Mercurial > repos > jjohnson > iedb_api

annotate iedb_api.py @ 0:991424605492 draft

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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
author jjohnson
date Mon, 17 Feb 2020 16:04:07 -0500
parents
children 4a89ba6cfc63
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991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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1 #!/usr/bin/env python
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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2 """
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jjohnson
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3 """
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jjohnson
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4 import sys
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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5 import os.path
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
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6 import re
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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7 import optparse
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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8 import urllib
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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9 import urllib2
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10 from optparse import OptionParser
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11
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12 mhci_methods = ['recommended','consensus','netmhcpan','ann','smmpmbec','smm','comblib_sidney2008','netmhccons','pickpocket']
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13 mhcii_methods = ['recommended','consensus3','NetMHCIIpan','nn_align','smm_align','comblib','tepitope']
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14 processing_methods = ['recommended','consensus','netmhcpan','ann','smmpmbec','smm','comblib_sidney2008']
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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15 mhcnp_methods = ['mhcnp']
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16 bcell_methods = ['Bepipred','Chou-FasmanEmini','Karplus-Schulz','Kolaskar-Tongaonkar','Parker']
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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17 prediction_methods = {'mhci':mhci_methods,'mhcii':mhcii_methods,'processing':processing_methods,'mhcnp':mhcnp_methods,'bcell':bcell_methods}
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19 def warn_err(msg,exit_code=1):
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20 sys.stderr.write(msg)
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21 if exit_code:
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22 sys.exit(exit_code)
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23
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24
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25 def __main__():
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26 #Parse Command Line
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27 parser = optparse.OptionParser()
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28 parser.add_option( '-p', '--prediction', dest='prediction', default='mhci', choices=['mhci','mhcii','processing','mhcnp','bcell'], help='IEDB API prediction service' )
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29 parser.add_option( '-s', '--sequence', dest='sequence', action="append", default=None, help='Peptide Sequence' )
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30 parser.add_option( '-m', '--method', dest='method', default='recommended', choices=['recommended','consensus','netmhcpan','ann','smmpmbec','smm','comblib_sidney2008','netmhccons','pickpocket' ], help='prediction method' )
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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31 parser.add_option( '-a', '--allele', dest='allele', action="append", default=[], help='Alleles for which to make predictions' )
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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32 parser.add_option( '-l', '--length', dest='length', action="append", default=[], choices=['8', '9', '10', '11', '12', '13', '14', '15'], help='lengths for which to make predictions, 1 per allele' )
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
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33 parser.add_option( '-i', '--input', dest='input', default=None, help='Input file for peptide sequences (fasta or tabular)' )
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34 parser.add_option( '-c', '--column', dest='column', default=None, help='Peptide Column in a tabular input file' )
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35 parser.add_option( '-C', '--id_column', dest='id_column', default=None, help='ID Column in a tabular input file' )
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36 parser.add_option( '-o', '--output', dest='output', default=None, help='Output file for query results' )
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37 parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr' )
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38 (options, args) = parser.parse_args()
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39
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40 aapat = '^[ABCDEFGHIKLMNPQRSTVWY]+$'
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41
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42 if not options.allele and options.prediction != 'bcell':
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43 warn_err('-a allele required\n', exit_code=1)
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44
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45 if not (options.sequence or options.input):
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46 warn_err('NO Sequences given: either -s sequence or -i input_file is required\n', exit_code=1)
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47
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48 if options.output != None:
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49 try:
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50 outputPath = os.path.abspath(options.output)
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51 outputFile = open(outputPath, 'w')
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52 except Exception, e:
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53 warn_err("Unable to open output file: %s\n" % e, exit_code=1)
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54 else:
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55 outputFile = sys.stdout
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56
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57 url = 'http://tools-api.iedb.org/tools_api/%s/' % options.prediction
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58
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59 #TODO parse alleles from the options.alleles file
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60 alleles = ','.join(options.allele)
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61 lengths = ','.join(options.length)
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62 method = options.method
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63
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64 results = []
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65 global header
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66 header = None
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67
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68 sequence_text = []
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69 def add_seq(seqid,seq):
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70 sequence_text.append(">%s\n%s" % (seqid if seqid else "peptide%d" % len(sequence_text),seq))
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71
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72 def query(url,seq,allele,length,seqid=None,method='recommended'):
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73 global header
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74 params = dict()
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75 if method:
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76 params['method'] = method
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77 params['sequence_text'] = seq
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78 params['allele'] = allele
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79 params['length'] = length
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80 data = urllib.urlencode(params)
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81 request = urllib2.Request(url, data)
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82 if options.debug:
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83 print >> sys.stderr, "url %s %s %s" % (request.get_full_url(), seqid if seqid else "None", seq)
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84 response = None
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85 response = urllib2.urlopen(request)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
86 if response and response.getcode() == 200:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
87 resp_data = response.readlines()
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
88 for line in resp_data:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
89 if line.find('eptide') > 0:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
90 header = "#%s%s" % ("ID\t" if seqid else "", line)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
91 continue
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
92 if seqid:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
93 results.append("%s\t%s" % (seqid,line))
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
94 else:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
95 results.append(line)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
96 elif not response:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
97 warn_err("NO response from IEDB server\n", exit_code=3)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
98 else:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
99 warn_err("Error connecting to IEDB server\n", exit_code=response.getcode())
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
100
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
101 if options.sequence:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
102 for i,seq in enumerate(options.sequence):
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
103 query(url,seq,alleles,lengths,seqid=None,method=method)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
104 if options.input:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
105 try:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
106 fh = open(options.input,'r')
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
107 if options.column: ## tabular
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
108 col = int(options.column)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
109 idcol = int(options.id_column) if options.id_column else None
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
110 for i,line in enumerate(fh):
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
111 fields = line.split('\t')
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
112 if len(fields) > col:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
113 seq = re.sub('[_*]','',fields[col])
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
114 if re.match(aapat,seq):
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
115 seqid = fields[idcol] if idcol != None and idcol < len(fields) else None
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
116 query(url,seq,alleles,lengths,seqid=seqid,method=method)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
117 else:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
118 warn_err('Line %d, Not a peptide: %s\n' % (i,seq),exit_code=None)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
119 else: ## fasta
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
120 seqid = None
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
121 seq = ''
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
122 for i,line in enumerate(fh):
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
123 if line.startswith('>'):
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
124 if seqid and len(seq) > 0:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
125 query(url,seq,alleles,lengths,seqid=seqid,method=method)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
126 seqid = line[1:].strip()
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
127 seq = ''
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
128 else:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
129 seq += line.strip()
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
130 if seqid and len(seq) > 0:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
131 query(url,seq,alleles,lengths,seqid=seqid,method=method)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
132 fh.close()
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
133 except Exception, e:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
134 warn_err("Unable to open input file: %s\n" % e, exit_code=1)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
135
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
136 if header:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
137 outputFile.write(header)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
138 for line in results:
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
139 outputFile.write(line)
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
140
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
141 if __name__ == "__main__": __main__()
991424605492 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/iedb_api commit bbca4d5248b883344319e7a9f42c82d20a11cf0d"
jjohnson
parents:
diff changeset
142