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62,700 | def get_by_name ( self , name ) : san_managers = self . _client . get_all ( ) result = [ x for x in san_managers if x [ 'name' ] == name ] return result [ 0 ] if result else None | Gets a SAN Manager by name . |
62,701 | def get_by_provider_display_name ( self , provider_display_name ) : san_managers = self . _client . get_all ( ) result = [ x for x in san_managers if x [ 'providerDisplayName' ] == provider_display_name ] return result [ 0 ] if result else None | Gets a SAN Manager by provider display name . |
62,702 | def update_configuration ( self , configuration ) : return self . _client . update ( configuration , uri = self . URI + "/configuration" ) | Updates the metrics configuration with the new values . Overwrites the existing configuration . |
62,703 | def delete_all ( self , filter = None , timeout = - 1 ) : return self . _client . delete_all ( filter = filter , timeout = timeout ) | Delete an SNMPv3 User based on User name specified in filter . The user will be deleted only if it has no associated destinations . |
62,704 | def update_ports ( self , ports , id_or_uri ) : ports = merge_default_values ( ports , { 'type' : 'port' } ) uri = self . _client . build_uri ( id_or_uri ) + "/update-ports" return self . _client . update ( uri = uri , resource = ports ) | Updates the switch ports . Only the ports under the management of OneView and those that are unlinked are supported for update . |
62,705 | def from_json_file ( cls , file_name ) : with open ( file_name ) as json_data : config = json . load ( json_data ) return cls ( config ) | Construct OneViewClient using a json file . |
62,706 | def from_environment_variables ( cls ) : ip = os . environ . get ( 'ONEVIEWSDK_IP' , '' ) image_streamer_ip = os . environ . get ( 'ONEVIEWSDK_IMAGE_STREAMER_IP' , '' ) api_version = int ( os . environ . get ( 'ONEVIEWSDK_API_VERSION' , OneViewClient . DEFAULT_API_VERSION ) ) ssl_certificate = os . environ . get ( 'ONEVIEWSDK_SSL_CERTIFICATE' , '' ) username = os . environ . get ( 'ONEVIEWSDK_USERNAME' , '' ) auth_login_domain = os . environ . get ( 'ONEVIEWSDK_AUTH_LOGIN_DOMAIN' , '' ) password = os . environ . get ( 'ONEVIEWSDK_PASSWORD' , '' ) proxy = os . environ . get ( 'ONEVIEWSDK_PROXY' , '' ) sessionID = os . environ . get ( 'ONEVIEWSDK_SESSIONID' , '' ) timeout = os . environ . get ( 'ONEVIEWSDK_CONNECTION_TIMEOUT' ) config = dict ( ip = ip , image_streamer_ip = image_streamer_ip , api_version = api_version , ssl_certificate = ssl_certificate , credentials = dict ( userName = username , authLoginDomain = auth_login_domain , password = password , sessionID = sessionID ) , proxy = proxy , timeout = timeout ) return cls ( config ) | Construct OneViewClient using environment variables . |
62,707 | def create_image_streamer_client ( self ) : image_streamer = ImageStreamerClient ( self . __image_streamer_ip , self . __connection . get_session_id ( ) , self . __connection . _apiVersion , self . __connection . _sslBundle ) return image_streamer | Create the Image Streamer API Client . |
62,708 | def certificate_authority ( self ) : if not self . __certificate_authority : self . __certificate_authority = CertificateAuthority ( self . __connection ) return self . __certificate_authority | Gets the Certificate Authority API client . |
62,709 | def connections ( self ) : if not self . __connections : self . __connections = Connections ( self . __connection ) return self . __connections | Gets the Connections API client . |
62,710 | def fcoe_networks ( self ) : if not self . __fcoe_networks : self . __fcoe_networks = FcoeNetworks ( self . __connection ) return self . __fcoe_networks | Gets the FcoeNetworks API client . |
62,711 | def fabrics ( self ) : if not self . __fabrics : self . __fabrics = Fabrics ( self . __connection ) return self . __fabrics | Gets the Fabrics API client . |
62,712 | def restores ( self ) : if not self . __restores : self . __restores = Restores ( self . __connection ) return self . __restores | Gets the Restores API client . |
62,713 | def scopes ( self ) : if not self . __scopes : self . __scopes = Scopes ( self . __connection ) return self . __scopes | Gets the Scopes API client . |
62,714 | def datacenters ( self ) : if not self . __datacenters : self . __datacenters = Datacenters ( self . __connection ) return self . __datacenters | Gets the Datacenters API client . |
62,715 | def network_sets ( self ) : if not self . __network_sets : self . __network_sets = NetworkSets ( self . __connection ) return self . __network_sets | Gets the NetworkSets API client . |
62,716 | def server_hardware ( self ) : if not self . __server_hardware : self . __server_hardware = ServerHardware ( self . __connection ) return self . __server_hardware | Gets the ServerHardware API client . |
62,717 | def server_hardware_types ( self ) : if not self . __server_hardware_types : self . __server_hardware_types = ServerHardwareTypes ( self . __connection ) return self . __server_hardware_types | Gets the ServerHardwareTypes API client . |
62,718 | def id_pools_vsn_ranges ( self ) : if not self . __id_pools_vsn_ranges : self . __id_pools_vsn_ranges = IdPoolsRanges ( 'vsn' , self . __connection ) return self . __id_pools_vsn_ranges | Gets the IdPoolsRanges API Client for VSN Ranges . |
62,719 | def id_pools_vmac_ranges ( self ) : if not self . __id_pools_vmac_ranges : self . __id_pools_vmac_ranges = IdPoolsRanges ( 'vmac' , self . __connection ) return self . __id_pools_vmac_ranges | Gets the IdPoolsRanges API Client for VMAC Ranges . |
62,720 | def id_pools_vwwn_ranges ( self ) : if not self . __id_pools_vwwn_ranges : self . __id_pools_vwwn_ranges = IdPoolsRanges ( 'vwwn' , self . __connection ) return self . __id_pools_vwwn_ranges | Gets the IdPoolsRanges API Client for VWWN Ranges . |
62,721 | def id_pools_ipv4_ranges ( self ) : if not self . __id_pools_ipv4_ranges : self . __id_pools_ipv4_ranges = IdPoolsIpv4Ranges ( self . __connection ) return self . __id_pools_ipv4_ranges | Gets the IdPoolsIpv4Ranges API client . |
62,722 | def id_pools_ipv4_subnets ( self ) : if not self . __id_pools_ipv4_subnets : self . __id_pools_ipv4_subnets = IdPoolsIpv4Subnets ( self . __connection ) return self . __id_pools_ipv4_subnets | Gets the IdPoolsIpv4Subnets API client . |
62,723 | def id_pools ( self ) : if not self . __id_pools : self . __id_pools = IdPools ( self . __connection ) return self . __id_pools | Gets the IdPools API client . |
62,724 | def switches ( self ) : if not self . __switches : self . __switches = Switches ( self . __connection ) return self . __switches | Gets the Switches API client . |
62,725 | def roles ( self ) : if not self . __roles : self . __roles = Roles ( self . __connection ) return self . __roles | Gets the Roles API client . |
62,726 | def switch_types ( self ) : if not self . __switch_types : self . __switch_types = SwitchTypes ( self . __connection ) return self . __switch_types | Gets the SwitchTypes API client . |
62,727 | def logical_switches ( self ) : if not self . __logical_switches : self . __logical_switches = LogicalSwitches ( self . __connection ) return self . __logical_switches | Gets the LogicalSwitches API client . |
62,728 | def tasks ( self ) : if not self . __tasks : self . __tasks = Tasks ( self . __connection ) return self . __tasks | Gets the Tasks API client . |
62,729 | def enclosure_groups ( self ) : if not self . __enclosure_groups : self . __enclosure_groups = EnclosureGroups ( self . __connection ) return self . __enclosure_groups | Gets the EnclosureGroups API client . |
62,730 | def logical_enclosures ( self ) : if not self . __logical_enclosures : self . __logical_enclosures = LogicalEnclosures ( self . __connection ) return self . __logical_enclosures | Gets the LogicalEnclosures API client . |
62,731 | def metric_streaming ( self ) : if not self . __metric_streaming : self . __metric_streaming = MetricStreaming ( self . __connection ) return self . __metric_streaming | Gets the MetricStreaming API client . |
62,732 | def interconnects ( self ) : if not self . __interconnects : self . __interconnects = Interconnects ( self . __connection ) return self . __interconnects | Gets the Interconnects API client . |
62,733 | def interconnect_link_topologies ( self ) : if not self . __interconnect_link_topologies : self . __interconnect_link_topologies = InterconnectLinkTopologies ( self . __connection ) return self . __interconnect_link_topologies | Gets the InterconnectLinkTopologies API client . |
62,734 | def sas_interconnect_types ( self ) : if not self . __sas_interconnect_types : self . __sas_interconnect_types = SasInterconnectTypes ( self . __connection ) return self . __sas_interconnect_types | Gets the SasInterconnectTypes API client . |
62,735 | def internal_link_sets ( self ) : if not self . __internal_link_sets : self . __internal_link_sets = InternalLinkSets ( self . __connection ) return self . __internal_link_sets | Gets the InternalLinkSets API client . |
62,736 | def logical_interconnect_groups ( self ) : if not self . __logical_interconnect_groups : self . __logical_interconnect_groups = LogicalInterconnectGroups ( self . __connection ) return self . __logical_interconnect_groups | Gets the LogicalInterconnectGroups API client . |
62,737 | def sas_logical_interconnects ( self ) : if not self . __sas_logical_interconnects : self . __sas_logical_interconnects = SasLogicalInterconnects ( self . __connection ) return self . __sas_logical_interconnects | Gets the SasLogicalInterconnects API client . |
62,738 | def logical_downlinks ( self ) : if not self . __logical_downlinks : self . __logical_downlinks = LogicalDownlinks ( self . __connection ) return self . __logical_downlinks | Gets the LogicalDownlinks API client . |
62,739 | def power_devices ( self ) : if not self . __power_devices : self . __power_devices = PowerDevices ( self . __connection ) return self . __power_devices | Gets the PowerDevices API client . |
62,740 | def unmanaged_devices ( self ) : if not self . __unmanaged_devices : self . __unmanaged_devices = UnmanagedDevices ( self . __connection ) return self . __unmanaged_devices | Gets the Unmanaged Devices API client . |
62,741 | def racks ( self ) : if not self . __racks : self . __racks = Racks ( self . __connection ) return self . __racks | Gets the Racks API client . |
62,742 | def san_managers ( self ) : if not self . __san_managers : self . __san_managers = SanManagers ( self . __connection ) return self . __san_managers | Gets the SanManagers API client . |
62,743 | def endpoints ( self ) : if not self . __endpoints : self . __endpoints = Endpoints ( self . __connection ) return self . __endpoints | Gets the Endpoints API client . |
62,744 | def storage_systems ( self ) : if not self . __storage_systems : self . __storage_systems = StorageSystems ( self . __connection ) return self . __storage_systems | Gets the StorageSystems API client . |
62,745 | def storage_pools ( self ) : if not self . __storage_pools : self . __storage_pools = StoragePools ( self . __connection ) return self . __storage_pools | Gets the StoragePools API client . |
62,746 | def storage_volume_templates ( self ) : if not self . __storage_volume_templates : self . __storage_volume_templates = StorageVolumeTemplates ( self . __connection ) return self . __storage_volume_templates | Gets the StorageVolumeTemplates API client . |
62,747 | def storage_volume_attachments ( self ) : if not self . __storage_volume_attachments : self . __storage_volume_attachments = StorageVolumeAttachments ( self . __connection ) return self . __storage_volume_attachments | Gets the StorageVolumeAttachments API client . |
62,748 | def firmware_drivers ( self ) : if not self . __firmware_drivers : self . __firmware_drivers = FirmwareDrivers ( self . __connection ) return self . __firmware_drivers | Gets the FirmwareDrivers API client . |
62,749 | def firmware_bundles ( self ) : if not self . __firmware_bundles : self . __firmware_bundles = FirmwareBundles ( self . __connection ) return self . __firmware_bundles | Gets the FirmwareBundles API client . |
62,750 | def volumes ( self ) : if not self . __volumes : self . __volumes = Volumes ( self . __connection ) return self . __volumes | Gets the Volumes API client . |
62,751 | def sas_logical_jbod_attachments ( self ) : if not self . __sas_logical_jbod_attachments : self . __sas_logical_jbod_attachments = SasLogicalJbodAttachments ( self . __connection ) return self . __sas_logical_jbod_attachments | Gets the SAS Logical JBOD Attachments client . |
62,752 | def managed_sans ( self ) : if not self . __managed_sans : self . __managed_sans = ManagedSANs ( self . __connection ) return self . __managed_sans | Gets the Managed SANs API client . |
62,753 | def migratable_vc_domains ( self ) : if not self . __migratable_vc_domains : self . __migratable_vc_domains = MigratableVcDomains ( self . __connection ) return self . __migratable_vc_domains | Gets the VC Migration Manager API client . |
62,754 | def sas_interconnects ( self ) : if not self . __sas_interconnects : self . __sas_interconnects = SasInterconnects ( self . __connection ) return self . __sas_interconnects | Gets the SAS Interconnects API client . |
62,755 | def sas_logical_interconnect_groups ( self ) : if not self . __sas_logical_interconnect_groups : self . __sas_logical_interconnect_groups = SasLogicalInterconnectGroups ( self . __connection ) return self . __sas_logical_interconnect_groups | Gets the SasLogicalInterconnectGroups API client . |
62,756 | def drive_enclosures ( self ) : if not self . __drive_enclures : self . __drive_enclures = DriveEnclosures ( self . __connection ) return self . __drive_enclures | Gets the Drive Enclosures API client . |
62,757 | def sas_logical_jbods ( self ) : if not self . __sas_logical_jbods : self . __sas_logical_jbods = SasLogicalJbods ( self . __connection ) return self . __sas_logical_jbods | Gets the SAS Logical JBODs API client . |
62,758 | def labels ( self ) : if not self . __labels : self . __labels = Labels ( self . __connection ) return self . __labels | Gets the Labels API client . |
62,759 | def index_resources ( self ) : if not self . __index_resources : self . __index_resources = IndexResources ( self . __connection ) return self . __index_resources | Gets the Index Resources API client . |
62,760 | def alerts ( self ) : if not self . __alerts : self . __alerts = Alerts ( self . __connection ) return self . __alerts | Gets the Alerts API client . |
62,761 | def events ( self ) : if not self . __events : self . __events = Events ( self . __connection ) return self . __events | Gets the Events API client . |
62,762 | def os_deployment_servers ( self ) : if not self . __os_deployment_servers : self . __os_deployment_servers = OsDeploymentServers ( self . __connection ) return self . __os_deployment_servers | Gets the Os Deployment Servers API client . |
62,763 | def certificate_rabbitmq ( self ) : if not self . __certificate_rabbitmq : self . __certificate_rabbitmq = CertificateRabbitMQ ( self . __connection ) return self . __certificate_rabbitmq | Gets the Certificate RabbitMQ API client . |
62,764 | def users ( self ) : if not self . __users : self . __users = Users ( self . __connection ) return self . __users | Gets the Users API client . |
62,765 | def appliance_device_read_community ( self ) : if not self . __appliance_device_read_community : self . __appliance_device_read_community = ApplianceDeviceReadCommunity ( self . __connection ) return self . __appliance_device_read_community | Gets the ApplianceDeviceReadCommunity API client . |
62,766 | def appliance_device_snmp_v1_trap_destinations ( self ) : if not self . __appliance_device_snmp_v1_trap_destinations : self . __appliance_device_snmp_v1_trap_destinations = ApplianceDeviceSNMPv1TrapDestinations ( self . __connection ) return self . __appliance_device_snmp_v1_trap_destinations | Gets the ApplianceDeviceSNMPv1TrapDestinations API client . |
62,767 | def appliance_device_snmp_v3_trap_destinations ( self ) : if not self . __appliance_device_snmp_v3_trap_destinations : self . __appliance_device_snmp_v3_trap_destinations = ApplianceDeviceSNMPv3TrapDestinations ( self . __connection ) return self . __appliance_device_snmp_v3_trap_destinations | Gets the ApplianceDeviceSNMPv3TrapDestinations API client . |
62,768 | def appliance_device_snmp_v3_users ( self ) : if not self . __appliance_device_snmp_v3_users : self . __appliance_device_snmp_v3_users = ApplianceDeviceSNMPv3Users ( self . __connection ) return self . __appliance_device_snmp_v3_users | Gets the ApplianceDeviceSNMPv3Users API client . |
62,769 | def appliance_node_information ( self ) : if not self . __appliance_node_information : self . __appliance_node_information = ApplianceNodeInformation ( self . __connection ) return self . __appliance_node_information | Gets the ApplianceNodeInformation API client . |
62,770 | def appliance_time_and_locale_configuration ( self ) : if not self . __appliance_time_and_locale_configuration : self . __appliance_time_and_locale_configuration = ApplianceTimeAndLocaleConfiguration ( self . __connection ) return self . __appliance_time_and_locale_configuration | Gets the ApplianceTimeAndLocaleConfiguration API client . |
62,771 | def versions ( self ) : if not self . __versions : self . __versions = Versions ( self . __connection ) return self . __versions | Gets the Version API client . |
62,772 | def backups ( self ) : if not self . __backups : self . __backups = Backups ( self . __connection ) return self . __backups | Gets the Backup API client . |
62,773 | def login_details ( self ) : if not self . __login_details : self . __login_details = LoginDetails ( self . __connection ) return self . __login_details | Gets the login details |
62,774 | def get_available_networks ( self , ** kwargs ) : query_string = '&' . join ( '{}={}' . format ( key , value ) for key , value in kwargs . items ( ) if value ) uri = self . URI + "{}?{}" . format ( "/available-networks" , query_string ) return self . _helper . do_get ( uri ) | Retrieves the list of Ethernet networks Fibre Channel networks and network sets that are available to a server profile template along with their respective ports . The scopeUris serverHardwareTypeUri and enclosureGroupUri parameters should be specified to get the available networks for a new server profile template . The serverHardwareTypeUri enclosureGroupUri and profileTemplateUri should be specified to get available networks for an existing server profile template . The scopeUris parameter is ignored when the profileTemplateUri is specified . |
62,775 | def get_all_without_ethernet ( self , start = 0 , count = - 1 , filter = '' , sort = '' ) : without_ethernet_client = ResourceClient ( self . _connection , "/rest/logical-downlinks/withoutEthernet" ) return without_ethernet_client . get_all ( start , count , filter = filter , sort = sort ) | Gets a paginated collection of logical downlinks without ethernet . The collection is based on optional sorting and filtering and is constrained by start and count parameters . |
62,776 | def get_without_ethernet ( self , id_or_uri ) : uri = self . _client . build_uri ( id_or_uri ) + "/withoutEthernet" return self . _client . get ( uri ) | Gets the logical downlink with the specified ID without ethernet . |
62,777 | def update_firmware ( self , firmware_information , force = False ) : firmware_uri = "{}/firmware" . format ( self . data [ "uri" ] ) result = self . _helper . update ( firmware_information , firmware_uri , force = force ) self . refresh ( ) return result | Installs firmware to the member interconnects of a SAS Logical Interconnect . |
62,778 | def get_firmware ( self ) : firmware_uri = "{}/firmware" . format ( self . data [ "uri" ] ) return self . _helper . do_get ( firmware_uri ) | Gets baseline firmware information for a SAS Logical Interconnect . |
62,779 | def update_compliance_all ( self , information , timeout = - 1 ) : uri = self . URI + "/compliance" result = self . _helper . update ( information , uri , timeout = timeout ) return result | Returns SAS Logical Interconnects to a consistent state . The current SAS Logical Interconnect state is compared to the associated SAS Logical Interconnect group . |
62,780 | def replace_drive_enclosure ( self , information ) : uri = "{}/replaceDriveEnclosure" . format ( self . data [ "uri" ] ) result = self . _helper . create ( information , uri ) self . refresh ( ) return result | When a drive enclosure has been physically replaced initiate the replacement operation that enables the new drive enclosure to take over as a replacement for the prior drive enclosure . The request requires specification of both the serial numbers of the original drive enclosure and its replacement to be provided . |
62,781 | def update_configuration ( self ) : uri = "{}/configuration" . format ( self . data [ "uri" ] ) result = self . _helper . update ( { } , uri ) self . refresh ( ) return result | Asynchronously applies or re - applies the SAS Logical Interconnect configuration to all managed interconnects of a SAS Logical Interconnect . |
62,782 | def mutationhash ( strings , nedit ) : maxlen = max ( [ len ( string ) for string in strings ] ) indexes = generate_idx ( maxlen , nedit ) muthash = defaultdict ( set ) for string in strings : muthash [ string ] . update ( [ string ] ) for x in substitution_set ( string , indexes ) : muthash [ x ] . update ( [ string ] ) return muthash | produce a hash with each key a nedit distance substitution for a set of strings . values of the hash is the set of strings the substitution could have come from |
62,783 | def substitution_set ( string , indexes ) : strlen = len ( string ) return { mutate_string ( string , x ) for x in indexes if valid_substitution ( strlen , x ) } | for a string return a set of all possible substitutions |
62,784 | def valid_substitution ( strlen , index ) : values = index [ 0 ] return all ( [ strlen > i for i in values ] ) | skip performing substitutions that are outside the bounds of the string |
62,785 | def acgt_match ( string ) : search = re . compile ( r'[^ACGT]' ) . search return not bool ( search ( string ) ) | returns True if sting consist of only A C G T |
62,786 | def stream_fastq ( file_handler ) : next_element = '' for i , line in enumerate ( file_handler ) : next_element += line if i % 4 == 3 : yield next_element next_element = '' | Generator which gives all four lines if a fastq read as one string |
62,787 | def read_fastq ( filename ) : if not filename : return itertools . cycle ( ( None , ) ) if filename == "-" : filename_fh = sys . stdin elif filename . endswith ( 'gz' ) : if is_python3 : filename_fh = gzip . open ( filename , mode = 'rt' ) else : filename_fh = BufferedReader ( gzip . open ( filename , mode = 'rt' ) ) else : filename_fh = open ( filename ) return stream_fastq ( filename_fh ) | return a stream of FASTQ entries handling gzipped and empty files |
62,788 | def write_fastq ( filename ) : if filename : if filename . endswith ( 'gz' ) : filename_fh = gzip . open ( filename , mode = 'wb' ) else : filename_fh = open ( filename , mode = 'w' ) else : filename_fh = None return filename_fh | return a handle for FASTQ writing handling gzipped files |
62,789 | def detect_alignment_annotations ( queryalignment , tags = False ) : annotations = set ( ) for k , v in BARCODEINFO . items ( ) : if tags : if queryalignment . has_tag ( v . bamtag ) : annotations . add ( k ) else : if v . readprefix in queryalignment . qname : annotations . add ( k ) return annotations | detects the annotations present in a SAM file inspecting either the tags or the query names and returns a set of annotations present |
62,790 | def detect_fastq_annotations ( fastq_file ) : annotations = set ( ) queryread = tz . first ( read_fastq ( fastq_file ) ) for k , v in BARCODEINFO . items ( ) : if v . readprefix in queryread : annotations . add ( k ) return annotations | detects annotations preesent in a FASTQ file by examining the first read |
62,791 | def construct_transformed_regex ( annotations ) : re_string = '.*' if "cellular" in annotations : re_string += ":CELL_(?P<CB>.*)" if "molecular" in annotations : re_string += ":UMI_(?P<MB>\w*)" if "sample" in annotations : re_string += ":SAMPLE_(?P<SB>\w*)" if re_string == ".*" : logger . error ( "No annotation present on this file, aborting." ) sys . exit ( 1 ) return re_string | construct a regex that matches possible fields in a transformed file annotations is a set of which keys in BARCODEINFO are present in the file |
62,792 | def _infer_transform_options ( transform ) : TransformOptions = collections . namedtuple ( "TransformOptions" , [ 'CB' , 'dual_index' , 'triple_index' , 'MB' , 'SB' ] ) CB = False SB = False MB = False dual_index = False triple_index = False for rx in transform . values ( ) : if not rx : continue if "CB1" in rx : if "CB3" in rx : triple_index = True else : dual_index = True if "SB" in rx : SB = True if "CB" in rx : CB = True if "MB" in rx : MB = True return TransformOptions ( CB = CB , dual_index = dual_index , triple_index = triple_index , MB = MB , SB = SB ) | figure out what transform options should be by examining the provided regexes for keywords |
62,793 | def _extract_readnum ( read_dict ) : pat = re . compile ( r"(?P<readnum>/\d+)$" ) parts = pat . split ( read_dict [ "name" ] ) if len ( parts ) == 3 : name , readnum , endofline = parts read_dict [ "name" ] = name read_dict [ "readnum" ] = readnum else : read_dict [ "readnum" ] = "" return read_dict | Extract read numbers from old - style fastqs . |
62,794 | def sparse ( csv , sparse ) : import pandas as pd df = pd . read_csv ( csv , index_col = 0 , header = 0 ) pd . Series ( df . index ) . to_csv ( sparse + ".rownames" , index = False ) pd . Series ( df . columns . values ) . to_csv ( sparse + ".colnames" , index = False ) with open ( sparse , "w+b" ) as out_handle : scipy . io . mmwrite ( out_handle , scipy . sparse . csr_matrix ( df ) ) | Convert a CSV file to a sparse matrix with rows and column names saved as companion files . |
62,795 | def cb_histogram ( fastq , umi_histogram ) : annotations = detect_fastq_annotations ( fastq ) re_string = construct_transformed_regex ( annotations ) parser_re = re . compile ( re_string ) cb_counter = collections . Counter ( ) umi_counter = collections . Counter ( ) for read in read_fastq ( fastq ) : match = parser_re . search ( read ) . groupdict ( ) cb = match [ 'CB' ] cb_counter [ cb ] += 1 if umi_histogram : umi = match [ 'MB' ] umi_counter [ ( cb , umi ) ] += 1 for bc , count in cb_counter . most_common ( ) : sys . stdout . write ( '{}\t{}\n' . format ( bc , count ) ) if umi_histogram : with open ( umi_histogram , "w" ) as umi_handle : for cbumi , count in umi_counter . most_common ( ) : umi_handle . write ( '{}\t{}\t{}\n' . format ( cbumi [ 0 ] , cbumi [ 1 ] , count ) ) | Counts the number of reads for each cellular barcode |
62,796 | def umi_histogram ( fastq ) : annotations = detect_fastq_annotations ( fastq ) re_string = construct_transformed_regex ( annotations ) parser_re = re . compile ( re_string ) counter = collections . Counter ( ) for read in read_fastq ( fastq ) : match = parser_re . search ( read ) . groupdict ( ) counter [ match [ 'MB' ] ] += 1 for bc , count in counter . most_common ( ) : sys . stdout . write ( '{}\t{}\n' . format ( bc , count ) ) | Counts the number of reads for each UMI |
62,797 | def get_cb_depth_set ( cb_histogram , cb_cutoff ) : cb_keep_set = set ( ) if not cb_histogram : return cb_keep_set with read_cbhistogram ( cb_histogram ) as fh : cb_map = dict ( p . strip ( ) . split ( ) for p in fh ) cb_keep_set = set ( [ k for k , v in cb_map . items ( ) if int ( v ) > cb_cutoff ] ) logger . info ( 'Keeping %d out of %d cellular barcodes.' % ( len ( cb_keep_set ) , len ( cb_map ) ) ) return cb_keep_set | Returns a set of barcodes with a minimum number of reads |
62,798 | def guess_depth_cutoff ( cb_histogram ) : with read_cbhistogram ( cb_histogram ) as fh : cb_vals = [ int ( p . strip ( ) . split ( ) [ 1 ] ) for p in fh ] histo = np . histogram ( np . log10 ( cb_vals ) , bins = 50 ) vals = histo [ 0 ] edges = histo [ 1 ] mids = np . array ( [ ( edges [ i ] + edges [ i + 1 ] ) / 2 for i in range ( edges . size - 1 ) ] ) wdensity = vals * ( 10 ** mids ) / sum ( vals * ( 10 ** mids ) ) baseline = np . median ( wdensity ) wdensity = list ( wdensity ) peak = wdensity . index ( max ( wdensity [ len ( wdensity ) / 2 : ] ) ) cutoff = None for index , dens in reversed ( list ( enumerate ( wdensity [ 1 : peak ] ) ) ) : if dens < 2 * baseline : cutoff = index break if not cutoff : return None else : cutoff = 10 ** mids [ cutoff ] logger . info ( 'Setting barcode cutoff to %d' % cutoff ) return cutoff | Guesses at an appropriate barcode cutoff |
62,799 | def cb_filter ( fastq , bc1 , bc2 , bc3 , cores , nedit ) : with open_gzipsafe ( bc1 ) as bc1_fh : bc1 = set ( cb . strip ( ) for cb in bc1_fh ) if bc2 : with open_gzipsafe ( bc2 ) as bc2_fh : bc2 = set ( cb . strip ( ) for cb in bc2_fh ) if bc3 : with open_gzipsafe ( bc3 ) as bc3_fh : bc3 = set ( cb . strip ( ) for cb in bc3_fh ) annotations = detect_fastq_annotations ( fastq ) re_string = construct_transformed_regex ( annotations ) if nedit == 0 : filter_cb = partial ( exact_barcode_filter , bc1 = bc1 , bc2 = bc2 , bc3 = bc3 , re_string = re_string ) else : bc1hash = MutationHash ( bc1 , nedit ) bc2hash = None bc3hash = None if bc2 : bc2hash = MutationHash ( bc2 , nedit ) if bc3 : bc3hash = MutationHash ( bc3 , nedit ) filter_cb = partial ( correcting_barcode_filter , bc1hash = bc1hash , bc2hash = bc2hash , bc3hash = bc3hash , re_string = re_string ) p = multiprocessing . Pool ( cores ) chunks = tz . partition_all ( 10000 , read_fastq ( fastq ) ) bigchunks = tz . partition_all ( cores , chunks ) for bigchunk in bigchunks : for chunk in p . map ( filter_cb , list ( bigchunk ) ) : for read in chunk : sys . stdout . write ( read ) | Filters reads with non - matching barcodes Expects formatted fastq files . |
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