|
0
|
1 #!/usr/bin/env python
|
|
|
2 """
|
|
|
3 #
|
|
|
4 #------------------------------------------------------------------------------
|
|
|
5 # University of Minnesota
|
|
|
6 # Copyright 2015, Regents of the University of Minnesota
|
|
|
7 #------------------------------------------------------------------------------
|
|
|
8 # Author:
|
|
|
9 #
|
|
|
10 # James E Johnson
|
|
|
11 #
|
|
|
12 #------------------------------------------------------------------------------
|
|
|
13 """
|
|
|
14
|
|
|
15 import json
|
|
|
16 import logging
|
|
|
17 import optparse
|
|
|
18 from optparse import OptionParser
|
|
|
19 import os
|
|
|
20 import sys
|
|
|
21 import re
|
|
|
22 import urllib
|
|
|
23 import urllib2
|
|
|
24 try:
|
|
|
25 import xml.etree.cElementTree as ET
|
|
|
26 except ImportError:
|
|
|
27 import xml.etree.ElementTree as ET
|
|
|
28
|
|
|
29 def warn_err(msg,exit_code=1):
|
|
|
30 sys.stderr.write(msg)
|
|
|
31 if exit_code:
|
|
|
32 sys.exit(exit_code)
|
|
|
33
|
|
|
34 def read_fasta(fp):
|
|
|
35 name, seq = None, []
|
|
|
36 for line in fp:
|
|
|
37 line = line.rstrip()
|
|
|
38 if line.startswith(">"):
|
|
|
39 if name: yield (name, ''.join(seq))
|
|
|
40 name, seq = line, []
|
|
|
41 else:
|
|
|
42 seq.append(line)
|
|
|
43 if name: yield (name, ''.join(seq))
|
|
|
44
|
|
|
45 def read_mzid(fp):
|
|
|
46 peptides = []
|
|
|
47 for event, elem in ET.iterparse(fp):
|
|
|
48 if event == 'end':
|
|
|
49 if re.search('PeptideSequence',elem.tag):
|
|
|
50 peptides.append(elem.text)
|
|
|
51 return peptides
|
|
|
52
|
|
|
53 def read_pepxml(fp):
|
|
|
54 peptides = []
|
|
|
55 for event, elem in ET.iterparse(fp):
|
|
|
56 if event == 'end':
|
|
|
57 if re.search('search_hit',elem.tag):
|
|
|
58 peptides.append(elem.get('peptide'))
|
|
|
59 return peptides
|
|
|
60
|
|
|
61 def __main__():
|
|
|
62 #Parse Command Line
|
|
|
63 parser = optparse.OptionParser()
|
|
|
64 # unipept API
|
|
|
65 parser.add_option( '-A', '--api', dest='unipept', default='pept2lca', choices=['pept2lca','pept2taxa','pept2prot'], help='The unipept application: pept2lca, pept2taxa, or pept2prot' )
|
|
|
66 # files
|
|
|
67 parser.add_option( '-t', '--tabular', dest='tabular', default=None, help='A tabular file that contains a peptide column' )
|
|
|
68 parser.add_option( '-c', '--column', dest='column', type='int', default=0, help='The column (zero-based) in the tabular file that contains peptide sequences' )
|
|
|
69 parser.add_option( '-f', '--fasta', dest='fasta', default=None, help='A fasta file containing peptide sequences' )
|
|
|
70 parser.add_option( '-m', '--mzid', dest='mzid', default=None, help='A mxIdentML file containing peptide sequences' )
|
|
|
71 parser.add_option( '-p', '--pepxml', dest='pepxml', default=None, help='A pepxml file containing peptide sequences' )
|
|
|
72 # Unipept Flags
|
|
|
73 parser.add_option( '-e', '--equate_il', dest='equate_il', action='store_true', default=False, help='isoleucine (I) and leucine (L) are equated when matching tryptic peptides to UniProt records' )
|
|
|
74 parser.add_option( '-x', '--extra', dest='extra', action='store_true', default=False, help='return the complete lineage of the taxonomic lowest common ancestor' )
|
|
|
75 parser.add_option( '-n', '--names', dest='names', action='store_true', default=False, help='return the names of all ranks in the lineage of the taxonomic lowest common ancestor' )
|
|
|
76 # Warn vs Error Flag
|
|
|
77 parser.add_option( '-S', '--strict', dest='strict', action='store_true', default=False, help='Print exit on invalid peptide' )
|
|
|
78 # outputs
|
|
|
79 parser.add_option( '-J', '--json', dest='json', default=None, help='Output file path for json formatted results')
|
|
|
80 parser.add_option( '-T', '--tsv', dest='tsv', default=None, help='Output file path for TAB-separated-values (.tsv) formatted results')
|
|
|
81 parser.add_option( '-C', '--csv', dest='csv', default=None, help='Output file path for Comma-separated-values (.csv) formatted results')
|
|
|
82 parser.add_option( '-M', '--mismatch', dest='mismatch', default=None, help='Output file path for peptide with no matches' )
|
|
|
83 (options, args) = parser.parse_args()
|
|
|
84 invalid_ec = 2 if options.strict else None
|
|
|
85 peptides = []
|
|
|
86 pep_pat = '^([ABCDEFGHIKLMNPQRSTVWXYZ]+)$'
|
|
|
87 ## Get peptide sequences
|
|
|
88 if options.mzid:
|
|
|
89 peptides += read_mzid(options.mzid)
|
|
|
90 if options.pepxml:
|
|
|
91 peptides += read_pepxml(options.pepxml)
|
|
|
92 if options.tabular:
|
|
|
93 with open(options.tabular) as fp:
|
|
|
94 for i,line in enumerate(fp):
|
|
|
95 if line.strip() == '' or line.startswith('#'):
|
|
|
96 continue
|
|
|
97 fields = line.rstrip('\n').split('\t')
|
|
|
98 peptide = fields[options.column]
|
|
|
99 if not re.match(pep_pat,peptide):
|
|
|
100 warn_err('"%s" is not a peptide (line %d column %d of tabular file: %s)\n' % (peptide,i,options.column,options.tabular),exit_code=invalid_ec)
|
|
|
101 peptides.append(peptide)
|
|
|
102 if options.fasta:
|
|
|
103 with open(options.fasta) as fp:
|
|
|
104 for id, peptide in read_fasta(fp):
|
|
|
105 if not re.match(pep_pat,peptide):
|
|
|
106 warn_err('"%s" is not a peptide (id %s of fasta file: %s)\n' % (peptide,id,options.fasta),exit_code=invalid_ec)
|
|
|
107 peptides.append(peptide)
|
|
|
108 if args and len(args) > 0:
|
|
|
109 for i,peptide in enumerate(args):
|
|
|
110 if not re.match(pep_pat,peptide):
|
|
|
111 warn_err('"%s" is not a peptide (arg %d)\n' % (peptide,i),exit_code=invalid_ec)
|
|
|
112 peptides.append(peptide)
|
|
|
113 if len(peptides) < 1:
|
|
|
114 warn_err("No peptides input!",exit_code=1)
|
|
|
115 ## unipept
|
|
|
116 post_data = []
|
|
|
117 if options.equate_il:
|
|
|
118 post_data.append(("equate_il","true"))
|
|
|
119 if options.names:
|
|
|
120 post_data.append(("extra","true"))
|
|
|
121 post_data.append(("names","true"))
|
|
|
122 elif options.extra:
|
|
|
123 post_data.append(("extra","true"))
|
|
|
124 post_data += [('input[]', x) for x in peptides]
|
|
|
125 headers = {'Content-Type': 'application/x-www-form-urlencoded', 'Accept': 'application/json'}
|
|
|
126 url = 'http://api.unipept.ugent.be/api/v1/%s' % options.unipept
|
|
|
127 req = urllib2.Request( url, headers = headers, data = urllib.urlencode(post_data) )
|
|
|
128 resp = json.loads( urllib2.urlopen( req ).read() )
|
|
|
129 ## output results
|
|
|
130 if not (options.mismatch or options.json or options.tsv or options.csv):
|
|
|
131 print >> sys.stdout, str(resp)
|
|
|
132 if options.mismatch:
|
|
|
133 peptides_matched = []
|
|
|
134 for i,pdict in enumerate(resp):
|
|
|
135 peptides_matched.append(pdict['peptide'])
|
|
|
136 with open(options.mismatch,'w') as outputFile:
|
|
|
137 for peptide in peptides:
|
|
|
138 if not peptide in peptides_matched:
|
|
|
139 outputFile.write("%s\n" % peptide)
|
|
|
140 if options.json:
|
|
|
141 with open(options.json,'w') as outputFile:
|
|
|
142 outputFile.write(str(resp))
|
|
|
143 if options.tsv or options.csv:
|
|
|
144 # 'pept2lca','pept2taxa','pept2prot'
|
|
|
145 pept2lca_column_order = [ 'peptide','superkingdom','kingdom','subkingdom','superphylum','phylum','subphylum','superclass','class_','subclass','infraclass','superorder','order','suborder','infraorder','parvorder','superfamily','family','subfamily','tribe','subtribe','genus','subgenus','species_group','species_subgroup','species','subspecies','varietas','forma' ]
|
|
|
146 pept2prot_column_order = [ 'peptide','uniprot_id','taxon_id','taxon_name','ec_references','go_references','refseq_ids','refseq_protein_ids','insdc_ids','insdc_protein_ids']
|
|
|
147 column_order = pept2prot_column_order if options.unipept == 'pept2prot' else pept2lca_column_order
|
|
|
148 found_keys = set()
|
|
|
149 results = []
|
|
|
150 for i,pdict in enumerate(resp):
|
|
|
151 results.append(pdict)
|
|
|
152 found_keys |= set(pdict.keys())
|
|
|
153 # print >> sys.stderr, "%s\n%s" % (pdict.keys(),found_keys)
|
|
|
154 column_names = []
|
|
|
155 column_keys = []
|
|
|
156 for col in column_order:
|
|
|
157 if col in found_keys:
|
|
|
158 column_names.append(col)
|
|
|
159 column_keys.append(col)
|
|
|
160 elif options.extra or options.names:
|
|
|
161 col_id = col+'_id'
|
|
|
162 col_name = col+'_name'
|
|
|
163 if options.extra:
|
|
|
164 if col_id in found_keys:
|
|
|
165 column_names.append(col_id)
|
|
|
166 column_keys.append(col_id)
|
|
|
167 if options.names:
|
|
|
168 if col_name in found_keys:
|
|
|
169 column_names.append(col)
|
|
|
170 column_keys.append(col_name)
|
|
|
171 else:
|
|
|
172 if col+'_name' in found_keys:
|
|
|
173 column_names.append(col)
|
|
|
174 column_keys.append(col+'_name')
|
|
|
175 elif col+'_id' in found_keys:
|
|
|
176 column_names.append(col)
|
|
|
177 column_keys.append(col+'_id')
|
|
|
178 # print >> sys.stderr, "%s\n%s" % (column_names,column_keys)
|
|
|
179 taxa = []
|
|
|
180 for i,pdict in enumerate(results):
|
|
|
181 vals = [str(pdict[x]) if x in pdict and pdict[x] else '' for x in column_keys]
|
|
|
182 taxa.append(vals)
|
|
|
183 if options.tsv:
|
|
|
184 with open(options.tsv,'w') as outputFile:
|
|
|
185 outputFile.write("#%s\n"% '\t'.join(column_names))
|
|
|
186 for vals in taxa:
|
|
|
187 outputFile.write("%s\n"% '\t'.join(vals))
|
|
|
188 if options.csv:
|
|
|
189 with open(options.csv,'w') as outputFile:
|
|
|
190 outputFile.write("%s\n"% ','.join(column_names))
|
|
|
191 for vals in taxa:
|
|
|
192 outputFile.write("%s\n"% ','.join(['"%s"' % (v if v else '') for v in vals]))
|
|
|
193
|
|
|
194 if __name__ == "__main__" : __main__()
|
