Mercurial > repos > jjohnson > iedb_api

annotate iedb_api.py @ 3:153d5fa7af53 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
author jjohnson
date Wed, 26 Feb 2020 16:27:06 -0500
parents 4a89ba6cfc63
children a14128950578
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
1 #!/usr/bin/env python
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
2
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
3 import argparse
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
4 import os.path
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
5 import re
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
6 import sys
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
7 import time
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
8 from urllib.error import HTTPError
3
153d5fa7af53 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
jjohnson
parents: 1
diff changeset
9 from urllib.parse import unquote, urlencode
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
10 from urllib.request import urlopen
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
11
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
12 mhci_methods = ['recommended', 'consensus',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
13 'netmhcpan_ba', 'netmhcpan_el',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
14 'ann', 'smmpmbec', 'smm',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
15 'comblib_sidney2008', 'netmhccons',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
16 'pickpocket', 'netmhcstabpan']
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
17 mhcii_methods = ['recommended', 'consensus', 'NetMHCIIpan',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
18 'nn_align', 'smm_align', 'comblib', 'tepitope']
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
19 processing_methods = ['recommended', 'netmhcpan', 'ann',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
20 'smmpmbec', 'smm', 'comblib_sidney2008',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
21 'netmhccons', 'pickpocket']
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
22 mhcnp_methods = ['mhcnp', 'netmhcpan']
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
23 bcell_methods = ['Bepipred', 'Chou-Fasman', 'Emini', 'Karplus-Schulz',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
24 'Kolaskar-Tongaonkar', 'Parker', 'Bepipred-2.0']
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
25 prediction_methods = {'mhci': mhci_methods,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
26 'mhcii': mhcii_methods,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
27 'processing': processing_methods,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
28 'mhcnp': mhcnp_methods,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
29 'bcell': bcell_methods}
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
30 all_methods = set(mhci_methods + mhcii_methods +
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
31 mhcnp_methods + bcell_methods)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
32 prediction_lengths = {'mhci': range(8, 16),
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
33 'mhcii': range(11, 31),
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
34 'processing': range(8, 15),
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
35 'mhcnp': range(8, 12),
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
36 'bcell': range(8, 16)}
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
37
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
38
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
39 def warn_err(msg, exit_code=1):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
40 sys.stderr.write(msg)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
41 if exit_code:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
42 sys.exit(exit_code)
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
43
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
44
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
45 def __main__():
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
46 # Parse Command Line
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
47 parser = argparse.ArgumentParser(description='', epilog='')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
48 parser.add_argument('-p', '--prediction',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
49 default='mhci',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
50 choices=prediction_methods.keys(),
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
51 help='IEDB API prediction service')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
52 parser.add_argument('-s', '--sequence',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
53 action="append",
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
54 default=None,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
55 help='Peptide Sequence')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
56 parser.add_argument('-m', '--method',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
57 default='recommended',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
58 choices=all_methods,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
59 help='prediction method')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
60 parser.add_argument('-P', '--proteasome',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
61 default=None,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
62 choices=['immuno', 'constitutive'],
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
63 help='IEDB processing proteasome type')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
64 parser.add_argument('-a', '--allele',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
65 action="append",
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
66 default=[],
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
67 help='Alleles for which to make predictions')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
68 parser.add_argument('-l', '--length',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
69 action="append",
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
70 default=[],
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
71 help='lengths for which to make predictions, ' +
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
72 '1 per allele')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
73 parser.add_argument('-w', '--window_size',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
74 type=int,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
75 default=None,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
76 help='window_size for bcell prediction')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
77 parser.add_argument('-i', '--input',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
78 default=None,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
79 help='Input file for peptide sequences ' +
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
80 '(fasta or tabular)')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
81 parser.add_argument('-c', '--column',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
82 default=None,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
83 help='Peptide Column in a tabular input file')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
84 parser.add_argument('-C', '--id_column',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
85 default=None,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
86 help='ID Column in a tabular input file')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
87 parser.add_argument('-o', '--output',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
88 default=None,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
89 help='Output file for query results')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
90 parser.add_argument('-O', '--output2',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
91 default='iedb_results2',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
92 help='Output file for secondary query results')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
93 parser.add_argument('-t', '--timeout',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
94 type=int,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
95 default=600,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
96 help='Seconds to wait for server response')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
97 parser.add_argument('-r', '--retries',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
98 type=int,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
99 default=5,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
100 help='Number of times to retry server query')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
101 parser.add_argument('-S', '--sleep',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
102 type=int,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
103 default=300,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
104 help='Seconds to wait between retries')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
105 parser.add_argument('-d', '--debug',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
106 action='store_true',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
107 default=False,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
108 help='Turn on wrapper debugging to stderr')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
109 args = parser.parse_args()
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
110
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
111 aapat = '^[ABCDEFGHIKLMNPQRSTVWY]+$'
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
112
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
113 if not args.allele and args.prediction != 'bcell':
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
114 warn_err('-a allele required\n', exit_code=1)
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
115
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
116 if not (args.sequence or args.input):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
117 warn_err('NO Sequences given: ' +
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
118 'either -s sequence or -i input_file is required\n',
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
119 exit_code=1)
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
120
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
121 if args.output is not None:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
122 try:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
123 outputPath = os.path.abspath(args.output)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
124 outputFile = open(outputPath, 'w')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
125 except Exception as e:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
126 warn_err("Unable to open output file: %s\n" % e, exit_code=1)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
127 else:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
128 outputFile = sys.stdout
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
129
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
130 url = 'http://tools-cluster-interface.iedb.org/tools_api/%s/' %\
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
131 args.prediction
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
132 len_param = 'length' if args.prediction != 'bcell' else 'window_size'
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
133
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
134 # TODO parse alleles from the args.alleles file
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
135 alleles = ','.join(args.allele) if args.prediction != 'bcell' else None
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
136 lengths = ','.join(args.length)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
137 if args.prediction == 'bcell':
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
138 lengths = args.window_size
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
139 method = args.method
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
140 proteasome = args.proteasome if args.prediction == 'processcing' else None
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
141 global header
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
142 header = None
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
143 results = []
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
144 global header2
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
145 header2 = None
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
146 results2 = []
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
147
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
148 sequence_text = []
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
149
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
150 def add_seq(seqid, seq):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
151 sid = seqid if seqid else "peptide%d" % len(sequence_text)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
152 sequence_text.append(">%s\n%s" % (sid, seq))
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
153
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
154 def query(url, seq, allele, length, seqid=None, method='recommended'):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
155 global header
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
156 global header2
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
157 params = dict()
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
158 if method:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
159 params['method'] = method.encode()
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
160 if proteasome:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
161 params['proteasome'] = proteasome.encode()
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
162 params['sequence_text'] = seq.encode()
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
163 if allele is not None:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
164 params['allele'] = allele.encode()
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
165 if length is not None:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
166 params[len_param] = str(length).encode()
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
167 req_data = urlencode(params)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
168 if args.debug:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
169 print('url %s %s' % (url, unquote(req_data)), file=sys.stderr)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
170 retries = max(0, args.retries) + 1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
171 for retry in range(1, retries):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
172 response = None
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
173 try:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
174 response = urlopen(url, data=req_data.encode('utf-8'),
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
175 timeout=args.timeout)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
176 if response and response.getcode() == 200:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
177 data = [line.decode() for line in response.readlines()]
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
178 if args.debug:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
179 print(data, file=sys.stderr)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
180 rslts = results
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
181 for ln, line in enumerate(data):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
182 if line.lower().find('invalid') >= 0:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
183 msg = '%s %s\n%s' % (url, unquote(req_data),
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
184 ''.join(data))
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
185 warn_err(msg, exit_code=1)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
186 if line.find('eptide') > 0:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
187 header = "#%s%s" %\
3
153d5fa7af53 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
jjohnson
parents: 1
diff changeset
188 ("ID\t" if seqid else "", line)
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
189 if args.debug:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
190 print(header, file=sys.stderr)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
191 continue
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
192 elif method == 'Bepipred' and line.find('Residue') > 0:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
193 header2 = "#%s%s" %\
3
153d5fa7af53 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 250d6261ba8c695446f845f2f31c6cca8d87a427-dirty"
jjohnson
parents: 1
diff changeset
194 ("ID\t" if seqid else "", line)
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
195 if args.debug:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
196 print(header2, file=sys.stderr)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
197 rslts = results2
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
198 continue
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
199 if seqid:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
200 rslts.extend("%s\t%s" % (seqid, line))
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
201 else:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
202 rslts.extend(line)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
203 break
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
204 else:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
205 code = response.getcode() if response else 1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
206 warn_err("Error connecting to IEDB server\n",
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
207 exit_code=code)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
208 except HTTPError as e:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
209 code = None if retry < args.retries else e.code
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
210 warn_err("%d of %d Error connecting to IEDB server %s\n" %
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
211 (retry, retries, e),
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
212 exit_code=code)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
213 time.sleep(args.sleep)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
214 except Exception as e:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
215 warn_err("Error connecting to IEDB server %s\n" % e,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
216 exit_code=3)
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
217
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
218 if args.sequence:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
219 for i, seq in enumerate(args.sequence):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
220 query(url, seq, alleles, lengths, seqid=None, method=method)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
221 if args.input:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
222 try:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
223 fh = open(args.input, 'r')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
224 if args.column: # tabular
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
225 col = int(args.column)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
226 idcol = int(args.id_column) if args.id_column else None
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
227 for i, line in enumerate(fh):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
228 fields = line.split('\t')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
229 if len(fields) > col:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
230 seq = re.sub('[_*]', '', fields[col])
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
231 if re.match(aapat, seq):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
232 if idcol is not None and idcol < len(fields):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
233 seqid = fields[idcol]
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
234 else:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
235 seqid = None
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
236 query(url, seq, alleles, lengths,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
237 seqid=seqid, method=method)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
238 else:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
239 warn_err('Line %d, Not a peptide: %s\n' % (i, seq),
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
240 exit_code=None)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
241 else: # fasta
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
242 seqid = None
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
243 seq = ''
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
244 for i, line in enumerate(fh):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
245 if line.startswith('>'):
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
246 if seqid and len(seq) > 0:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
247 query(url, seq, alleles, lengths,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
248 seqid=seqid, method=method)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
249 seqid = line[1:].strip()
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
250 seq = ''
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
251 else:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
252 seq += line.strip()
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
253 if seqid and len(seq) > 0:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
254 query(url, seq, alleles, lengths,
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
255 seqid=seqid, method=method)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
256 fh.close()
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
257 except Exception as e:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
258 warn_err("Unable to open input file: %s\n" % e, exit_code=1)
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
259
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
260 if header:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
261 outputFile.write(header)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
262 for line in results:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
263 outputFile.write(line)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
264 if results2:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
265 if args.output2:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
266 try:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
267 outPath = os.path.abspath(args.output2)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
268 outFile = open(outPath, 'w')
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
269 except Exception as e:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
270 warn_err("Unable to open output file: %s\n" % e, exit_code=1)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
271 else:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
272 outFile = sys.stdout
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
273 if header2:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
274 outFile.write(header2)
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
275 for line in results2:
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
276 outFile.write(line)
0
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
277
1
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
278
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
279 if __name__ == "__main__":
4a89ba6cfc63 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit 18698e056ccc2d6d37836bd22728e2d8765e92ec"
jjohnson
parents: 0
diff changeset
280 __main__()