ 13 ] = '#SCG duplicates' continue name , code , info = line [ 0 ] , line [ 1 ] , line info = [ to_int ( i ) for i in info ] if id_type is False : # try to use name and code ID if 'UNK' in code or 'unknown' in code : code = name if ( name != code ) and ( name and code in g2info ) : print ( '# duplicate name or code in table(s)' , file = sys . stderr ) print ( '# %s and/or %s' % ( name , code ) , file = sys . stderr ) exit ( ) if name not in g2info : g2info [ name ] = { item : stat for item , stat in zip ( header , info ) } if code not in g2info : g2info [ code ] = { item : stat for item , stat in zip ( header , info ) } else : if id_type == 'name' : ID = name elif id_type == 'code' : ID = code else : print ( '# specify name or code column using -id' , file = sys . stderr ) exit ( ) ID = ID . replace ( ' ' , '' ) g2info [ ID ] = { item : stat for item , stat in zip ( header , info ) } if g2info [ ID ] [ 'genome size (bp)' ] == '' : g2info [ ID ] [ 'genome size (bp)' ] = 0 return g2info | 60 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L174-L213 | [
"def",
"minutes_for_sessions_in_range",
"(",
"self",
",",
"start_session_label",
",",
"end_session_label",
")",
":",
"first_minute",
",",
"_",
"=",
"self",
".",
"open_and_close_for_session",
"(",
"start_session_label",
")",
"_",
",",
"last_minute",
"=",
"self",
".",
"open_and_close_for_session",
"(",
"end_session_label",
")",
"return",
"self",
".",
"minutes_in_range",
"(",
"first_minute",
",",
"last_minute",
")"
] |
convert checkM genome info tables to dictionary | def parse_checkM_tables ( tables ) : g2info = { } for table in tables : for line in open ( table ) : line = line . strip ( ) . split ( '\t' ) if line [ 0 ] . startswith ( 'Bin Id' ) : header = line header [ 8 ] = 'genome size (bp)' header [ 5 ] = '#SCGs' header [ 6 ] = '#SCG duplicates' continue ID , info = line [ 0 ] , line info = [ to_int ( i ) for i in info ] ID = ID . replace ( ' ' , '' ) g2info [ ID ] = { item : stat for item , stat in zip ( header , info ) } if g2info [ ID ] [ 'genome size (bp)' ] == '' : g2info [ ID ] [ 'genome size (bp)' ] = 0 return g2info | 61 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L215-L235 | [
"def",
"start_transmit",
"(",
"self",
",",
"blocking",
"=",
"False",
",",
"start_packet_groups",
"=",
"True",
",",
"*",
"ports",
")",
":",
"port_list",
"=",
"self",
".",
"set_ports_list",
"(",
"*",
"ports",
")",
"if",
"start_packet_groups",
":",
"port_list_for_packet_groups",
"=",
"self",
".",
"ports",
".",
"values",
"(",
")",
"port_list_for_packet_groups",
"=",
"self",
".",
"set_ports_list",
"(",
"*",
"port_list_for_packet_groups",
")",
"self",
".",
"api",
".",
"call_rc",
"(",
"'ixClearTimeStamp {}'",
".",
"format",
"(",
"port_list_for_packet_groups",
")",
")",
"self",
".",
"api",
".",
"call_rc",
"(",
"'ixStartPacketGroups {}'",
".",
"format",
"(",
"port_list_for_packet_groups",
")",
")",
"self",
".",
"api",
".",
"call_rc",
"(",
"'ixStartTransmit {}'",
".",
"format",
"(",
"port_list",
")",
")",
"time",
".",
"sleep",
"(",
"0.2",
")",
"if",
"blocking",
":",
"self",
".",
"wait_transmit",
"(",
"*",
"ports",
")"
] |
get genome lengths | def genome_lengths ( fastas , info ) : if info is False : info = { } for genome in fastas : name = genome . rsplit ( '.' , 1 ) [ 0 ] . rsplit ( '/' , 1 ) [ - 1 ] . rsplit ( '.contigs' ) [ 0 ] if name in info : continue length = 0 fragments = 0 for seq in parse_fasta ( genome ) : length += len ( seq [ 1 ] ) fragments += 1 info [ name ] = { 'genome size (bp)' : length , '# contigs' : fragments } return info | 62 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/cluster_ani.py#L237-L253 | [
"def",
"serverinfo",
"(",
"url",
"=",
"'http://localhost:8080/manager'",
",",
"timeout",
"=",
"180",
")",
":",
"data",
"=",
"_wget",
"(",
"'serverinfo'",
",",
"{",
"}",
",",
"url",
",",
"timeout",
"=",
"timeout",
")",
"if",
"data",
"[",
"'res'",
"]",
"is",
"False",
":",
"return",
"{",
"'error'",
":",
"data",
"[",
"'msg'",
"]",
"}",
"ret",
"=",
"{",
"}",
"data",
"[",
"'msg'",
"]",
".",
"pop",
"(",
"0",
")",
"for",
"line",
"in",
"data",
"[",
"'msg'",
"]",
":",
"tmp",
"=",
"line",
".",
"split",
"(",
"':'",
")",
"ret",
"[",
"tmp",
"[",
"0",
"]",
".",
"strip",
"(",
")",
"]",
"=",
"tmp",
"[",
"1",
"]",
".",
"strip",
"(",
")",
"return",
"ret"
] |
Returns a list of db keys to route the given call to . | def get_dbs ( self , attr , args , kwargs , * * fkwargs ) : if not self . _ready : if not self . setup_router ( args = args , kwargs = kwargs , * * fkwargs ) : raise self . UnableToSetupRouter ( ) retval = self . _pre_routing ( attr = attr , args = args , kwargs = kwargs , * * fkwargs ) if retval is not None : args , kwargs = retval if not ( args or kwargs ) : return self . cluster . hosts . keys ( ) try : db_nums = self . _route ( attr = attr , args = args , kwargs = kwargs , * * fkwargs ) except Exception as e : self . _handle_exception ( e ) db_nums = [ ] return self . _post_routing ( attr = attr , db_nums = db_nums , args = args , kwargs = kwargs , * * fkwargs ) | 63 | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L50-L81 | [
"async",
"def",
"write",
"(",
"self",
",",
"writer",
":",
"Any",
",",
"close_boundary",
":",
"bool",
"=",
"True",
")",
"->",
"None",
":",
"if",
"not",
"self",
".",
"_parts",
":",
"return",
"for",
"part",
",",
"encoding",
",",
"te_encoding",
"in",
"self",
".",
"_parts",
":",
"await",
"writer",
".",
"write",
"(",
"b'--'",
"+",
"self",
".",
"_boundary",
"+",
"b'\\r\\n'",
")",
"await",
"writer",
".",
"write",
"(",
"part",
".",
"_binary_headers",
")",
"if",
"encoding",
"or",
"te_encoding",
":",
"w",
"=",
"MultipartPayloadWriter",
"(",
"writer",
")",
"if",
"encoding",
":",
"w",
".",
"enable_compression",
"(",
"encoding",
")",
"if",
"te_encoding",
":",
"w",
".",
"enable_encoding",
"(",
"te_encoding",
")",
"await",
"part",
".",
"write",
"(",
"w",
")",
"# type: ignore",
"await",
"w",
".",
"write_eof",
"(",
")",
"else",
":",
"await",
"part",
".",
"write",
"(",
"writer",
")",
"await",
"writer",
".",
"write",
"(",
"b'\\r\\n'",
")",
"if",
"close_boundary",
":",
"await",
"writer",
".",
"write",
"(",
"b'--'",
"+",
"self",
".",
"_boundary",
"+",
"b'--\\r\\n'",
")"
] |
Call method to perform any setup | def setup_router ( self , args , kwargs , * * fkwargs ) : self . _ready = self . _setup_router ( args = args , kwargs = kwargs , * * fkwargs ) return self . _ready | 64 | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L87-L93 | [
"def",
"load_stl_ascii",
"(",
"file_obj",
")",
":",
"# the first line is the header",
"header",
"=",
"file_obj",
".",
"readline",
"(",
")",
"# make sure header is a string, not bytes",
"if",
"hasattr",
"(",
"header",
",",
"'decode'",
")",
":",
"try",
":",
"header",
"=",
"header",
".",
"decode",
"(",
"'utf-8'",
")",
"except",
"BaseException",
":",
"header",
"=",
"''",
"# save header to metadata",
"metadata",
"=",
"{",
"'header'",
":",
"header",
"}",
"# read all text into one string",
"text",
"=",
"file_obj",
".",
"read",
"(",
")",
"# convert bytes to string",
"if",
"hasattr",
"(",
"text",
",",
"'decode'",
")",
":",
"text",
"=",
"text",
".",
"decode",
"(",
"'utf-8'",
")",
"# split by endsolid keyword",
"text",
"=",
"text",
".",
"lower",
"(",
")",
".",
"split",
"(",
"'endsolid'",
")",
"[",
"0",
"]",
"# create array of splits",
"blob",
"=",
"np",
".",
"array",
"(",
"text",
".",
"strip",
"(",
")",
".",
"split",
"(",
")",
")",
"# there are 21 'words' in each face",
"face_len",
"=",
"21",
"# length of blob should be multiple of face_len",
"if",
"(",
"len",
"(",
"blob",
")",
"%",
"face_len",
")",
"!=",
"0",
":",
"raise",
"HeaderError",
"(",
"'Incorrect length STL file!'",
")",
"face_count",
"=",
"int",
"(",
"len",
"(",
"blob",
")",
"/",
"face_len",
")",
"# this offset is to be added to a fixed set of tiled indices",
"offset",
"=",
"face_len",
"*",
"np",
".",
"arange",
"(",
"face_count",
")",
".",
"reshape",
"(",
"(",
"-",
"1",
",",
"1",
")",
")",
"normal_index",
"=",
"np",
".",
"tile",
"(",
"[",
"2",
",",
"3",
",",
"4",
"]",
",",
"(",
"face_count",
",",
"1",
")",
")",
"+",
"offset",
"vertex_index",
"=",
"np",
".",
"tile",
"(",
"[",
"8",
",",
"9",
",",
"10",
",",
"12",
",",
"13",
",",
"14",
",",
"16",
",",
"17",
",",
"18",
"]",
",",
"(",
"face_count",
",",
"1",
")",
")",
"+",
"offset",
"# faces are groups of three sequential vertices",
"faces",
"=",
"np",
".",
"arange",
"(",
"face_count",
"*",
"3",
")",
".",
"reshape",
"(",
"(",
"-",
"1",
",",
"3",
")",
")",
"face_normals",
"=",
"blob",
"[",
"normal_index",
"]",
".",
"astype",
"(",
"'<f8'",
")",
"vertices",
"=",
"blob",
"[",
"vertex_index",
".",
"reshape",
"(",
"(",
"-",
"1",
",",
"3",
")",
")",
"]",
".",
"astype",
"(",
"'<f8'",
")",
"return",
"{",
"'vertices'",
":",
"vertices",
",",
"'faces'",
":",
"faces",
",",
"'metadata'",
":",
"metadata",
",",
"'face_normals'",
":",
"face_normals",
"}"
] |
Perform routing and return db_nums | def _route ( self , attr , args , kwargs , * * fkwargs ) : return self . cluster . hosts . keys ( ) | 65 | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L111-L115 | [
"def",
"get_thumbnail",
"(",
"self",
",",
"video_path",
",",
"at_time",
"=",
"0.5",
")",
":",
"filename",
"=",
"os",
".",
"path",
".",
"basename",
"(",
"video_path",
")",
"filename",
",",
"__",
"=",
"os",
".",
"path",
".",
"splitext",
"(",
"filename",
")",
"_",
",",
"image_path",
"=",
"tempfile",
".",
"mkstemp",
"(",
"suffix",
"=",
"'_{}.jpg'",
".",
"format",
"(",
"filename",
")",
")",
"video_duration",
"=",
"self",
".",
"get_media_info",
"(",
"video_path",
")",
"[",
"'duration'",
"]",
"if",
"at_time",
">",
"video_duration",
":",
"raise",
"exceptions",
".",
"InvalidTimeError",
"(",
")",
"thumbnail_time",
"=",
"at_time",
"cmds",
"=",
"[",
"self",
".",
"ffmpeg_path",
",",
"'-i'",
",",
"video_path",
",",
"'-vframes'",
",",
"'1'",
"]",
"cmds",
".",
"extend",
"(",
"[",
"'-ss'",
",",
"str",
"(",
"thumbnail_time",
")",
",",
"'-y'",
",",
"image_path",
"]",
")",
"process",
"=",
"self",
".",
"_spawn",
"(",
"cmds",
")",
"self",
".",
"_check_returncode",
"(",
"process",
")",
"if",
"not",
"os",
".",
"path",
".",
"getsize",
"(",
"image_path",
")",
":",
"# we somehow failed to generate thumbnail",
"os",
".",
"unlink",
"(",
"image_path",
")",
"raise",
"exceptions",
".",
"InvalidTimeError",
"(",
")",
"return",
"image_path"
] |
Iterates through all connections which were previously listed as unavailable and marks any that have expired their retry_timeout as being up . | def check_down_connections ( self ) : now = time . time ( ) for db_num , marked_down_at in self . _down_connections . items ( ) : if marked_down_at + self . retry_timeout <= now : self . mark_connection_up ( db_num ) | 66 | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L175-L184 | [
"def",
"transform_sparql_construct",
"(",
"rdf",
",",
"construct_query",
")",
":",
"logging",
".",
"debug",
"(",
"\"performing SPARQL CONSTRUCT transformation\"",
")",
"if",
"construct_query",
"[",
"0",
"]",
"==",
"'@'",
":",
"# actual query should be read from file",
"construct_query",
"=",
"file",
"(",
"construct_query",
"[",
"1",
":",
"]",
")",
".",
"read",
"(",
")",
"logging",
".",
"debug",
"(",
"\"CONSTRUCT query: %s\"",
",",
"construct_query",
")",
"newgraph",
"=",
"Graph",
"(",
")",
"for",
"triple",
"in",
"rdf",
".",
"query",
"(",
"construct_query",
")",
":",
"newgraph",
".",
"add",
"(",
"triple",
")",
"return",
"newgraph"
] |
Marks all connections which were previously listed as unavailable as being up . | def flush_down_connections ( self ) : self . _get_db_attempts = 0 for db_num in self . _down_connections . keys ( ) : self . mark_connection_up ( db_num ) | 67 | https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/routers/base.py#L186-L192 | [
"def",
"_op_generic_Ctz",
"(",
"self",
",",
"args",
")",
":",
"wtf_expr",
"=",
"claripy",
".",
"BVV",
"(",
"self",
".",
"_from_size",
",",
"self",
".",
"_from_size",
")",
"for",
"a",
"in",
"reversed",
"(",
"range",
"(",
"self",
".",
"_from_size",
")",
")",
":",
"bit",
"=",
"claripy",
".",
"Extract",
"(",
"a",
",",
"a",
",",
"args",
"[",
"0",
"]",
")",
"wtf_expr",
"=",
"claripy",
".",
"If",
"(",
"bit",
"==",
"1",
",",
"claripy",
".",
"BVV",
"(",
"a",
",",
"self",
".",
"_from_size",
")",
",",
"wtf_expr",
")",
"return",
"wtf_expr"
] |
Compute standby power | def standby ( df , resolution = '24h' , time_window = None ) : if df . empty : raise EmptyDataFrame ( ) df = pd . DataFrame ( df ) # if df was a pd.Series, convert to DataFrame def parse_time ( t ) : if isinstance ( t , numbers . Number ) : return pd . Timestamp . utcfromtimestamp ( t ) . time ( ) else : return pd . Timestamp ( t ) . time ( ) # first filter based on the time-window if time_window is not None : t_start = parse_time ( time_window [ 0 ] ) t_end = parse_time ( time_window [ 1 ] ) if t_start > t_end : # start before midnight df = df [ ( df . index . time >= t_start ) | ( df . index . time < t_end ) ] else : df = df [ ( df . index . time >= t_start ) & ( df . index . time < t_end ) ] return df . resample ( resolution ) . min ( ) | 68 | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/analysis.py#L72-L115 | [
"def",
"generate_http_manifest",
"(",
"self",
")",
":",
"base_path",
"=",
"os",
".",
"path",
".",
"dirname",
"(",
"self",
".",
"translate_path",
"(",
"self",
".",
"path",
")",
")",
"self",
".",
"dataset",
"=",
"dtoolcore",
".",
"DataSet",
".",
"from_uri",
"(",
"base_path",
")",
"admin_metadata_fpath",
"=",
"os",
".",
"path",
".",
"join",
"(",
"base_path",
",",
"\".dtool\"",
",",
"\"dtool\"",
")",
"with",
"open",
"(",
"admin_metadata_fpath",
")",
"as",
"fh",
":",
"admin_metadata",
"=",
"json",
".",
"load",
"(",
"fh",
")",
"http_manifest",
"=",
"{",
"\"admin_metadata\"",
":",
"admin_metadata",
",",
"\"manifest_url\"",
":",
"self",
".",
"generate_url",
"(",
"\".dtool/manifest.json\"",
")",
",",
"\"readme_url\"",
":",
"self",
".",
"generate_url",
"(",
"\"README.yml\"",
")",
",",
"\"overlays\"",
":",
"self",
".",
"generate_overlay_urls",
"(",
")",
",",
"\"item_urls\"",
":",
"self",
".",
"generate_item_urls",
"(",
")",
"}",
"return",
"bytes",
"(",
"json",
".",
"dumps",
"(",
"http_manifest",
")",
",",
"\"utf-8\"",
")"
] |
Compute the share of the standby power in the total consumption . | def share_of_standby ( df , resolution = '24h' , time_window = None ) : p_sb = standby ( df , resolution , time_window ) df = df . resample ( resolution ) . mean ( ) p_tot = df . sum ( ) p_standby = p_sb . sum ( ) share_standby = p_standby / p_tot res = share_standby . iloc [ 0 ] return res | 69 | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/analysis.py#L118-L146 | [
"def",
"getAsKmlPngAnimation",
"(",
"self",
",",
"session",
",",
"projectFile",
"=",
"None",
",",
"path",
"=",
"None",
",",
"documentName",
"=",
"None",
",",
"colorRamp",
"=",
"None",
",",
"alpha",
"=",
"1.0",
",",
"noDataValue",
"=",
"0",
",",
"drawOrder",
"=",
"0",
",",
"cellSize",
"=",
"None",
",",
"resampleMethod",
"=",
"'NearestNeighbour'",
")",
":",
"# Prepare rasters",
"timeStampedRasters",
"=",
"self",
".",
"_assembleRasterParams",
"(",
"projectFile",
",",
"self",
".",
"rasters",
")",
"# Make sure the raster field is valid",
"converter",
"=",
"RasterConverter",
"(",
"sqlAlchemyEngineOrSession",
"=",
"session",
")",
"# Configure color ramp",
"if",
"isinstance",
"(",
"colorRamp",
",",
"dict",
")",
":",
"converter",
".",
"setCustomColorRamp",
"(",
"colorRamp",
"[",
"'colors'",
"]",
",",
"colorRamp",
"[",
"'interpolatedPoints'",
"]",
")",
"else",
":",
"converter",
".",
"setDefaultColorRamp",
"(",
"colorRamp",
")",
"if",
"documentName",
"is",
"None",
":",
"documentName",
"=",
"self",
".",
"fileExtension",
"kmlString",
",",
"binaryPngStrings",
"=",
"converter",
".",
"getAsKmlPngAnimation",
"(",
"tableName",
"=",
"WMSDatasetRaster",
".",
"tableName",
",",
"timeStampedRasters",
"=",
"timeStampedRasters",
",",
"rasterIdFieldName",
"=",
"'id'",
",",
"rasterFieldName",
"=",
"'raster'",
",",
"documentName",
"=",
"documentName",
",",
"alpha",
"=",
"alpha",
",",
"drawOrder",
"=",
"drawOrder",
",",
"cellSize",
"=",
"cellSize",
",",
"noDataValue",
"=",
"noDataValue",
",",
"resampleMethod",
"=",
"resampleMethod",
")",
"if",
"path",
":",
"directory",
"=",
"os",
".",
"path",
".",
"dirname",
"(",
"path",
")",
"archiveName",
"=",
"(",
"os",
".",
"path",
".",
"split",
"(",
"path",
")",
"[",
"1",
"]",
")",
".",
"split",
"(",
"'.'",
")",
"[",
"0",
"]",
"kmzPath",
"=",
"os",
".",
"path",
".",
"join",
"(",
"directory",
",",
"(",
"archiveName",
"+",
"'.kmz'",
")",
")",
"with",
"ZipFile",
"(",
"kmzPath",
",",
"'w'",
")",
"as",
"kmz",
":",
"kmz",
".",
"writestr",
"(",
"archiveName",
"+",
"'.kml'",
",",
"kmlString",
")",
"for",
"index",
",",
"binaryPngString",
"in",
"enumerate",
"(",
"binaryPngStrings",
")",
":",
"kmz",
".",
"writestr",
"(",
"'raster{0}.png'",
".",
"format",
"(",
"index",
")",
",",
"binaryPngString",
")",
"return",
"kmlString",
",",
"binaryPngStrings"
] |
Toggle counter for gas boilers | def count_peaks ( ts ) : on_toggles = ts . diff ( ) > 3000 shifted = np . logical_not ( on_toggles . shift ( 1 ) ) result = on_toggles & shifted count = result . sum ( ) return count | 70 | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/analysis.py#L149-L169 | [
"def",
"users",
"(",
"self",
",",
"start",
"=",
"1",
",",
"num",
"=",
"10",
",",
"sortField",
"=",
"\"fullName\"",
",",
"sortOrder",
"=",
"\"asc\"",
",",
"role",
"=",
"None",
")",
":",
"users",
"=",
"[",
"]",
"url",
"=",
"self",
".",
"_url",
"+",
"\"/users\"",
"params",
"=",
"{",
"\"f\"",
":",
"\"json\"",
",",
"\"start\"",
":",
"start",
",",
"\"num\"",
":",
"num",
"}",
"if",
"not",
"role",
"is",
"None",
":",
"params",
"[",
"'role'",
"]",
"=",
"role",
"if",
"not",
"sortField",
"is",
"None",
":",
"params",
"[",
"'sortField'",
"]",
"=",
"sortField",
"if",
"not",
"sortOrder",
"is",
"None",
":",
"params",
"[",
"'sortOrder'",
"]",
"=",
"sortOrder",
"from",
".",
"_community",
"import",
"Community",
"res",
"=",
"self",
".",
"_post",
"(",
"url",
"=",
"url",
",",
"param_dict",
"=",
"params",
",",
"securityHandler",
"=",
"self",
".",
"_securityHandler",
",",
"proxy_url",
"=",
"self",
".",
"_proxy_url",
",",
"proxy_port",
"=",
"self",
".",
"_proxy_port",
")",
"if",
"\"users\"",
"in",
"res",
":",
"if",
"len",
"(",
"res",
"[",
"'users'",
"]",
")",
">",
"0",
":",
"parsed",
"=",
"urlparse",
".",
"urlparse",
"(",
"self",
".",
"_url",
")",
"if",
"parsed",
".",
"netloc",
".",
"lower",
"(",
")",
".",
"find",
"(",
"'arcgis.com'",
")",
"==",
"-",
"1",
":",
"cURL",
"=",
"\"%s://%s/%s/sharing/rest/community\"",
"%",
"(",
"parsed",
".",
"scheme",
",",
"parsed",
".",
"netloc",
",",
"parsed",
".",
"path",
"[",
"1",
":",
"]",
".",
"split",
"(",
"'/'",
")",
"[",
"0",
"]",
")",
"else",
":",
"cURL",
"=",
"\"%s://%s/sharing/rest/community\"",
"%",
"(",
"parsed",
".",
"scheme",
",",
"parsed",
".",
"netloc",
")",
"com",
"=",
"Community",
"(",
"url",
"=",
"cURL",
",",
"securityHandler",
"=",
"self",
".",
"_securityHandler",
",",
"proxy_url",
"=",
"self",
".",
"_proxy_url",
",",
"proxy_port",
"=",
"self",
".",
"_proxy_port",
")",
"for",
"r",
"in",
"res",
"[",
"'users'",
"]",
":",
"users",
".",
"append",
"(",
"com",
".",
"users",
".",
"user",
"(",
"r",
"[",
"\"username\"",
"]",
")",
")",
"res",
"[",
"'users'",
"]",
"=",
"users",
"return",
"res"
] |
Calculate the ratio of input vs . norm over a given interval . | def load_factor ( ts , resolution = None , norm = None ) : if norm is None : norm = ts . max ( ) if resolution is not None : ts = ts . resample ( rule = resolution ) . mean ( ) lf = ts / norm return lf | 71 | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/analysis.py#L172-L199 | [
"def",
"unbind",
"(",
"self",
",",
"devices_to_unbind",
")",
":",
"if",
"self",
".",
"entity_api_key",
"==",
"\"\"",
":",
"return",
"{",
"'status'",
":",
"'failure'",
",",
"'response'",
":",
"'No API key found in request'",
"}",
"url",
"=",
"self",
".",
"base_url",
"+",
"\"api/0.1.0/subscribe/unbind\"",
"headers",
"=",
"{",
"\"apikey\"",
":",
"self",
".",
"entity_api_key",
"}",
"data",
"=",
"{",
"\"exchange\"",
":",
"\"amq.topic\"",
",",
"\"keys\"",
":",
"devices_to_unbind",
",",
"\"queue\"",
":",
"self",
".",
"entity_id",
"}",
"with",
"self",
".",
"no_ssl_verification",
"(",
")",
":",
"r",
"=",
"requests",
".",
"delete",
"(",
"url",
",",
"json",
"=",
"data",
",",
"headers",
"=",
"headers",
")",
"print",
"(",
"r",
")",
"response",
"=",
"dict",
"(",
")",
"if",
"\"No API key\"",
"in",
"str",
"(",
"r",
".",
"content",
".",
"decode",
"(",
"\"utf-8\"",
")",
")",
":",
"response",
"[",
"\"status\"",
"]",
"=",
"\"failure\"",
"r",
"=",
"json",
".",
"loads",
"(",
"r",
".",
"content",
".",
"decode",
"(",
"\"utf-8\"",
")",
")",
"[",
"'message'",
"]",
"elif",
"'unbind'",
"in",
"str",
"(",
"r",
".",
"content",
".",
"decode",
"(",
"\"utf-8\"",
")",
")",
":",
"response",
"[",
"\"status\"",
"]",
"=",
"\"success\"",
"r",
"=",
"r",
".",
"content",
".",
"decode",
"(",
"\"utf-8\"",
")",
"else",
":",
"response",
"[",
"\"status\"",
"]",
"=",
"\"failure\"",
"r",
"=",
"r",
".",
"content",
".",
"decode",
"(",
"\"utf-8\"",
")",
"response",
"[",
"\"response\"",
"]",
"=",
"str",
"(",
"r",
")",
"return",
"response"
] |
get top hits after sorting by column number | def top_hits ( hits , num , column , reverse ) : hits . sort ( key = itemgetter ( column ) , reverse = reverse ) for hit in hits [ 0 : num ] : yield hit | 72 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/besthits.py#L17-L23 | [
"def",
"_openResources",
"(",
"self",
")",
":",
"try",
":",
"rate",
",",
"data",
"=",
"scipy",
".",
"io",
".",
"wavfile",
".",
"read",
"(",
"self",
".",
"_fileName",
",",
"mmap",
"=",
"True",
")",
"except",
"Exception",
"as",
"ex",
":",
"logger",
".",
"warning",
"(",
"ex",
")",
"logger",
".",
"warning",
"(",
"\"Unable to read wav with memmory mapping. Trying without now.\"",
")",
"rate",
",",
"data",
"=",
"scipy",
".",
"io",
".",
"wavfile",
".",
"read",
"(",
"self",
".",
"_fileName",
",",
"mmap",
"=",
"False",
")",
"self",
".",
"_array",
"=",
"data",
"self",
".",
"attributes",
"[",
"'rate'",
"]",
"=",
"rate"
] |
parse b6 output with sorting | def numBlast_sort ( blast , numHits , evalueT , bitT ) : header = [ '#query' , 'target' , 'pident' , 'alen' , 'mismatch' , 'gapopen' , 'qstart' , 'qend' , 'tstart' , 'tend' , 'evalue' , 'bitscore' ] yield header hmm = { h : [ ] for h in header } for line in blast : if line . startswith ( '#' ) : continue line = line . strip ( ) . split ( '\t' ) # Evalue and Bitscore thresholds line [ 10 ] , line [ 11 ] = float ( line [ 10 ] ) , float ( line [ 11 ] ) evalue , bit = line [ 10 ] , line [ 11 ] if evalueT is not False and evalue > evalueT : continue if bitT is not False and bit < bitT : continue for i , h in zip ( line , header ) : hmm [ h ] . append ( i ) hmm = pd . DataFrame ( hmm ) for query , df in hmm . groupby ( by = [ '#query' ] ) : df = df . sort_values ( by = [ 'bitscore' ] , ascending = False ) for hit in df [ header ] . values [ 0 : numHits ] : yield hit | 73 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/besthits.py#L25-L50 | [
"def",
"bind_texture",
"(",
"texture",
")",
":",
"if",
"not",
"getattr",
"(",
"texture",
",",
"'image'",
",",
"None",
")",
":",
"texture",
".",
"image",
"=",
"load_image",
"(",
"texture",
".",
"path",
")",
"glEnable",
"(",
"texture",
".",
"image",
".",
"target",
")",
"glBindTexture",
"(",
"texture",
".",
"image",
".",
"target",
",",
"texture",
".",
"image",
".",
"id",
")",
"gl",
".",
"glTexParameterf",
"(",
"texture",
".",
"image",
".",
"target",
",",
"gl",
".",
"GL_TEXTURE_WRAP_S",
",",
"gl",
".",
"GL_CLAMP_TO_EDGE",
")",
"gl",
".",
"glTexParameterf",
"(",
"texture",
".",
"image",
".",
"target",
",",
"gl",
".",
"GL_TEXTURE_WRAP_T",
",",
"gl",
".",
"GL_CLAMP_TO_EDGE",
")"
] |
parse b6 output | def numBlast ( blast , numHits , evalueT = False , bitT = False , sort = False ) : if sort is True : for hit in numBlast_sort ( blast , numHits , evalueT , bitT ) : yield hit return header = [ '#query' , 'target' , 'pident' , 'alen' , 'mismatch' , 'gapopen' , 'qstart' , 'qend' , 'tstart' , 'tend' , 'evalue' , 'bitscore' ] yield header prev , hits = None , [ ] for line in blast : line = line . strip ( ) . split ( '\t' ) ID = line [ 0 ] line [ 10 ] , line [ 11 ] = float ( line [ 10 ] ) , float ( line [ 11 ] ) evalue , bit = line [ 10 ] , line [ 11 ] if ID != prev : if len ( hits ) > 0 : # column is 1 + line index for hit in top_hits ( hits , numHits , 11 , True ) : yield hit hits = [ ] if evalueT == False and bitT == False : hits . append ( line ) elif evalue <= evalueT and bitT == False : hits . append ( line ) elif evalue <= evalueT and bit >= bitT : hits . append ( line ) elif evalueT == False and bit >= bitT : hits . append ( line ) prev = ID for hit in top_hits ( hits , numHits , 11 , True ) : yield hit | 74 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/besthits.py#L52-L85 | [
"def",
"__getBio",
"(",
"self",
",",
"web",
")",
":",
"bio",
"=",
"web",
".",
"find_all",
"(",
"\"div\"",
",",
"{",
"\"class\"",
":",
"\"user-profile-bio\"",
"}",
")",
"if",
"bio",
":",
"try",
":",
"bio",
"=",
"bio",
"[",
"0",
"]",
".",
"text",
"if",
"bio",
"and",
"GitHubUser",
".",
"isASCII",
"(",
"bio",
")",
":",
"bioText",
"=",
"bio",
".",
"replace",
"(",
"\"\\n\"",
",",
"\"\"",
")",
"bioText",
"=",
"bioText",
".",
"replace",
"(",
"\"\\t\"",
",",
"\" \"",
")",
".",
"replace",
"(",
"\"\\\"\"",
",",
"\"\"",
")",
"bioText",
"=",
"bioText",
".",
"replace",
"(",
"\"\\'\"",
",",
"\"\"",
")",
".",
"replace",
"(",
"\"\\\\\"",
",",
"\"\"",
")",
"self",
".",
"bio",
"=",
"bioText",
"else",
":",
"self",
".",
"bio",
"=",
"\"\"",
"except",
"IndexError",
"as",
"error",
":",
"print",
"(",
"\"There was an error with the user \"",
"+",
"self",
".",
"name",
")",
"print",
"(",
"error",
")",
"except",
"AttributeError",
"as",
"error",
":",
"print",
"(",
"\"There was an error with the user \"",
"+",
"self",
".",
"name",
")",
"print",
"(",
"error",
")"
] |
parse hmm domain table output this version is faster but does not work unless the table is sorted | def numDomtblout ( domtblout , numHits , evalueT , bitT , sort ) : if sort is True : for hit in numDomtblout_sort ( domtblout , numHits , evalueT , bitT ) : yield hit return header = [ '#target name' , 'target accession' , 'tlen' , 'query name' , 'query accession' , 'qlen' , 'full E-value' , 'full score' , 'full bias' , 'domain #' , '# domains' , 'domain c-Evalue' , 'domain i-Evalue' , 'domain score' , 'domain bias' , 'hmm from' , 'hmm to' , 'seq from' , 'seq to' , 'env from' , 'env to' , 'acc' , 'target description' ] yield header prev , hits = None , [ ] for line in domtblout : if line . startswith ( '#' ) : continue # parse line and get description line = line . strip ( ) . split ( ) desc = ' ' . join ( line [ 18 : ] ) line = line [ 0 : 18 ] line . append ( desc ) # create ID based on query name and domain number ID = line [ 0 ] + line [ 9 ] # domain c-Evalue and domain score thresholds line [ 11 ] , line [ 13 ] = float ( line [ 11 ] ) , float ( line [ 13 ] ) evalue , bitscore = line [ 11 ] , line [ 13 ] line [ 11 ] , line [ 13 ] = evalue , bitscore if ID != prev : if len ( hits ) > 0 : for hit in top_hits ( hits , numHits , 13 , True ) : yield hit hits = [ ] if evalueT == False and bitT == False : hits . append ( line ) elif evalue <= evalueT and bitT == False : hits . append ( line ) elif evalue <= evalueT and bit >= bitT : hits . append ( line ) elif evalueT == False and bit >= bitT : hits . append ( line ) prev = ID for hit in top_hits ( hits , numHits , 13 , True ) : yield hit | 75 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/besthits.py#L121-L168 | [
"def",
"files_comments_delete",
"(",
"self",
",",
"*",
",",
"file",
":",
"str",
",",
"id",
":",
"str",
",",
"*",
"*",
"kwargs",
")",
"->",
"SlackResponse",
":",
"kwargs",
".",
"update",
"(",
"{",
"\"file\"",
":",
"file",
",",
"\"id\"",
":",
"id",
"}",
")",
"return",
"self",
".",
"api_call",
"(",
"\"files.comments.delete\"",
",",
"json",
"=",
"kwargs",
")"
] |
convert stockholm to fasta | def stock2fa ( stock ) : seqs = { } for line in stock : if line . startswith ( '#' ) is False and line . startswith ( ' ' ) is False and len ( line ) > 3 : id , seq = line . strip ( ) . split ( ) id = id . rsplit ( '/' , 1 ) [ 0 ] id = re . split ( '[0-9]\|' , id , 1 ) [ - 1 ] if id not in seqs : seqs [ id ] = [ ] seqs [ id ] . append ( seq ) if line . startswith ( '//' ) : break return seqs | 76 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/stockholm2fa.py#L11-L26 | [
"def",
"list_tables",
"(",
")",
":",
"tables",
"=",
"[",
"]",
"try",
":",
"table_list",
"=",
"DYNAMODB_CONNECTION",
".",
"list_tables",
"(",
")",
"while",
"True",
":",
"for",
"table_name",
"in",
"table_list",
"[",
"u'TableNames'",
"]",
":",
"tables",
".",
"append",
"(",
"get_table",
"(",
"table_name",
")",
")",
"if",
"u'LastEvaluatedTableName'",
"in",
"table_list",
":",
"table_list",
"=",
"DYNAMODB_CONNECTION",
".",
"list_tables",
"(",
"table_list",
"[",
"u'LastEvaluatedTableName'",
"]",
")",
"else",
":",
"break",
"except",
"DynamoDBResponseError",
"as",
"error",
":",
"dynamodb_error",
"=",
"error",
".",
"body",
"[",
"'__type'",
"]",
".",
"rsplit",
"(",
"'#'",
",",
"1",
")",
"[",
"1",
"]",
"if",
"dynamodb_error",
"==",
"'ResourceNotFoundException'",
":",
"logger",
".",
"error",
"(",
"'No tables found'",
")",
"elif",
"dynamodb_error",
"==",
"'AccessDeniedException'",
":",
"logger",
".",
"debug",
"(",
"'Your AWS API keys lack access to listing tables. '",
"'That is an issue if you are trying to use regular '",
"'expressions in your table configuration.'",
")",
"elif",
"dynamodb_error",
"==",
"'UnrecognizedClientException'",
":",
"logger",
".",
"error",
"(",
"'Invalid security token. Are your AWS API keys correct?'",
")",
"else",
":",
"logger",
".",
"error",
"(",
"(",
"'Unhandled exception: {0}: {1}. '",
"'Please file a bug report at '",
"'https://github.com/sebdah/dynamic-dynamodb/issues'",
")",
".",
"format",
"(",
"dynamodb_error",
",",
"error",
".",
"body",
"[",
"'message'",
"]",
")",
")",
"except",
"JSONResponseError",
"as",
"error",
":",
"logger",
".",
"error",
"(",
"'Communication error: {0}'",
".",
"format",
"(",
"error",
")",
")",
"sys",
".",
"exit",
"(",
"1",
")",
"return",
"tables"
] |
Return boolean time series following given week schedule . | def week_schedule ( index , on_time = None , off_time = None , off_days = None ) : if on_time is None : on_time = '9:00' if off_time is None : off_time = '17:00' if off_days is None : off_days = [ 'Sunday' , 'Monday' ] if not isinstance ( on_time , datetime . time ) : on_time = pd . to_datetime ( on_time , format = '%H:%M' ) . time ( ) if not isinstance ( off_time , datetime . time ) : off_time = pd . to_datetime ( off_time , format = '%H:%M' ) . time ( ) times = ( index . time >= on_time ) & ( index . time < off_time ) & ( ~ index . weekday_name . isin ( off_days ) ) return pd . Series ( times , index = index ) | 77 | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/utils.py#L10-L47 | [
"def",
"removeAllEntitlements",
"(",
"self",
",",
"appId",
")",
":",
"params",
"=",
"{",
"\"f\"",
":",
"\"json\"",
",",
"\"appId\"",
":",
"appId",
"}",
"url",
"=",
"self",
".",
"_url",
"+",
"\"/licenses/removeAllEntitlements\"",
"return",
"self",
".",
"_post",
"(",
"url",
"=",
"url",
",",
"param_dict",
"=",
"params",
",",
"proxy_url",
"=",
"self",
".",
"_proxy_url",
",",
"proxy_port",
"=",
"self",
".",
"_proxy_port",
")"
] |
Draw a carpet plot of a pandas timeseries . | def carpet ( timeseries , * * kwargs ) : # define optional input parameters cmap = kwargs . pop ( 'cmap' , cm . coolwarm ) norm = kwargs . pop ( 'norm' , LogNorm ( ) ) interpolation = kwargs . pop ( 'interpolation' , 'nearest' ) cblabel = kwargs . pop ( 'zlabel' , timeseries . name if timeseries . name else '' ) title = kwargs . pop ( 'title' , 'carpet plot: ' + timeseries . name if timeseries . name else '' ) # data preparation if timeseries . dropna ( ) . empty : print ( 'skipped {} - no data' . format ( title ) ) return ts = timeseries . resample ( '15min' ) . interpolate ( ) vmin = max ( 0.1 , kwargs . pop ( 'vmin' , ts [ ts > 0 ] . min ( ) ) ) vmax = max ( vmin , kwargs . pop ( 'vmax' , ts . quantile ( .999 ) ) ) # convert to dataframe with date as index and time as columns by # first replacing the index by a MultiIndex mpldatetimes = date2num ( ts . index . to_pydatetime ( ) ) ts . index = pd . MultiIndex . from_arrays ( [ np . floor ( mpldatetimes ) , 2 + mpldatetimes % 1 ] ) # '2 +': matplotlib bug workaround. # and then unstacking the second index level to columns df = ts . unstack ( ) # data plotting fig , ax = plt . subplots ( ) # define the extent of the axes (remark the +- 0.5 for the y axis in order to obtain aligned date ticks) extent = [ df . columns [ 0 ] , df . columns [ - 1 ] , df . index [ - 1 ] + 0.5 , df . index [ 0 ] - 0.5 ] im = plt . imshow ( df , vmin = vmin , vmax = vmax , extent = extent , cmap = cmap , aspect = 'auto' , norm = norm , interpolation = interpolation , * * kwargs ) # figure formatting # x axis ax . xaxis_date ( ) ax . xaxis . set_major_locator ( HourLocator ( interval = 2 ) ) ax . xaxis . set_major_formatter ( DateFormatter ( '%H:%M' ) ) ax . xaxis . grid ( True ) plt . xlabel ( 'UTC Time' ) # y axis ax . yaxis_date ( ) dmin , dmax = ax . yaxis . get_data_interval ( ) number_of_days = ( num2date ( dmax ) - num2date ( dmin ) ) . days # AutoDateLocator is not suited in case few data is available if abs ( number_of_days ) <= 35 : ax . yaxis . set_major_locator ( DayLocator ( ) ) else : ax . yaxis . set_major_locator ( AutoDateLocator ( ) ) ax . yaxis . set_major_formatter ( DateFormatter ( "%a, %d %b %Y" ) ) # plot colorbar cbticks = np . logspace ( np . log10 ( vmin ) , np . log10 ( vmax ) , 11 , endpoint = True ) cb = plt . colorbar ( format = '%.0f' , ticks = cbticks ) cb . set_label ( cblabel ) # plot title plt . title ( title ) return im | 78 | https://github.com/opengridcc/opengrid/blob/69b8da3c8fcea9300226c45ef0628cd6d4307651/opengrid/library/plotting.py#L34-L125 | [
"async",
"def",
"remove",
"(",
"self",
",",
"von_wallet",
":",
"Wallet",
")",
"->",
"None",
":",
"LOGGER",
".",
"debug",
"(",
"'WalletManager.remove >>> wallet %s'",
",",
"von_wallet",
")",
"await",
"von_wallet",
".",
"remove",
"(",
")",
"LOGGER",
".",
"debug",
"(",
"'WalletManager.remove <<<'",
")"
] |
calculate percent identity | def calc_pident_ignore_gaps ( a , b ) : m = 0 # matches mm = 0 # mismatches for A , B in zip ( list ( a ) , list ( b ) ) : if A == '-' or A == '.' or B == '-' or B == '.' : continue if A == B : m += 1 else : mm += 1 try : return float ( float ( m ) / float ( ( m + mm ) ) ) * 100 except : return 0 | 79 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L34-L50 | [
"def",
"BuildChecks",
"(",
"self",
",",
"request",
")",
":",
"result",
"=",
"[",
"]",
"if",
"request",
".",
"HasField",
"(",
"\"start_time\"",
")",
"or",
"request",
".",
"HasField",
"(",
"\"end_time\"",
")",
":",
"def",
"FilterTimestamp",
"(",
"file_stat",
",",
"request",
"=",
"request",
")",
":",
"return",
"file_stat",
".",
"HasField",
"(",
"\"st_mtime\"",
")",
"and",
"(",
"file_stat",
".",
"st_mtime",
"<",
"request",
".",
"start_time",
"or",
"file_stat",
".",
"st_mtime",
">",
"request",
".",
"end_time",
")",
"result",
".",
"append",
"(",
"FilterTimestamp",
")",
"if",
"request",
".",
"HasField",
"(",
"\"min_file_size\"",
")",
"or",
"request",
".",
"HasField",
"(",
"\"max_file_size\"",
")",
":",
"def",
"FilterSize",
"(",
"file_stat",
",",
"request",
"=",
"request",
")",
":",
"return",
"file_stat",
".",
"HasField",
"(",
"\"st_size\"",
")",
"and",
"(",
"file_stat",
".",
"st_size",
"<",
"request",
".",
"min_file_size",
"or",
"file_stat",
".",
"st_size",
">",
"request",
".",
"max_file_size",
")",
"result",
".",
"append",
"(",
"FilterSize",
")",
"if",
"request",
".",
"HasField",
"(",
"\"perm_mode\"",
")",
":",
"def",
"FilterPerms",
"(",
"file_stat",
",",
"request",
"=",
"request",
")",
":",
"return",
"(",
"file_stat",
".",
"st_mode",
"&",
"request",
".",
"perm_mask",
")",
"!=",
"request",
".",
"perm_mode",
"result",
".",
"append",
"(",
"FilterPerms",
")",
"if",
"request",
".",
"HasField",
"(",
"\"uid\"",
")",
":",
"def",
"FilterUID",
"(",
"file_stat",
",",
"request",
"=",
"request",
")",
":",
"return",
"file_stat",
".",
"st_uid",
"!=",
"request",
".",
"uid",
"result",
".",
"append",
"(",
"FilterUID",
")",
"if",
"request",
".",
"HasField",
"(",
"\"gid\"",
")",
":",
"def",
"FilterGID",
"(",
"file_stat",
",",
"request",
"=",
"request",
")",
":",
"return",
"file_stat",
".",
"st_gid",
"!=",
"request",
".",
"gid",
"result",
".",
"append",
"(",
"FilterGID",
")",
"if",
"request",
".",
"HasField",
"(",
"\"path_regex\"",
")",
":",
"regex",
"=",
"request",
".",
"path_regex",
"def",
"FilterPath",
"(",
"file_stat",
",",
"regex",
"=",
"regex",
")",
":",
"\"\"\"Suppress any filename not matching the regular expression.\"\"\"",
"return",
"not",
"regex",
".",
"Search",
"(",
"file_stat",
".",
"pathspec",
".",
"Basename",
"(",
")",
")",
"result",
".",
"append",
"(",
"FilterPath",
")",
"if",
"request",
".",
"HasField",
"(",
"\"data_regex\"",
")",
":",
"def",
"FilterData",
"(",
"file_stat",
",",
"*",
"*",
"_",
")",
":",
"\"\"\"Suppress files that do not match the content.\"\"\"",
"return",
"not",
"self",
".",
"TestFileContent",
"(",
"file_stat",
")",
"result",
".",
"append",
"(",
"FilterData",
")",
"return",
"result"
] |
skip column if either is a gap | def remove_gaps ( A , B ) : a_seq , b_seq = [ ] , [ ] for a , b in zip ( list ( A ) , list ( B ) ) : if a == '-' or a == '.' or b == '-' or b == '.' : continue a_seq . append ( a ) b_seq . append ( b ) return '' . join ( a_seq ) , '' . join ( b_seq ) | 80 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L52-L62 | [
"def",
"get_needful_files",
"(",
"self",
")",
":",
"manifest",
"=",
"self",
".",
"storage",
".",
"load_manifest",
"(",
")",
"if",
"self",
".",
"keep_unhashed_files",
":",
"if",
"PY3",
":",
"needful_files",
"=",
"set",
"(",
"manifest",
".",
"keys",
"(",
")",
"|",
"manifest",
".",
"values",
"(",
")",
")",
"else",
":",
"needful_files",
"=",
"set",
"(",
"manifest",
".",
"keys",
"(",
")",
"+",
"manifest",
".",
"values",
"(",
")",
")",
"needful_files",
"=",
"{",
"self",
".",
"storage",
".",
"clean_name",
"(",
"file",
")",
"for",
"file",
"in",
"needful_files",
"}",
"else",
":",
"needful_files",
"=",
"set",
"(",
"manifest",
".",
"values",
"(",
")",
")",
"return",
"{",
"self",
".",
"process_file",
"(",
"file",
")",
"for",
"file",
"in",
"needful_files",
"}"
] |
compare pairs of sequences | def compare_seqs ( seqs ) : A , B , ignore_gaps = seqs a , b = A [ 1 ] , B [ 1 ] # actual sequences if len ( a ) != len ( b ) : print ( '# reads are not the same length' , file = sys . stderr ) exit ( ) if ignore_gaps is True : pident = calc_pident_ignore_gaps ( a , b ) else : pident = calc_pident ( a , b ) return A [ 0 ] , B [ 0 ] , pident | 81 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L64-L77 | [
"def",
"color_electrodes",
"(",
"self",
",",
"config_nr",
",",
"ax",
")",
":",
"electrodes",
"=",
"np",
".",
"loadtxt",
"(",
"options",
".",
"config_file",
",",
"skiprows",
"=",
"1",
")",
"electrodes",
"=",
"self",
".",
"configs",
"[",
"~",
"np",
".",
"isnan",
"(",
"self",
".",
"configs",
")",
".",
"any",
"(",
"1",
")",
"]",
"electrodes",
"=",
"electrodes",
".",
"astype",
"(",
"int",
")",
"conf",
"=",
"[",
"]",
"for",
"dim",
"in",
"range",
"(",
"0",
",",
"electrodes",
".",
"shape",
"[",
"1",
"]",
")",
":",
"c",
"=",
"electrodes",
"[",
"config_nr",
",",
"dim",
"]",
"# c = c.partition('0')",
"a",
"=",
"np",
".",
"round",
"(",
"c",
"/",
"10000",
")",
"-",
"1",
"b",
"=",
"np",
".",
"mod",
"(",
"c",
",",
"10000",
")",
"-",
"1",
"conf",
".",
"append",
"(",
"a",
")",
"conf",
".",
"append",
"(",
"b",
")",
"Ex",
",",
"Ez",
"=",
"elem",
".",
"get_electrodes",
"(",
")",
"color",
"=",
"[",
"'#ffed00'",
",",
"'#ffed00'",
",",
"'#ff0000'",
",",
"'#ff0000'",
"]",
"ax",
".",
"scatter",
"(",
"Ex",
"[",
"conf",
"]",
",",
"Ez",
"[",
"conf",
"]",
",",
"c",
"=",
"color",
",",
"marker",
"=",
"'s'",
",",
"s",
"=",
"60",
",",
"clip_on",
"=",
"False",
",",
"edgecolors",
"=",
"'k'",
")"
] |
calculate Levenshtein ratio of sequences | def compare_seqs_leven ( seqs ) : A , B , ignore_gaps = seqs a , b = remove_gaps ( A [ 1 ] , B [ 1 ] ) # actual sequences if len ( a ) != len ( b ) : print ( '# reads are not the same length' , file = sys . stderr ) exit ( ) pident = lr ( a , b ) * 100 return A [ 0 ] , B [ 0 ] , pident | 82 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L79-L89 | [
"def",
"create_calcs",
"(",
"self",
")",
":",
"specs",
"=",
"self",
".",
"_combine_core_aux_specs",
"(",
")",
"for",
"spec",
"in",
"specs",
":",
"spec",
"[",
"'dtype_out_time'",
"]",
"=",
"_prune_invalid_time_reductions",
"(",
"spec",
")",
"return",
"[",
"Calc",
"(",
"*",
"*",
"sp",
")",
"for",
"sp",
"in",
"specs",
"]"
] |
make pairwise sequence comparisons between aligned sequences | def pairwise_compare ( afa , leven , threads , print_list , ignore_gaps ) : # load sequences into dictionary seqs = { seq [ 0 ] : seq for seq in nr_fasta ( [ afa ] , append_index = True ) } num_seqs = len ( seqs ) # define all pairs pairs = ( ( i [ 0 ] , i [ 1 ] , ignore_gaps ) for i in itertools . combinations ( list ( seqs . values ( ) ) , 2 ) ) pool = multithread ( threads ) # calc percent identity between all pairs - parallelize if leven is True : pident = pool . map ( compare_seqs_leven , pairs ) else : compare = pool . imap_unordered ( compare_seqs , pairs ) pident = [ i for i in tqdm ( compare , total = ( num_seqs * num_seqs ) / 2 ) ] pool . close ( ) pool . terminate ( ) pool . join ( ) return to_dictionary ( pident , print_list ) | 83 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L91-L110 | [
"def",
"refresh",
"(",
"self",
")",
"->",
"None",
":",
"if",
"not",
"self",
":",
"self",
".",
"values",
"[",
":",
"]",
"=",
"0.",
"elif",
"len",
"(",
"self",
")",
"==",
"1",
":",
"values",
"=",
"list",
"(",
"self",
".",
"_toy2values",
".",
"values",
"(",
")",
")",
"[",
"0",
"]",
"self",
".",
"values",
"[",
":",
"]",
"=",
"self",
".",
"apply_timefactor",
"(",
"values",
")",
"else",
":",
"for",
"idx",
",",
"date",
"in",
"enumerate",
"(",
"timetools",
".",
"TOY",
".",
"centred_timegrid",
"(",
"self",
".",
"simulationstep",
")",
")",
":",
"values",
"=",
"self",
".",
"interp",
"(",
"date",
")",
"self",
".",
"values",
"[",
"idx",
"]",
"=",
"self",
".",
"apply_timefactor",
"(",
"values",
")"
] |
print matrix of pidents to stdout | def print_pairwise ( pw , median = False ) : names = sorted ( set ( [ i for i in pw ] ) ) if len ( names ) != 0 : if '>' in names [ 0 ] : yield [ '#' ] + [ i . split ( '>' ) [ 1 ] for i in names if '>' in i ] else : yield [ '#' ] + names for a in names : if '>' in a : yield [ a . split ( '>' ) [ 1 ] ] + [ pw [ a ] [ b ] for b in names ] else : out = [ ] for b in names : if b in pw [ a ] : if median is False : out . append ( max ( pw [ a ] [ b ] ) ) else : out . append ( np . median ( pw [ a ] [ b ] ) ) else : out . append ( '-' ) yield [ a ] + out | 84 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L132-L155 | [
"def",
"from_manifest",
"(",
"app",
",",
"filename",
",",
"raw",
"=",
"False",
",",
"*",
"*",
"kwargs",
")",
":",
"cfg",
"=",
"current_app",
".",
"config",
"if",
"current_app",
".",
"config",
".",
"get",
"(",
"'TESTING'",
")",
":",
"return",
"# Do not spend time here when testing",
"path",
"=",
"_manifests",
"[",
"app",
"]",
"[",
"filename",
"]",
"if",
"not",
"raw",
"and",
"cfg",
".",
"get",
"(",
"'CDN_DOMAIN'",
")",
"and",
"not",
"cfg",
".",
"get",
"(",
"'CDN_DEBUG'",
")",
":",
"scheme",
"=",
"'https'",
"if",
"cfg",
".",
"get",
"(",
"'CDN_HTTPS'",
")",
"else",
"request",
".",
"scheme",
"prefix",
"=",
"'{}://'",
".",
"format",
"(",
"scheme",
")",
"if",
"not",
"path",
".",
"startswith",
"(",
"'/'",
")",
":",
"# CDN_DOMAIN has no trailing slash",
"path",
"=",
"'/'",
"+",
"path",
"return",
"''",
".",
"join",
"(",
"(",
"prefix",
",",
"cfg",
"[",
"'CDN_DOMAIN'",
"]",
",",
"path",
")",
")",
"elif",
"not",
"raw",
"and",
"kwargs",
".",
"get",
"(",
"'external'",
",",
"False",
")",
":",
"if",
"path",
".",
"startswith",
"(",
"'/'",
")",
":",
"# request.host_url has a trailing slash",
"path",
"=",
"path",
"[",
"1",
":",
"]",
"return",
"''",
".",
"join",
"(",
"(",
"request",
".",
"host_url",
",",
"path",
")",
")",
"return",
"path"
] |
print stats for comparisons | def print_comps ( comps ) : if comps == [ ] : print ( 'n/a' ) else : print ( '# min: %s, max: %s, mean: %s' % ( min ( comps ) , max ( comps ) , np . mean ( comps ) ) ) | 85 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L157-L165 | [
"def",
"readSources",
"(",
"self",
")",
":",
"for",
"sourceCount",
",",
"sourceElement",
"in",
"enumerate",
"(",
"self",
".",
"root",
".",
"findall",
"(",
"\".sources/source\"",
")",
")",
":",
"# shall we just read the UFO here?",
"filename",
"=",
"sourceElement",
".",
"attrib",
".",
"get",
"(",
"'filename'",
")",
"# filename is a path relaive to the documentpath. resolve first.",
"sourcePath",
"=",
"os",
".",
"path",
".",
"abspath",
"(",
"os",
".",
"path",
".",
"join",
"(",
"os",
".",
"path",
".",
"dirname",
"(",
"self",
".",
"path",
")",
",",
"filename",
")",
")",
"sourceName",
"=",
"sourceElement",
".",
"attrib",
".",
"get",
"(",
"'name'",
")",
"if",
"sourceName",
"is",
"None",
":",
"# if the source element has no name attribute",
"# (some authoring tools do not need them)",
"# then we should make a temporary one. We still need it for reference.",
"sourceName",
"=",
"\"temp_master.%d\"",
"%",
"(",
"sourceCount",
")",
"self",
".",
"reportProgress",
"(",
"\"prep\"",
",",
"'load'",
",",
"sourcePath",
")",
"if",
"not",
"os",
".",
"path",
".",
"exists",
"(",
"sourcePath",
")",
":",
"raise",
"MutatorError",
"(",
"\"Source not found at %s\"",
"%",
"sourcePath",
")",
"sourceObject",
"=",
"self",
".",
"_instantiateFont",
"(",
"sourcePath",
")",
"# read the locations",
"sourceLocationObject",
"=",
"None",
"sourceLocationObject",
"=",
"self",
".",
"locationFromElement",
"(",
"sourceElement",
")",
"if",
"sourceLocationObject",
"is",
"None",
":",
"raise",
"MutatorError",
"(",
"\"No location defined for source %s\"",
"%",
"sourceName",
")",
"# read lib flag",
"for",
"libElement",
"in",
"sourceElement",
".",
"findall",
"(",
"'.lib'",
")",
":",
"if",
"libElement",
".",
"attrib",
".",
"get",
"(",
"'copy'",
")",
"==",
"'1'",
":",
"self",
".",
"libSource",
"=",
"sourceName",
"# read the groups flag",
"for",
"groupsElement",
"in",
"sourceElement",
".",
"findall",
"(",
"'.groups'",
")",
":",
"if",
"groupsElement",
".",
"attrib",
".",
"get",
"(",
"'copy'",
")",
"==",
"'1'",
":",
"self",
".",
"groupsSource",
"=",
"sourceName",
"# read the info flag",
"for",
"infoElement",
"in",
"sourceElement",
".",
"findall",
"(",
"\".info\"",
")",
":",
"if",
"infoElement",
".",
"attrib",
".",
"get",
"(",
"'copy'",
")",
"==",
"'1'",
":",
"self",
".",
"infoSource",
"=",
"sourceName",
"if",
"infoElement",
".",
"attrib",
".",
"get",
"(",
"'mute'",
")",
"==",
"'1'",
":",
"self",
".",
"muted",
"[",
"'info'",
"]",
".",
"append",
"(",
"sourceName",
")",
"# read the features flag",
"for",
"featuresElement",
"in",
"sourceElement",
".",
"findall",
"(",
"\".features\"",
")",
":",
"if",
"featuresElement",
".",
"attrib",
".",
"get",
"(",
"'copy'",
")",
"==",
"'1'",
":",
"if",
"self",
".",
"featuresSource",
"is",
"not",
"None",
":",
"self",
".",
"featuresSource",
"=",
"None",
"else",
":",
"self",
".",
"featuresSource",
"=",
"sourceName",
"mutedGlyphs",
"=",
"[",
"]",
"for",
"glyphElement",
"in",
"sourceElement",
".",
"findall",
"(",
"\".glyph\"",
")",
":",
"glyphName",
"=",
"glyphElement",
".",
"attrib",
".",
"get",
"(",
"'name'",
")",
"if",
"glyphName",
"is",
"None",
":",
"continue",
"if",
"glyphElement",
".",
"attrib",
".",
"get",
"(",
"'mute'",
")",
"==",
"'1'",
":",
"if",
"not",
"sourceName",
"in",
"self",
".",
"muted",
"[",
"'glyphs'",
"]",
":",
"self",
".",
"muted",
"[",
"'glyphs'",
"]",
"[",
"sourceName",
"]",
"=",
"[",
"]",
"self",
".",
"muted",
"[",
"'glyphs'",
"]",
"[",
"sourceName",
"]",
".",
"append",
"(",
"glyphName",
")",
"for",
"kerningElement",
"in",
"sourceElement",
".",
"findall",
"(",
"\".kerning\"",
")",
":",
"if",
"kerningElement",
".",
"attrib",
".",
"get",
"(",
"'mute'",
")",
"==",
"'1'",
":",
"self",
".",
"muted",
"[",
"'kerning'",
"]",
".",
"append",
"(",
"sourceName",
")",
"# store",
"self",
".",
"sources",
"[",
"sourceName",
"]",
"=",
"sourceObject",
",",
"sourceLocationObject",
"self",
".",
"reportProgress",
"(",
"\"prep\"",
",",
"'done'",
")"
] |
print min . pident within each clade and then matrix of between - clade max . | def compare_clades ( pw ) : names = sorted ( set ( [ i for i in pw ] ) ) for i in range ( 0 , 4 ) : wi , bt = { } , { } for a in names : for b in pw [ a ] : if ';' not in a or ';' not in b : continue pident = pw [ a ] [ b ] cA , cB = a . split ( ';' ) [ i ] , b . split ( ';' ) [ i ] if i == 0 and '_' in cA and '_' in cB : cA = cA . rsplit ( '_' , 1 ) [ 1 ] cB = cB . rsplit ( '_' , 1 ) [ 1 ] elif '>' in cA or '>' in cB : cA = cA . split ( '>' ) [ 1 ] cB = cB . split ( '>' ) [ 1 ] if cA == cB : if cA not in wi : wi [ cA ] = [ ] wi [ cA ] . append ( pident ) else : if cA not in bt : bt [ cA ] = { } if cB not in bt [ cA ] : bt [ cA ] [ cB ] = [ ] bt [ cA ] [ cB ] . append ( pident ) print ( '\n# min. within' ) for clade , pidents in list ( wi . items ( ) ) : print ( '\t' . join ( [ 'wi:%s' % str ( i ) , clade , str ( min ( pidents ) ) ] ) ) # print matrix of maximum between groups comps = [ ] print ( '\n# max. between' ) for comp in print_pairwise ( bt ) : if comp is not None : print ( '\t' . join ( [ 'bt:%s' % str ( i ) ] + [ str ( j ) for j in comp ] ) ) if comp [ 0 ] != '#' : comps . extend ( [ j for j in comp [ 1 : ] if j != '-' ] ) print_comps ( comps ) # print matrix of median between groups comps = [ ] print ( '\n# median between' ) for comp in print_pairwise ( bt , median = True ) : if comp is not None : print ( '\t' . join ( [ 'bt:%s' % str ( i ) ] + [ str ( j ) for j in comp ] ) ) if comp [ 0 ] != '#' : comps . extend ( [ j for j in comp [ 1 : ] if j != '-' ] ) print_comps ( comps ) | 86 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L167-L216 | [
"def",
"AddKeywordsForName",
"(",
"self",
",",
"name",
",",
"keywords",
")",
":",
"data_store",
".",
"DB",
".",
"IndexAddKeywordsForName",
"(",
"self",
".",
"urn",
",",
"name",
",",
"keywords",
")"
] |
convert matrix to dictionary of comparisons | def matrix2dictionary ( matrix ) : pw = { } for line in matrix : line = line . strip ( ) . split ( '\t' ) if line [ 0 ] . startswith ( '#' ) : names = line [ 1 : ] continue a = line [ 0 ] for i , pident in enumerate ( line [ 1 : ] ) : b = names [ i ] if a not in pw : pw [ a ] = { } if b not in pw : pw [ b ] = { } if pident != '-' : pident = float ( pident ) pw [ a ] [ b ] = pident pw [ b ] [ a ] = pident return pw | 87 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/compare_aligned.py#L218-L239 | [
"async",
"def",
"postprocess_websocket",
"(",
"self",
",",
"response",
":",
"Optional",
"[",
"Response",
"]",
",",
"websocket_context",
":",
"Optional",
"[",
"WebsocketContext",
"]",
"=",
"None",
",",
")",
"->",
"Response",
":",
"websocket_",
"=",
"(",
"websocket_context",
"or",
"_websocket_ctx_stack",
".",
"top",
")",
".",
"websocket",
"functions",
"=",
"(",
"websocket_context",
"or",
"_websocket_ctx_stack",
".",
"top",
")",
".",
"_after_websocket_functions",
"blueprint",
"=",
"websocket_",
".",
"blueprint",
"if",
"blueprint",
"is",
"not",
"None",
":",
"functions",
"=",
"chain",
"(",
"functions",
",",
"self",
".",
"after_websocket_funcs",
"[",
"blueprint",
"]",
")",
"functions",
"=",
"chain",
"(",
"functions",
",",
"self",
".",
"after_websocket_funcs",
"[",
"None",
"]",
")",
"for",
"function",
"in",
"functions",
":",
"response",
"=",
"await",
"function",
"(",
"response",
")",
"session_",
"=",
"(",
"websocket_context",
"or",
"_request_ctx_stack",
".",
"top",
")",
".",
"session",
"if",
"not",
"self",
".",
"session_interface",
".",
"is_null_session",
"(",
"session_",
")",
":",
"if",
"response",
"is",
"None",
"and",
"isinstance",
"(",
"session_",
",",
"SecureCookieSession",
")",
"and",
"session_",
".",
"modified",
":",
"self",
".",
"logger",
".",
"exception",
"(",
"\"Secure Cookie Session modified during websocket handling. \"",
"\"These modifications will be lost as a cookie cannot be set.\"",
")",
"else",
":",
"await",
"self",
".",
"save_session",
"(",
"session_",
",",
"response",
")",
"return",
"response"
] |
Set argument parser option . | def setoption ( parser , metadata = None ) : parser . add_argument ( '-v' , action = 'version' , version = __version__ ) subparsers = parser . add_subparsers ( help = 'sub commands help' ) create_cmd = subparsers . add_parser ( 'create' ) create_cmd . add_argument ( 'name' , help = 'Specify Python package name.' ) create_cmd . add_argument ( '-d' , dest = 'description' , action = 'store' , help = 'Short description about your package.' ) create_cmd . add_argument ( '-a' , dest = 'author' , action = 'store' , required = True , help = 'Python package author name.' ) create_cmd . add_argument ( '-e' , dest = 'email' , action = 'store' , required = True , help = 'Python package author email address.' ) create_cmd . add_argument ( '-l' , dest = 'license' , choices = metadata . licenses ( ) . keys ( ) , default = 'GPLv3+' , help = 'Specify license. (default: %(default)s)' ) create_cmd . add_argument ( '-s' , dest = 'status' , choices = metadata . status ( ) . keys ( ) , default = 'Alpha' , help = ( 'Specify development status. ' '(default: %(default)s)' ) ) create_cmd . add_argument ( '--no-check' , action = 'store_true' , help = 'No checking package name in PyPI.' ) create_cmd . add_argument ( '--with-samples' , action = 'store_true' , help = 'Generate package with sample code.' ) group = create_cmd . add_mutually_exclusive_group ( required = True ) group . add_argument ( '-U' , dest = 'username' , action = 'store' , help = 'Specify GitHub username.' ) group . add_argument ( '-u' , dest = 'url' , action = 'store' , type = valid_url , help = 'Python package homepage url.' ) create_cmd . add_argument ( '-o' , dest = 'outdir' , action = 'store' , default = os . path . abspath ( os . path . curdir ) , help = 'Specify output directory. (default: $PWD)' ) list_cmd = subparsers . add_parser ( 'list' ) list_cmd . add_argument ( '-l' , dest = 'licenses' , action = 'store_true' , help = 'show license choices.' ) | 88 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L12-L51 | [
"def",
"write",
"(",
"self",
",",
"splits",
"=",
"None",
",",
"mergers",
"=",
"None",
",",
"dividends",
"=",
"None",
",",
"stock_dividends",
"=",
"None",
")",
":",
"self",
".",
"write_frame",
"(",
"'splits'",
",",
"splits",
")",
"self",
".",
"write_frame",
"(",
"'mergers'",
",",
"mergers",
")",
"self",
".",
"write_dividend_data",
"(",
"dividends",
",",
"stock_dividends",
")",
"# Use IF NOT EXISTS here to allow multiple writes if desired.",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS splits_sids \"",
"\"ON splits(sid)\"",
")",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS splits_effective_date \"",
"\"ON splits(effective_date)\"",
")",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS mergers_sids \"",
"\"ON mergers(sid)\"",
")",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS mergers_effective_date \"",
"\"ON mergers(effective_date)\"",
")",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS dividends_sid \"",
"\"ON dividends(sid)\"",
")",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS dividends_effective_date \"",
"\"ON dividends(effective_date)\"",
")",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS dividend_payouts_sid \"",
"\"ON dividend_payouts(sid)\"",
")",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS dividends_payouts_ex_date \"",
"\"ON dividend_payouts(ex_date)\"",
")",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS stock_dividend_payouts_sid \"",
"\"ON stock_dividend_payouts(sid)\"",
")",
"self",
".",
"conn",
".",
"execute",
"(",
"\"CREATE INDEX IF NOT EXISTS stock_dividends_payouts_ex_date \"",
"\"ON stock_dividend_payouts(ex_date)\"",
")"
] |
Parse argument options . | def parse_options ( metadata ) : parser = argparse . ArgumentParser ( description = '%(prog)s usage:' , prog = __prog__ ) setoption ( parser , metadata = metadata ) return parser | 89 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L72-L77 | [
"def",
"bisine_wahwah_wave",
"(",
"frequency",
")",
":",
"#",
"# This is clearly intended to build on the bisine wave defined above,",
"# so we can start by generating that.",
"waves_a",
"=",
"bisine_wave",
"(",
"frequency",
")",
"#",
"# Then, by reversing axis 2, we swap the stereo channels. By mixing",
"# this with `waves_a`, we'll be able to create the desired effect.",
"waves_b",
"=",
"tf",
".",
"reverse",
"(",
"waves_a",
",",
"axis",
"=",
"[",
"2",
"]",
")",
"#",
"# Let's have the balance oscillate from left to right four times.",
"iterations",
"=",
"4",
"#",
"# Now, we compute the balance for each sample: `ts` has values",
"# in [0, 1] that indicate how much we should use `waves_a`.",
"xs",
"=",
"tf",
".",
"reshape",
"(",
"tf",
".",
"range",
"(",
"_samples",
"(",
")",
",",
"dtype",
"=",
"tf",
".",
"float32",
")",
",",
"[",
"1",
",",
"_samples",
"(",
")",
",",
"1",
"]",
")",
"thetas",
"=",
"xs",
"/",
"_samples",
"(",
")",
"*",
"iterations",
"ts",
"=",
"(",
"tf",
".",
"sin",
"(",
"math",
".",
"pi",
"*",
"2",
"*",
"thetas",
")",
"+",
"1",
")",
"/",
"2",
"#",
"# Finally, we can mix the two together, and we're done.",
"wave",
"=",
"ts",
"*",
"waves_a",
"+",
"(",
"1.0",
"-",
"ts",
")",
"*",
"waves_b",
"#",
"# Alternately, we can make the effect more pronounced by exaggerating",
"# the sample data. Let's emit both variations.",
"exaggerated_wave",
"=",
"wave",
"**",
"3.0",
"return",
"tf",
".",
"concat",
"(",
"[",
"wave",
",",
"exaggerated_wave",
"]",
",",
"axis",
"=",
"0",
")"
] |
Execute main processes . | def main ( ) : try : pkg_version = Update ( ) if pkg_version . updatable ( ) : pkg_version . show_message ( ) metadata = control . retreive_metadata ( ) parser = parse_options ( metadata ) argvs = sys . argv if len ( argvs ) <= 1 : parser . print_help ( ) sys . exit ( 1 ) args = parser . parse_args ( ) control . print_licences ( args , metadata ) control . check_repository_existence ( args ) control . check_package_existence ( args ) control . generate_package ( args ) except ( RuntimeError , BackendFailure , Conflict ) as exc : sys . stderr . write ( '{0}\n' . format ( exc ) ) sys . exit ( 1 ) | 90 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/commands.py#L80-L99 | [
"def",
"_pare_down_model",
"(",
"self",
",",
"strain_gempro",
",",
"genes_to_remove",
")",
":",
"# Filter out genes in genes_to_remove which do not show up in the model",
"strain_genes",
"=",
"[",
"x",
".",
"id",
"for",
"x",
"in",
"strain_gempro",
".",
"genes",
"]",
"genes_to_remove",
".",
"extend",
"(",
"self",
".",
"missing_in_orthology_matrix",
")",
"genes_to_remove",
"=",
"list",
"(",
"set",
"(",
"genes_to_remove",
")",
".",
"intersection",
"(",
"set",
"(",
"strain_genes",
")",
")",
")",
"if",
"len",
"(",
"genes_to_remove",
")",
"==",
"0",
":",
"log",
".",
"info",
"(",
"'{}: no genes marked non-functional'",
".",
"format",
"(",
"strain_gempro",
".",
"id",
")",
")",
"return",
"else",
":",
"log",
".",
"debug",
"(",
"'{}: {} genes to be marked non-functional'",
".",
"format",
"(",
"strain_gempro",
".",
"id",
",",
"len",
"(",
"genes_to_remove",
")",
")",
")",
"# If a COBRApy model exists, utilize the delete_model_genes method",
"if",
"strain_gempro",
".",
"model",
":",
"strain_gempro",
".",
"model",
".",
"_trimmed",
"=",
"False",
"strain_gempro",
".",
"model",
".",
"_trimmed_genes",
"=",
"[",
"]",
"strain_gempro",
".",
"model",
".",
"_trimmed_reactions",
"=",
"{",
"}",
"# Delete genes!",
"cobra",
".",
"manipulation",
".",
"delete_model_genes",
"(",
"strain_gempro",
".",
"model",
",",
"genes_to_remove",
")",
"if",
"strain_gempro",
".",
"model",
".",
"_trimmed",
":",
"log",
".",
"info",
"(",
"'{}: marked {} genes as non-functional, '",
"'deactivating {} reactions'",
".",
"format",
"(",
"strain_gempro",
".",
"id",
",",
"len",
"(",
"strain_gempro",
".",
"model",
".",
"_trimmed_genes",
")",
",",
"len",
"(",
"strain_gempro",
".",
"model",
".",
"_trimmed_reactions",
")",
")",
")",
"# Otherwise, just mark the genes as non-functional",
"else",
":",
"for",
"g",
"in",
"genes_to_remove",
":",
"strain_gempro",
".",
"genes",
".",
"get_by_id",
"(",
"g",
")",
".",
"functional",
"=",
"False",
"log",
".",
"info",
"(",
"'{}: marked {} genes as non-functional'",
".",
"format",
"(",
"strain_gempro",
".",
"id",
",",
"len",
"(",
"genes_to_remove",
")",
")",
")"
] |
Check key and set default vaule when it does not exists . | def _check_or_set_default_params ( self ) : if not hasattr ( self , 'date' ) : self . _set_param ( 'date' , datetime . utcnow ( ) . strftime ( '%Y-%m-%d' ) ) if not hasattr ( self , 'version' ) : self . _set_param ( 'version' , self . default_version ) # pylint: disable=no-member if not hasattr ( self , 'description' ) or self . description is None : getattr ( self , '_set_param' ) ( 'description' , self . warning_message ) | 91 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L44-L52 | [
"def",
"matchw",
"(",
"string",
",",
"templ",
",",
"wstr",
",",
"wchr",
")",
":",
"# ctypes.c_char(wstr.encode(encoding='UTF-8')",
"string",
"=",
"stypes",
".",
"stringToCharP",
"(",
"string",
")",
"templ",
"=",
"stypes",
".",
"stringToCharP",
"(",
"templ",
")",
"wstr",
"=",
"ctypes",
".",
"c_char",
"(",
"wstr",
".",
"encode",
"(",
"encoding",
"=",
"'UTF-8'",
")",
")",
"wchr",
"=",
"ctypes",
".",
"c_char",
"(",
"wchr",
".",
"encode",
"(",
"encoding",
"=",
"'UTF-8'",
")",
")",
"return",
"bool",
"(",
"libspice",
".",
"matchw_c",
"(",
"string",
",",
"templ",
",",
"wstr",
",",
"wchr",
")",
")"
] |
Move directory from working directory to output directory . | def move ( self ) : if not os . path . isdir ( self . outdir ) : os . makedirs ( self . outdir ) shutil . move ( self . tmpdir , os . path . join ( self . outdir , self . name ) ) | 92 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L169-L173 | [
"def",
"check_origin",
"(",
"self",
",",
"origin",
")",
":",
"mod_opts",
"=",
"self",
".",
"application",
".",
"mod_opts",
"if",
"mod_opts",
".",
"get",
"(",
"'cors_origin'",
")",
":",
"return",
"bool",
"(",
"_check_cors_origin",
"(",
"origin",
",",
"mod_opts",
"[",
"'cors_origin'",
"]",
")",
")",
"else",
":",
"return",
"super",
"(",
"AllEventsHandler",
",",
"self",
")",
".",
"check_origin",
"(",
"origin",
")"
] |
Initialize VCS repository . | def vcs_init ( self ) : VCS ( os . path . join ( self . outdir , self . name ) , self . pkg_data ) | 93 | https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/package.py#L185-L187 | [
"def",
"with_timestamps",
"(",
"self",
",",
"created_at",
"=",
"None",
",",
"updated_at",
"=",
"None",
")",
":",
"if",
"not",
"created_at",
":",
"created_at",
"=",
"self",
".",
"created_at",
"(",
")",
"if",
"not",
"updated_at",
":",
"updated_at",
"=",
"self",
".",
"updated_at",
"(",
")",
"return",
"self",
".",
"with_pivot",
"(",
"created_at",
",",
"updated_at",
")"
] |
Finds the location of the current Steam installation on Windows machines . Returns None for any non - Windows machines or for Windows machines where Steam is not installed . | def find_steam_location ( ) : if registry is None : return None key = registry . CreateKey ( registry . HKEY_CURRENT_USER , "Software\Valve\Steam" ) return registry . QueryValueEx ( key , "SteamPath" ) [ 0 ] | 94 | https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/winutils.py#L10-L20 | [
"def",
"remove_node",
"(",
"self",
",",
"node",
")",
":",
"affected_nodes",
"=",
"[",
"v",
"for",
"u",
",",
"v",
"in",
"self",
".",
"edges",
"(",
")",
"if",
"u",
"==",
"node",
"]",
"for",
"affected_node",
"in",
"affected_nodes",
":",
"node_cpd",
"=",
"self",
".",
"get_cpds",
"(",
"node",
"=",
"affected_node",
")",
"if",
"node_cpd",
":",
"node_cpd",
".",
"marginalize",
"(",
"[",
"node",
"]",
",",
"inplace",
"=",
"True",
")",
"if",
"self",
".",
"get_cpds",
"(",
"node",
"=",
"node",
")",
":",
"self",
".",
"remove_cpds",
"(",
"node",
")",
"super",
"(",
"BayesianModel",
",",
"self",
")",
".",
"remove_node",
"(",
"node",
")"
] |
Plot PCoA principal coordinates scaled by the relative abundances of otu_name . | def plot_PCoA ( cat_data , otu_name , unifrac , names , colors , xr , yr , outDir , save_as , plot_style ) : fig = plt . figure ( figsize = ( 14 , 8 ) ) ax = fig . add_subplot ( 111 ) for i , cat in enumerate ( cat_data ) : plt . scatter ( cat_data [ cat ] [ "pc1" ] , cat_data [ cat ] [ "pc2" ] , cat_data [ cat ] [ "size" ] , color = colors [ cat ] , alpha = 0.85 , marker = "o" , edgecolor = "black" , label = cat ) lgnd = plt . legend ( loc = "best" , scatterpoints = 3 , fontsize = 13 ) for i in range ( len ( colors . keys ( ) ) ) : lgnd . legendHandles [ i ] . _sizes = [ 80 ] # Change the legend marker size manually plt . title ( " " . join ( otu_name . split ( "_" ) ) , style = "italic" ) plt . ylabel ( "PC2 (Percent Explained Variance {:.3f}%)" . format ( float ( unifrac [ "varexp" ] [ 1 ] ) ) ) plt . xlabel ( "PC1 (Percent Explained Variance {:.3f}%)" . format ( float ( unifrac [ "varexp" ] [ 0 ] ) ) ) plt . xlim ( round ( xr [ 0 ] * 1.5 , 1 ) , round ( xr [ 1 ] * 1.5 , 1 ) ) plt . ylim ( round ( yr [ 0 ] * 1.5 , 1 ) , round ( yr [ 1 ] * 1.5 , 1 ) ) if plot_style : gu . ggplot2_style ( ax ) fc = "0.8" else : fc = "none" fig . savefig ( os . path . join ( outDir , "_" . join ( otu_name . split ( ) ) ) + "." + save_as , facecolor = fc , edgecolor = "none" , format = save_as , bbox_inches = "tight" , pad_inches = 0.2 ) plt . close ( fig ) | 95 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/PCoA_bubble.py#L36-L65 | [
"def",
"reset",
"(",
"cls",
")",
":",
"cls",
".",
"debug",
"=",
"False",
"cls",
".",
"disabled",
"=",
"False",
"cls",
".",
"overwrite",
"=",
"False",
"cls",
".",
"playback_only",
"=",
"False",
"cls",
".",
"recv_timeout",
"=",
"5",
"cls",
".",
"recv_endmarkers",
"=",
"[",
"]",
"cls",
".",
"recv_size",
"=",
"None"
] |
Split up the column data in a biom table by mapping category value . | def split_by_category ( biom_cols , mapping , category_id ) : columns = defaultdict ( list ) for i , col in enumerate ( biom_cols ) : columns [ mapping [ col [ 'id' ] ] [ category_id ] ] . append ( ( i , col ) ) return columns | 96 | https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/transpose_biom.py#L17-L25 | [
"def",
"sshagent_run",
"(",
"cmd",
")",
":",
"# Handle context manager modifications",
"wrapped_cmd",
"=",
"_prefix_commands",
"(",
"_prefix_env_vars",
"(",
"cmd",
")",
",",
"'remote'",
")",
"try",
":",
"host",
",",
"port",
"=",
"env",
".",
"host_string",
".",
"split",
"(",
"':'",
")",
"return",
"local",
"(",
"u\"ssh -p %s -A -o StrictHostKeyChecking=no %s@%s '%s'\"",
"%",
"(",
"port",
",",
"env",
".",
"user",
",",
"host",
",",
"wrapped_cmd",
")",
")",
"except",
"ValueError",
":",
"return",
"local",
"(",
"u\"ssh -A -o StrictHostKeyChecking=no %s@%s '%s'\"",
"%",
"(",
"env",
".",
"user",
",",
"env",
".",
"host_string",
",",
"wrapped_cmd",
")",
")"
] |
print line if starts with ... | def print_line ( l ) : print_lines = [ '# STOCKHOLM' , '#=GF' , '#=GS' , ' ' ] if len ( l . split ( ) ) == 0 : return True for start in print_lines : if l . startswith ( start ) : return True return False | 97 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/stockholm2oneline.py#L11-L21 | [
"def",
"setOverlayTransformTrackedDeviceRelative",
"(",
"self",
",",
"ulOverlayHandle",
",",
"unTrackedDevice",
")",
":",
"fn",
"=",
"self",
".",
"function_table",
".",
"setOverlayTransformTrackedDeviceRelative",
"pmatTrackedDeviceToOverlayTransform",
"=",
"HmdMatrix34_t",
"(",
")",
"result",
"=",
"fn",
"(",
"ulOverlayHandle",
",",
"unTrackedDevice",
",",
"byref",
"(",
"pmatTrackedDeviceToOverlayTransform",
")",
")",
"return",
"result",
",",
"pmatTrackedDeviceToOverlayTransform"
] |
convert stockholm to single line format | def stock2one ( stock ) : lines = { } for line in stock : line = line . strip ( ) if print_line ( line ) is True : yield line continue if line . startswith ( '//' ) : continue ID , seq = line . rsplit ( ' ' , 1 ) if ID not in lines : lines [ ID ] = '' else : # remove preceding white space seq = seq . strip ( ) lines [ ID ] += seq for ID , line in lines . items ( ) : yield '\t' . join ( [ ID , line ] ) yield '\n//' | 98 | https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/stockholm2oneline.py#L23-L44 | [
"def",
"Run",
"(",
"self",
")",
":",
"global",
"DB",
"# pylint: disable=global-statement",
"global",
"REL_DB",
"# pylint: disable=global-statement",
"global",
"BLOBS",
"# pylint: disable=global-statement",
"if",
"flags",
".",
"FLAGS",
".",
"list_storage",
":",
"self",
".",
"_ListStorageOptions",
"(",
")",
"sys",
".",
"exit",
"(",
"0",
")",
"try",
":",
"cls",
"=",
"DataStore",
".",
"GetPlugin",
"(",
"config",
".",
"CONFIG",
"[",
"\"Datastore.implementation\"",
"]",
")",
"except",
"KeyError",
":",
"msg",
"=",
"(",
"\"No Storage System %s found.\"",
"%",
"config",
".",
"CONFIG",
"[",
"\"Datastore.implementation\"",
"]",
")",
"if",
"config",
".",
"CONFIG",
"[",
"\"Datastore.implementation\"",
"]",
"==",
"\"SqliteDataStore\"",
":",
"msg",
"=",
"\"The SQLite datastore is no longer supported.\"",
"print",
"(",
"msg",
")",
"print",
"(",
"\"Available options:\"",
")",
"self",
".",
"_ListStorageOptions",
"(",
")",
"raise",
"ValueError",
"(",
"msg",
")",
"DB",
"=",
"cls",
"(",
")",
"# pylint: disable=g-bad-name",
"DB",
".",
"Initialize",
"(",
")",
"atexit",
".",
"register",
"(",
"DB",
".",
"Flush",
")",
"monitor_port",
"=",
"config",
".",
"CONFIG",
"[",
"\"Monitoring.http_port\"",
"]",
"if",
"monitor_port",
"!=",
"0",
":",
"DB",
".",
"InitializeMonitorThread",
"(",
")",
"# Initialize the blobstore.",
"blobstore_name",
"=",
"config",
".",
"CONFIG",
".",
"Get",
"(",
"\"Blobstore.implementation\"",
")",
"try",
":",
"cls",
"=",
"blob_store",
".",
"REGISTRY",
"[",
"blobstore_name",
"]",
"except",
"KeyError",
":",
"raise",
"ValueError",
"(",
"\"No blob store %s found.\"",
"%",
"blobstore_name",
")",
"BLOBS",
"=",
"blob_store",
".",
"BlobStoreValidationWrapper",
"(",
"cls",
"(",
")",
")",
"# Initialize a relational DB if configured.",
"rel_db_name",
"=",
"config",
".",
"CONFIG",
"[",
"\"Database.implementation\"",
"]",
"if",
"not",
"rel_db_name",
":",
"return",
"try",
":",
"cls",
"=",
"registry_init",
".",
"REGISTRY",
"[",
"rel_db_name",
"]",
"except",
"KeyError",
":",
"raise",
"ValueError",
"(",
"\"Database %s not found.\"",
"%",
"rel_db_name",
")",
"logging",
".",
"info",
"(",
"\"Using database implementation %s\"",
",",
"rel_db_name",
")",
"REL_DB",
"=",
"db",
".",
"DatabaseValidationWrapper",
"(",
"cls",
"(",
")",
")"
] |
Statics the methods . wut . | def math_func ( f ) : @ wraps ( f ) def wrapper ( * args , * * kwargs ) : if len ( args ) > 0 : return_type = type ( args [ 0 ] ) if kwargs . has_key ( 'return_type' ) : return_type = kwargs [ 'return_type' ] kwargs . pop ( 'return_type' ) return return_type ( f ( * args , * * kwargs ) ) args = list ( ( setify ( x ) for x in args ) ) return return_type ( f ( * args , * * kwargs ) ) return wrapper | 99 | https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/helpers.py#L8-L22 | [
"def",
"do_logout_service",
"(",
"request",
",",
"data",
",",
"binding",
",",
"config_loader_path",
"=",
"None",
",",
"next_page",
"=",
"None",
",",
"logout_error_template",
"=",
"'djangosaml2/logout_error.html'",
")",
":",
"logger",
".",
"debug",
"(",
"'Logout service started'",
")",
"conf",
"=",
"get_config",
"(",
"config_loader_path",
",",
"request",
")",
"state",
"=",
"StateCache",
"(",
"request",
".",
"session",
")",
"client",
"=",
"Saml2Client",
"(",
"conf",
",",
"state_cache",
"=",
"state",
",",
"identity_cache",
"=",
"IdentityCache",
"(",
"request",
".",
"session",
")",
")",
"if",
"'SAMLResponse'",
"in",
"data",
":",
"# we started the logout",
"logger",
".",
"debug",
"(",
"'Receiving a logout response from the IdP'",
")",
"response",
"=",
"client",
".",
"parse_logout_request_response",
"(",
"data",
"[",
"'SAMLResponse'",
"]",
",",
"binding",
")",
"state",
".",
"sync",
"(",
")",
"return",
"finish_logout",
"(",
"request",
",",
"response",
",",
"next_page",
"=",
"next_page",
")",
"elif",
"'SAMLRequest'",
"in",
"data",
":",
"# logout started by the IdP",
"logger",
".",
"debug",
"(",
"'Receiving a logout request from the IdP'",
")",
"subject_id",
"=",
"_get_subject_id",
"(",
"request",
".",
"session",
")",
"if",
"subject_id",
"is",
"None",
":",
"logger",
".",
"warning",
"(",
"'The session does not contain the subject id for user %s. Performing local logout'",
",",
"request",
".",
"user",
")",
"auth",
".",
"logout",
"(",
"request",
")",
"return",
"render",
"(",
"request",
",",
"logout_error_template",
",",
"status",
"=",
"403",
")",
"else",
":",
"http_info",
"=",
"client",
".",
"handle_logout_request",
"(",
"data",
"[",
"'SAMLRequest'",
"]",
",",
"subject_id",
",",
"binding",
",",
"relay_state",
"=",
"data",
".",
"get",
"(",
"'RelayState'",
",",
"''",
")",
")",
"state",
".",
"sync",
"(",
")",
"auth",
".",
"logout",
"(",
"request",
")",
"return",
"HttpResponseRedirect",
"(",
"get_location",
"(",
"http_info",
")",
")",
"else",
":",
"logger",
".",
"error",
"(",
"'No SAMLResponse or SAMLRequest parameter found'",
")",
"raise",
"Http404",
"(",
"'No SAMLResponse or SAMLRequest parameter found'",
")"
] |