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comparison align_dbspec.py @ 2:77ddaee887a8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
author galaxyp
date Fri, 01 Sep 2017 03:14:54 -0400
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1:8a30d6e5b97d 2:77ddaee887a8
1 #!/usr/bin/env python
2 import sys
3 import os
4 import argparse
5 import re
6 from Bio import SeqIO
7
8
9 def create_spectra_maps(specfiles, dbfiles, frregex, firstfr):
10 """Output something like
11 {'fr01', 'fr04'} # Normal filename set
12 and
13 {'fr03': ['fr02', 'fr03']} # pool definition
14 and
15 {'fr04': 'fr04', 'fr04b': 'fr04'} # rerun fraction, rerun may also be pool
16 """
17 specrange = get_fn_fractionmap(specfiles, frregex)
18 to_pool = []
19 poolmap, rerun_map, normal_fns = {}, [], set()
20 for i in range(0, len(dbfiles)):
21 num = i + firstfr
22 if num not in specrange:
23 to_pool.append(i)
24 elif to_pool and num in specrange:
25 to_pool.append(i)
26 poolmap[specrange[num][0]] = to_pool
27 to_pool = []
28 if not to_pool and specrange[num][0] in poolmap:
29 if poolmap[specrange[num][0]][-1] != i:
30 normal_fns.add((dbfiles[num - 1],
31 specfiles[specrange[num][0]]))
32 elif not to_pool:
33 normal_fns.add((dbfiles[num - 1], specfiles[specrange[num][0]]))
34 for num in sorted(specrange.keys()):
35 if len(specrange[num]) > 1:
36 rerun_map.append(specrange[num])
37 return normal_fns, rerun_map, poolmap
38
39
40 def get_fn_fractionmap(files, frregex):
41 fnfrmap = {}
42 for f_ix, fn in enumerate(files):
43 fnum = int(re.sub(frregex, '\\1', fn))
44 try:
45 fnfrmap[fnum].append(f_ix)
46 except KeyError:
47 fnfrmap[fnum] = [f_ix]
48 return fnfrmap
49
50
51 def pool_fasta_files(poolfiles):
52 acc_seq = {}
53 for fr in poolfiles:
54 for seq in SeqIO.parse(fr, 'fasta'):
55 sequence = str(seq.seq.upper())
56 try:
57 if sequence in acc_seq[seq.id]:
58 continue
59 except KeyError:
60 acc_seq[seq.id] = {sequence: 1}
61 yield seq
62 else:
63 acc_seq[seq.id][sequence] = 1
64 yield seq
65
66
67 def write_pooled_fasta(poolmap, specnames, dbfiles):
68 """Runs through poolmap and pooles output files, filtering out
69 duplicates"""
70 for outfr, infrs in poolmap.items():
71 outfn = os.path.join('aligned_out', os.path.basename(specnames[outfr]))
72 print('Pooling FASTA files {} - {} into: {}'.format(
73 dbfiles[infrs[0]], dbfiles[infrs[-1]], outfn))
74 with open(outfn, 'w') as fp:
75 SeqIO.write(pool_fasta_files([dbfiles[x] for x in infrs]), fp,
76 'fasta')
77
78
79 def write_nonpooled_fasta(fractions):
80 """Symlinks nonpooled db files"""
81 print('Symlinking non-pooled non-rerun files',
82 [(fr[0], os.path.join('aligned_out', os.path.basename(fr[1])))
83 for fr in fractions])
84 [os.symlink(fr[0], os.path.join('aligned_out', os.path.basename(fr[1])))
85 for fr in fractions]
86
87
88 def copy_rerun_fasta(rerun_map, specnames):
89 for dst_indices in rerun_map:
90 src = os.path.join(specnames[dst_indices[0]])
91 for outfn in [specnames[x] for x in dst_indices[1:]]:
92 print('Symlinking {} to {}'.format(src, outfn))
93 os.symlink(src, os.path.join('aligned_out', outfn))
94
95
96 def main():
97 args = parse_commandline()
98 with open(args.spectranames) as fp:
99 spectranames = [x.strip() for x in fp.read().strip().split('\n')]
100 vanilla_fr, rerun_map, poolmap = create_spectra_maps(spectranames,
101 args.dbfiles,
102 args.frspecregex,
103 args.firstfr)
104 write_pooled_fasta(poolmap, spectranames, args.dbfiles)
105 write_nonpooled_fasta(vanilla_fr)
106 copy_rerun_fasta(rerun_map, spectranames)
107
108
109 def parse_commandline():
110 parser = argparse.ArgumentParser(
111 formatter_class=argparse.RawTextHelpFormatter)
112 parser.add_argument('--specnames', dest='spectranames', help='File '
113 'containing spectra filenames with fractions. '
114 'Test data example illustrates reruns (fr03b, 09b) and'
115 ' pooled samples (fr05-09 are inside fr09 and fr09b).',
116 required=True)
117 parser.add_argument('--dbfiles', dest='dbfiles', help='FASTA db files',
118 nargs='+', required=True)
119 parser.add_argument('--frspec', dest='frspecregex', help='Fraction regex '
120 'to detect spectra fraction numbers', required=True)
121 parser.add_argument('--firstfr', dest='firstfr', help='First fraction nr',
122 type=int, required=True)
123 return parser.parse_args(sys.argv[1:])
124
125
126 if __name__ == '__main__':
127 main()