Hugging Face's logo

Spaces:
tracywong117
/
TIPars-UI
Sleeping

App Files Community
tracywong117 commited on
Commit
1d9cdb7
·
1 Parent(s): 5ae3d25

Add mafft and seqkit

Browse files
Files changed (46) hide show
  1. .gitattributes +2 -0
  2. Dockerfile +4 -0
  3. app.py +9 -0
  4. mafft-linux64/mafft.bat +3 -0
  5. mafft-linux64/mafftdir/bin/mafft +3 -0
  6. mafft-linux64/mafftdir/libexec/addsingle +3 -0
  7. mafft-linux64/mafftdir/libexec/contrafoldwrap +3 -0
  8. mafft-linux64/mafftdir/libexec/countlen +3 -0
  9. mafft-linux64/mafftdir/libexec/dash_alignments +3 -0
  10. mafft-linux64/mafftdir/libexec/dash_client +3 -0
  11. mafft-linux64/mafftdir/libexec/dash_sequences.fa +3 -0
  12. mafft-linux64/mafftdir/libexec/disttbfast +3 -0
  13. mafft-linux64/mafftdir/libexec/dndblast +3 -0
  14. mafft-linux64/mafftdir/libexec/dndfast7 +3 -0
  15. mafft-linux64/mafftdir/libexec/dndpre +3 -0
  16. mafft-linux64/mafftdir/libexec/dvtditr +3 -0
  17. mafft-linux64/mafftdir/libexec/f2cl +3 -0
  18. mafft-linux64/mafftdir/libexec/filter +3 -0
  19. mafft-linux64/mafftdir/libexec/getlag +3 -0
  20. mafft-linux64/mafftdir/libexec/hat3 +0 -0
  21. mafft-linux64/mafftdir/libexec/hex2maffttext +3 -0
  22. mafft-linux64/mafftdir/libexec/mafft-distance +3 -0
  23. mafft-linux64/mafftdir/libexec/mafft-homologs.1 +3 -0
  24. mafft-linux64/mafftdir/libexec/mafft-profile +3 -0
  25. mafft-linux64/mafftdir/libexec/mafft.1 +3 -0
  26. mafft-linux64/mafftdir/libexec/mafftash_premafft.pl +3 -0
  27. mafft-linux64/mafftdir/libexec/maffttext2hex +3 -0
  28. mafft-linux64/mafftdir/libexec/makedirectionlist +3 -0
  29. mafft-linux64/mafftdir/libexec/mccaskillwrap +3 -0
  30. mafft-linux64/mafftdir/libexec/multi2hat3s +3 -0
  31. mafft-linux64/mafftdir/libexec/nodepair +3 -0
  32. mafft-linux64/mafftdir/libexec/pairash +3 -0
  33. mafft-linux64/mafftdir/libexec/pairlocalalign +3 -0
  34. mafft-linux64/mafftdir/libexec/regtable2seq +3 -0
  35. mafft-linux64/mafftdir/libexec/replaceu +3 -0
  36. mafft-linux64/mafftdir/libexec/restoreu +3 -0
  37. mafft-linux64/mafftdir/libexec/score +3 -0
  38. mafft-linux64/mafftdir/libexec/seekquencer_premafft.pl +3 -0
  39. mafft-linux64/mafftdir/libexec/seq2regtable +3 -0
  40. mafft-linux64/mafftdir/libexec/setcore +3 -0
  41. mafft-linux64/mafftdir/libexec/setdirection +3 -0
  42. mafft-linux64/mafftdir/libexec/sextet5 +3 -0
  43. mafft-linux64/mafftdir/libexec/splittbfast +3 -0
  44. mafft-linux64/mafftdir/libexec/tbfast +3 -0
  45. mafft-linux64/mafftdir/libexec/version +3 -0
  46. seqkit +3 -0
.gitattributes CHANGED
@@ -34,3 +34,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
34
  *.zst filter=lfs diff=lfs merge=lfs -text
35
  *tfevents* filter=lfs diff=lfs merge=lfs -text
36
  *.jar filter=lfs diff=lfs merge=lfs -text
 
 
 
34
  *.zst filter=lfs diff=lfs merge=lfs -text
35
  *tfevents* filter=lfs diff=lfs merge=lfs -text
36
  *.jar filter=lfs diff=lfs merge=lfs -text
37
+ mafft-linux64/** filter=lfs diff=lfs merge=lfs -text
38
+ seqkit filter=lfs diff=lfs merge=lfs -text
Dockerfile CHANGED
@@ -73,6 +73,10 @@ COPY --chown=user:user ./ $HOME/app/
73
  # Install required Python dependencies
74
  RUN python3.11 -m pip install -r $HOME/app/requirements.txt
75
 
 
 
 
 
76
  # Expose the desired port
77
  EXPOSE 7860
78
 
 
73
  # Install required Python dependencies
74
  RUN python3.11 -m pip install -r $HOME/app/requirements.txt
75
 
76
+ # Install mafft
77
+ # RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.520-linux.tgz
78
+ # RUN tar xfvz mafft-7.520-linux.tgz
79
+
80
  # Expose the desired port
81
  EXPOSE 7860
82
 
app.py CHANGED
@@ -3,6 +3,15 @@ import subprocess
3
 
4
  def run_java():
5
  # Run the Java program using subprocess and redirect input/output
 
 
 
 
 
 
 
 
 
6
  subprocess.run(["tipars/tipars", "-t", "tipars/Benchmark_datasets/NDV/NDV_tree.nwk", "-s", "tipars/Benchmark_datasets/NDV/NDV_taxa.fas", "-a", "tipars/Benchmark_datasets/NDV/NDV_anc.fas", "-q", "tipars/Benchmark_datasets/NDV/NDV_query.fas", "-o", "tipars/Benchmark_datasets/NDV/tipars.tree"])
7
 
8
  return
 
3
 
4
  def run_java():
5
  # Run the Java program using subprocess and redirect input/output
6
+ command = ["mafft-linux64/mafft.bat", "--add", "tipars/Benchmark_datasets/NDV/NDV_query.fas", "--keeplength", "tipars/Benchmark_datasets/NDV/NDV_taxa.fas"]
7
+ with open("mafft_output.fas", "w") as output_file:
8
+ subprocess.run(command, stdout=output_file, text=True)
9
+ command = ["./seqkit", "seq", "-n", "tipars/Benchmark_datasets/NDV/NDV_query.fas"]
10
+ with open("query-name.txt", "w") as output_file:
11
+ subprocess.run(command, stdout=output_file, text=True)
12
+ command = ["./seqkit", "grep", "-f", "query-name.txt", "mafft_output.fas"]
13
+ with open("tipars/Benchmark_datasets/NDV/NDV_query.fas", "w") as output_file:
14
+ subprocess.run(command, stdout=output_file, text=True)
15
  subprocess.run(["tipars/tipars", "-t", "tipars/Benchmark_datasets/NDV/NDV_tree.nwk", "-s", "tipars/Benchmark_datasets/NDV/NDV_taxa.fas", "-a", "tipars/Benchmark_datasets/NDV/NDV_anc.fas", "-q", "tipars/Benchmark_datasets/NDV/NDV_query.fas", "-o", "tipars/Benchmark_datasets/NDV/tipars.tree"])
16
 
17
  return
mafft-linux64/mafft.bat ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f5e516270c66e7b2fd71ebcb2ecc3f56a5b63a53f888a8f4112030ec272c5275
3
+ size 284
mafft-linux64/mafftdir/bin/mafft ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:44d3dfba92152b488be137ff33d0fc5119388a9c465410310ee3efd6a6755b1a
3
+ size 109559
mafft-linux64/mafftdir/libexec/addsingle ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:93fc0ab87525e206afc060873fc669fca8c5f6469cca52ce705e2a54ecabf799
3
+ size 1316464
mafft-linux64/mafftdir/libexec/contrafoldwrap ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:df6ffd73aaf87424c1eb4ee53eaa3dfbc6245cb1a67222e516c644fba8e70d7c
3
+ size 928152
mafft-linux64/mafftdir/libexec/countlen ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:266b70d9b09bd4c273f279c26f0c03a4edd6853dae41489eb22a9eddd691cfd6
3
+ size 626008
mafft-linux64/mafftdir/libexec/dash_alignments ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:550a8b12ae02339bfe1e83c3a3a01df8f0029fbefab3f19f19bc8a3011eee012
3
+ size 139470
mafft-linux64/mafftdir/libexec/dash_client ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:7b2f1a8f8b922769fefaa0399b057aa20e93da5cece04b31e136b775093c6f9b
3
+ size 4232576
mafft-linux64/mafftdir/libexec/dash_sequences.fa ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5b9da9b530e7c6df2363f54715a4c0d042ab839bc48c835b6610b261ba737949
3
+ size 27687
mafft-linux64/mafftdir/libexec/disttbfast ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:686472e9173ce97deaedba569e999c06d87538394d61898557ac7155569c4c48
3
+ size 1341168
mafft-linux64/mafftdir/libexec/dndblast ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:81fbd47f15c424e077c6f5baa1044d0e39138538c0598e0f0125e18f95c48287
3
+ size 940432
mafft-linux64/mafftdir/libexec/dndfast7 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:081afdee709bb3c5b675e0a629fa4af7d24b57d080002529052a8438b5de1341
3
+ size 937616
mafft-linux64/mafftdir/libexec/dndpre ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:06fc0473eda58c1cac78eb6bf8bb8174cb955d5956cf385ab0548dbdf4035778
3
+ size 924048
mafft-linux64/mafftdir/libexec/dvtditr ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:18394172f8765efdab3e5c59b9af45cf5a5779d794104d9bd78098f695e3059c
3
+ size 1272528
mafft-linux64/mafftdir/libexec/f2cl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:b26f83e3123127ef7b95ee438a26fc51f69b7f52e50c9507458d1303b113e8c8
3
+ size 735312
mafft-linux64/mafftdir/libexec/filter ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:6a07af271f976bec14d2832ba7b363e28cca6ad252ad14eb5ff6d3f41fdd8fd8
3
+ size 866768
mafft-linux64/mafftdir/libexec/getlag ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e18db9a7c4beaa9d024b867ab1355146aa12eae8a8a19772d245bcbede10cd90
3
+ size 1202576
mafft-linux64/mafftdir/libexec/hat3 ADDED
File without changes
mafft-linux64/mafftdir/libexec/hex2maffttext ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:a5817c00d02c388b49b0f8e82a95da316b68aa42d8f901a0df65b3cb750d5e64
3
+ size 542776
mafft-linux64/mafftdir/libexec/mafft-distance ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:99622c60944e7059eef9b7703748a739c4b0aab64121b69fdd020b86e024da13
3
+ size 936344
mafft-linux64/mafftdir/libexec/mafft-homologs.1 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:af8149827654a2db14de0f4104a58681548af261b48fa1c74870aa08c870a847
3
+ size 4550
mafft-linux64/mafftdir/libexec/mafft-profile ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0dae2de229bb3602e0a882c5707871307ef900f4f98f918efe5f2f0a928f0de1
3
+ size 1200720
mafft-linux64/mafftdir/libexec/mafft.1 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:319b30bf9cd7a1cd1e64848950b84196268c8208faf5fc90d0e9d5ffe9fa6875
3
+ size 14771
mafft-linux64/mafftdir/libexec/mafftash_premafft.pl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0594ba064e06ad0b647a9927bc73541edd85fd18c09a65c7a5c849b318b93ef9
3
+ size 10475
mafft-linux64/mafftdir/libexec/maffttext2hex ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:4ced34fedac7ce84d43b93c93d36097c2457eecfeb08881a6557286a6cdcaf19
3
+ size 542776
mafft-linux64/mafftdir/libexec/makedirectionlist ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:b234bc0799e7f2933146150a4bddc096bbcaa055a389795fb73e3e41c2b412dc
3
+ size 1224280
mafft-linux64/mafftdir/libexec/mccaskillwrap ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e806073d87ba230f9cc738c6d3b1f1a77e87d4d07af20ddb9aa6cbef8793649a
3
+ size 929104
mafft-linux64/mafftdir/libexec/multi2hat3s ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:cb5c144cb2b21ebba354b241d621a6cacf0c0afc33ccb77c623e0bd50b7f89a1
3
+ size 985488
mafft-linux64/mafftdir/libexec/nodepair ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3d5ae99f0c17cff610642a1f03fa0bf56553293ad28ebad37fdf34fdde0da7a8
3
+ size 1264016
mafft-linux64/mafftdir/libexec/pairash ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:260013b2c9584106ab56a9ad1f79f0b9f405415d3f9ab4aea2e69545f70db95a
3
+ size 1214864
mafft-linux64/mafftdir/libexec/pairlocalalign ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ac836ab0af0e77dcc35980e4b47e833a276adf31071cc4a7733924396467750a
3
+ size 1239448
mafft-linux64/mafftdir/libexec/regtable2seq ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:0e8ddd6d899f0c19595653fe6d1f7401a0fe558c5b124baa48287978a607f822
3
+ size 866768
mafft-linux64/mafftdir/libexec/replaceu ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e920e5fa1fc8971a5d18a7a76d0921f31ec625556ed51840b77156d7bdb9e5cc
3
+ size 866768
mafft-linux64/mafftdir/libexec/restoreu ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:ffa82a31e389e0ac82625a49aba722631f50ec3b0d97dc9e011f60020cf8ad74
3
+ size 866768
mafft-linux64/mafftdir/libexec/score ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:3025b37b354304ab3f1336d9cdd101042c3f4f3ff7209a776fbf9dae32d42569
3
+ size 924040
mafft-linux64/mafftdir/libexec/seekquencer_premafft.pl ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:bfe2f4cd579c3734ac9a4979c9a1b577bef8993f5242c342019df2c490d82fd3
3
+ size 15541
mafft-linux64/mafftdir/libexec/seq2regtable ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:aaaf864d144698e33438bf14e5570d6966fad0a7956a937a8eb7eb913dbfaf1c
3
+ size 626104
mafft-linux64/mafftdir/libexec/setcore ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:bc6d64a4810b57f6aa6fe369ef2a8dbea4bd1ba4df3fc7f6dd4b67f0e2985d7c
3
+ size 1200784
mafft-linux64/mafftdir/libexec/setdirection ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:509ec44689e03f8fcfff5672e1a726405b5f233ffb382daa71bc280e619fc1f1
3
+ size 866768
mafft-linux64/mafftdir/libexec/sextet5 ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:9ad5cb4e12dc2e99551d96e52ea04cffcfd8c554aa2debe16f8ee96596911814
3
+ size 934032
mafft-linux64/mafftdir/libexec/splittbfast ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:65fbe482a70fb5976872c2cc370d7949b10dc6c0e62bf6107122a530b987799b
3
+ size 1227152
mafft-linux64/mafftdir/libexec/tbfast ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:e719be2cd84bb505eb022c7126eefb1c63456fe3b943c4a28613c9d97a779adf
3
+ size 1313168
mafft-linux64/mafftdir/libexec/version ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:5fc55d1c29b2292b820a6d32f6ac50ae396e1d6d9dce58005a7a589accbb6e27
3
+ size 538904
seqkit ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f0fbffd7e2d82cf9867fec96d8e809b34cd8f291e1d8678f550458fed1467187
3
+ size 18333696