Mercurial > repos > iuc > iedb_api

annotate iedb_api.py @ 1:6cf84410cb2e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 848c47fb29e9f1d319056a94a7dbd90129a4aafc"
author iuc
date Tue, 07 Apr 2020 23:20:35 -0400
parents fe3c43451319
children e95d3221b7f0
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fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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2
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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3 import argparse
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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4 import os.path
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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5 import re
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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6 import sys
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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7 import time
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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8 from urllib.error import HTTPError
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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9 from urllib.parse import unquote, urlencode
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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10 from urllib.request import urlopen
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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11
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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12 mhci_methods = ['recommended', 'consensus',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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13 'netmhcpan_ba', 'netmhcpan_el',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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14 'ann', 'smmpmbec', 'smm',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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15 'comblib_sidney2008', 'netmhccons',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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16 'pickpocket', 'netmhcstabpan']
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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17 mhcii_methods = ['recommended', 'consensus', 'NetMHCIIpan',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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18 'nn_align', 'smm_align', 'comblib', 'tepitope']
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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19 processing_methods = ['recommended', 'netmhcpan', 'ann',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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20 'smmpmbec', 'smm', 'comblib_sidney2008',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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21 'netmhccons', 'pickpocket']
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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22 mhcnp_methods = ['mhcnp', 'netmhcpan']
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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23 bcell_methods = ['Bepipred', 'Chou-Fasman', 'Emini', 'Karplus-Schulz',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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24 'Kolaskar-Tongaonkar', 'Parker', 'Bepipred-2.0']
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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25 prediction_methods = {'mhci': mhci_methods,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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26 'mhcii': mhcii_methods,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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27 'processing': processing_methods,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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28 'mhcnp': mhcnp_methods,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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29 'bcell': bcell_methods}
1
6cf84410cb2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 848c47fb29e9f1d319056a94a7dbd90129a4aafc"
iuc
parents: 0
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30 all_methods = set(mhci_methods + mhcii_methods + mhcnp_methods + bcell_methods)
0
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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31 prediction_lengths = {'mhci': range(8, 16),
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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32 'mhcii': range(11, 31),
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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33 'processing': range(8, 15),
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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34 'mhcnp': range(8, 12),
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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35 'bcell': range(8, 16)}
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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36
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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37
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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38 def parse_alleles(allelefile, lengths):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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39 alleles = []
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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40 lengths = []
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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41 with open(allelefile, 'r') as fh:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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42 for i, line in enumerate(fh):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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43 fields = line.strip().split(',')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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44 allele = fields[0].strip()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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45 if allele:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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46 if len(fields) > 1:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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47 for alen in fields[1:]:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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48 alleles.append(allele)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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49 lengths.append(alen)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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50 elif lengths:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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51 for alen in str(lengths).split(','):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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52 alleles.append(allele)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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53 lengths.append(alen)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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54 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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55 alleles.append(allele)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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56 return (alleles, lengths)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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57
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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58
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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59 def query(url, prediction, seq, allele, length, results,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
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60 seqid=None, method='recommended', proteasome=None,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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61 timeout=300, retries=3, sleep=300, debug=False):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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62 params = dict()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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63 if method:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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64 params['method'] = method.encode()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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65 if proteasome:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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66 params['proteasome'] = proteasome.encode()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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67 params['sequence_text'] = seq.strip().encode()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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68 if allele is not None:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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69 params['allele'] = allele.encode()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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70 if length is not None:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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71 if prediction == 'bcell':
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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72 params['window_size'] = str(length).encode()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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73 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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74 params['length'] = str(length).encode()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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75 req_data = urlencode(params)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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76 if debug:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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77 print('url %s %s' % (url, unquote(req_data)), file=sys.stderr)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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78 retries = max(0, retries) + 1
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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79 for retry in range(1, retries):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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80 response = None
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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81 try:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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82 response = urlopen(url, data=req_data.encode('utf-8'),
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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83 timeout=timeout)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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84 if response and response.getcode() == 200:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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85 data = [line.decode() for line in response.readlines()]
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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86 if debug:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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87 print(data, file=sys.stderr)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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88 rslts = results['prediction']['entries']
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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diff changeset
89 for ln, line in enumerate(data):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
90 if 'invalid' in line.lower() or 'tools_api.html' in line:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
91 msg = '%s %s\n%s' % (url, unquote(req_data),
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
92 ''.join(data))
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
93 warn_err(msg, exit_code=1)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
94 if line.find('eptide') > 0:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
95 results['prediction']['header'] = "#%s%s" %\
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
96 ("ID\t" if seqid else "", line)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
97 continue
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
98 elif method == 'Bepipred' and line.find('Residue') > 0:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
99 results['detail']['header'] = "#%s%s" %\
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
100 ("ID\t" if seqid else "", line)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
101 rslts = results['detail']['entries']
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
102 continue
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
103 if seqid:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
104 rslts.extend("%s\t%s" % (seqid, line))
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
105 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
106 rslts.extend(line)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
107 break
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
108 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
109 code = response.getcode() if response else 1
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
110 warn_err("Error connecting to IEDB server\n",
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
111 exit_code=code)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
112 except HTTPError as e:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
113 code = None if retry < retries else e.code
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
114 warn_err("%d of %d Error connecting to IEDB server %s\n" %
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
115 (retry, retries, e),
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
116 exit_code=code)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
117 time.sleep(sleep)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
118 except Exception as e:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
119 warn_err("Error connecting to IEDB server %s\n" % e,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
120 exit_code=3)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
121 return results
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
122
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
123
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
124 def warn_err(msg, exit_code=1):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
125 sys.stderr.write(msg)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
126 sys.stderr.flush()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
127 if exit_code:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
128 sys.exit(exit_code)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
129
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
130
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
131 def __main__():
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
132 # Parse Command Line
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
133 parser = argparse.ArgumentParser(description='', epilog='')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
134 parser.add_argument('-p', '--prediction',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
135 default='mhci',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
136 choices=prediction_methods.keys(),
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
137 help='IEDB API prediction service')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
138 parser.add_argument('-s', '--sequence',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
139 action="append",
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
140 default=None,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
141 help='Peptide Sequence')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
142 parser.add_argument('-m', '--method',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
143 default='recommended',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
144 choices=all_methods,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
145 help='prediction method')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
146 parser.add_argument('-P', '--proteasome',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
147 default=None,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
148 choices=['immuno', 'constitutive'],
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
149 help='IEDB processing proteasome type')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
150 parser.add_argument('-a', '--allele',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
151 action="append",
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
152 default=[],
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
153 help='Alleles for which to make predictions')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
154 parser.add_argument('-A', '--allelefile',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
155 default=None,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
156 help='File of HLA alleles')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
157 parser.add_argument('-l', '--length',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
158 action="append",
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
159 default=[],
1
6cf84410cb2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 848c47fb29e9f1d319056a94a7dbd90129a4aafc"
iuc
parents: 0
diff changeset
160 help='lengths for which to make predictions, '
0
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
161 '1 per allele')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
162 parser.add_argument('-w', '--window_size',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
163 type=int,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
164 default=None,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
165 help='window_size for bcell prediction')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
166 parser.add_argument('-i', '--input',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
167 default=None,
1
6cf84410cb2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 848c47fb29e9f1d319056a94a7dbd90129a4aafc"
iuc
parents: 0
diff changeset
168 help='Input file for peptide sequences '
0
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
169 '(fasta or tabular)')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
170 parser.add_argument('-c', '--column',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
171 default=None,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
172 help='Peptide Column in a tabular input file')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
173 parser.add_argument('-C', '--id_column',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
174 default=None,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
175 help='ID Column in a tabular input file')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
176 parser.add_argument('-o', '--output',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
177 default=None,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
178 help='Output file for query results')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
179 parser.add_argument('-O', '--output2',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
180 default='iedb_results2',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
181 help='Output file for secondary query results')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
182 parser.add_argument('-t', '--timeout',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
183 type=int,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
184 default=600,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
185 help='Seconds to wait for server response')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
186 parser.add_argument('-r', '--retries',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
187 type=int,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
188 default=5,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
189 help='Number of times to retry server query')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
190 parser.add_argument('-S', '--sleep',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
191 type=int,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
192 default=300,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
193 help='Seconds to wait between retries')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
194 parser.add_argument('-d', '--debug',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
195 action='store_true',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
196 default=False,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
197 help='Turn on wrapper debugging to stderr')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
198 args = parser.parse_args()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
199
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
200 aapat = '^[ABCDEFGHIKLMNPQRSTVWY]+$'
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
201
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
202 if args.prediction != 'bcell':
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
203 if not args.allele and not args.allelefile:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
204 warn_err('-a allele or -A allelefile required\n', exit_code=1)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
205
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
206 if not (args.sequence or args.input):
1
6cf84410cb2e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 848c47fb29e9f1d319056a94a7dbd90129a4aafc"
iuc
parents: 0
diff changeset
207 warn_err('NO Sequences given: '
0
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
208 'either -s sequence or -i input_file is required\n',
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
209 exit_code=1)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
210
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
211 if args.output is not None:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
212 try:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
213 outputPath = os.path.abspath(args.output)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
214 outputFile = open(outputPath, 'w')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
215 except Exception as e:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
216 warn_err("Unable to open output file: %s\n" % e, exit_code=1)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
217 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
218 outputFile = sys.stdout
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
219
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
220 # params
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
221 alleles = []
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
222 lengths = []
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
223 if args.prediction == 'bcell' and args.window_size is not None:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
224 lengths.append(str(args.window_size))
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
225 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
226 if args.allelefile:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
227 (alleles, lengths) = parse_alleles(args.allelefile, args.length)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
228 if args.allele:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
229 for i, allele in enumerate(args.allele):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
230 alleles.append(allele)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
231 alen = args.length[i] if i < len(args.length) else args.length[-1]
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
232 lengths.append(alen)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
233 allele = ','.join(alleles) if alleles else None
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
234 length = ','.join(lengths) if lengths else None
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
235 method = args.method
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
236 proteasome = args.proteasome if args.prediction == 'processcing' else None
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
237 url = 'http://tools-cluster-interface.iedb.org/tools_api/%s/' %\
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
238 args.prediction
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
239
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
240 # results
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
241 results = {'prediction': {'header': None, 'entries': []}, 'detail': {'header': None, 'entries': []}}
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
242
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
243 if args.sequence:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
244 for i, seq in enumerate(args.sequence):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
245 seqid = 'pep_%d' % i
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
246 query(url, args.prediction, seq, allele, length, results,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
247 seqid=seqid, method=method, proteasome=proteasome,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
248 timeout=args.timeout, retries=args.retries,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
249 sleep=args.sleep, debug=args.debug)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
250 if args.input:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
251 try:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
252 fh = open(args.input, 'r')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
253 if args.column: # tabular
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
254 col = int(args.column)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
255 idcol = int(args.id_column) if args.id_column else None
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
256 for i, line in enumerate(fh):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
257 fields = line.rstrip('\r\n').split('\t')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
258 if len(fields) > col:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
259 seq = re.sub('[_*]', '', fields[col].strip())
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
260 if re.match(aapat, seq):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
261 if idcol is not None and idcol < len(fields):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
262 seqid = fields[idcol]
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
263 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
264 seqid = 'pep_%d' % i
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
265 query(url, args.prediction, seq, allele, length,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
266 results, seqid=seqid,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
267 method=method, proteasome=proteasome,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
268 timeout=args.timeout, retries=args.retries,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
269 sleep=args.sleep, debug=args.debug)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
270 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
271 warn_err('Line %d, Not a peptide: %s\n' % (i, seq),
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
272 exit_code=None)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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273 else: # fasta
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
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274 seqid = None
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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275 seq = ''
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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276 for i, line in enumerate(fh):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
277 if line.startswith('>'):
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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278 if seqid and len(seq) > 0:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
279 query(url, args.prediction, seq, allele, length,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
280 results, seqid=seqid,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
281 method=method, proteasome=proteasome,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
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282 timeout=args.timeout, retries=args.retries,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
283 sleep=args.sleep, debug=args.debug)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
284 seqid = line[1:].strip()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
285 seq = ''
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
286 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
287 seq += line.strip()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
288 if seqid and len(seq) > 0:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
289 query(url, args.prediction, seq, allele, length,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
290 results, seqid=seqid,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
291 method=method, proteasome=proteasome,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
292 timeout=args.timeout, retries=args.retries,
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
293 sleep=args.sleep, debug=args.debug)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
294 fh.close()
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
295 except Exception as e:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
296 warn_err("Unable to open input file: %s\n" % e, exit_code=1)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
297
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
298 if results['prediction']['header']:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
299 outputFile.write(results['prediction']['header'])
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
300 for line in results['prediction']['entries']:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
301 outputFile.write(line)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
302 if results['detail']['entries']:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
303 if args.output2:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
304 try:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
305 outPath = os.path.abspath(args.output2)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
306 outFile = open(outPath, 'w')
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
307 except Exception as e:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
308 warn_err("Unable to open output file: %s\n" % e, exit_code=1)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
309 else:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
310 outFile = sys.stdout
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
311 if results['detail']['header']:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
312 outFile.write(results['detail']['header'])
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
313 for line in results['detail']['entries']:
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
314 outFile.write(line)
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
315
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
316
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
317 if __name__ == "__main__":
fe3c43451319 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 9aaa7c6c7241db52681b12939ebd908902830ef1"
iuc
parents:
diff changeset
318 __main__()