Mercurial > repos > iuc > meme_meme
annotate fimo_wrapper.py @ 3:798018a73e3f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author | iuc |
---|---|
date | Thu, 18 Feb 2016 10:23:12 -0500 |
parents | d20e391eb22f |
children |
rev | line source |
---|---|
1
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
1 #!/usr/bin/env python |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
2 import argparse |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
3 import os |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
4 import shutil |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
5 import string |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
6 import subprocess |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
7 import sys |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
8 import tempfile |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
9 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
10 BUFFSIZE = 1048576 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
11 # Translation table for reverse Complement, with ambiguity codes. |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
12 DNA_COMPLEMENT = string.maketrans("ACGTRYKMBDHVacgtrykmbdhv", "TGCAYRMKVHDBtgcayrmkvhdb") |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
13 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
14 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
15 def reverse(sequence): |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
16 # Reverse sequence string. |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
17 return sequence[::-1] |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
18 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
19 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
20 def dna_complement(sequence): |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
21 # Complement DNA sequence string. |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
22 return sequence.translate(DNA_COMPLEMENT) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
23 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
24 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
25 def dna_reverse_complement(sequence): |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
26 # Returns the reverse complement of the sequence. |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
27 sequence = reverse(sequence) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
28 return dna_complement(sequence) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
29 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
30 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
31 def stop_err(msg): |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
32 sys.stderr.write(msg) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
33 sys.exit(1) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
34 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
35 parser = argparse.ArgumentParser() |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
36 parser.add_argument('--input_motifs', dest='input_motifs', help='MEME output formatted files for input to fimo') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
37 parser.add_argument('--input_fasta', dest='input_fasta', help='Fassta sequence file') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
38 parser.add_argument('--options_type', dest='options_type', help='Basic or Advance options') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
39 parser.add_argument('--input_psp', dest='input_psp', default=None, help='File containing position specific priors') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
40 parser.add_argument('--input_prior_dist', dest='input_prior_dist', default=None, help='File containing binned distribution of priors') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
41 parser.add_argument('--alpha', dest='alpha', type=float, default=1.0, help='The alpha parameter for calculating position specific priors') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
42 parser.add_argument('--bgfile', dest='bgfile', default=None, help='Background file type, used only if not "default"') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
43 parser.add_argument('--max_strand', action='store_true', help='If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
44 parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
45 parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
46 parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
47 parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
48 parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
49 parser.add_argument('--output_path', dest='output_path', help='Output files directory') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
50 parser.add_argument('--parse_genomic_coord', action='store_true', help='Check each sequence header for UCSC style genomic coordinates') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
51 parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
52 parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
53 parser.add_argument('--gff_output', dest='gff_output', help='Gff output file') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
54 parser.add_argument('--html_output', dest='html_output', help='HTML output file') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
55 parser.add_argument('--interval_output', dest='interval_output', help='Interval output file') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
56 parser.add_argument('--txt_output', dest='txt_output', help='Text output file') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
57 parser.add_argument('--xml_output', dest='xml_output', help='XML output file') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
58 args = parser.parse_args() |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
59 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
60 fimo_cmd_list = ['fimo'] |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
61 if args.options_type == 'advanced': |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
62 fimo_cmd_list.append('--alpha %4f' % args.alpha) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
63 if args.bgfile is not None: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
64 fimo_cmd_list.append('--bgfile "%s"' % args.bgfile) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
65 if args.max_strand: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
66 fimo_cmd_list.append('--max-strand') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
67 fimo_cmd_list.append('--max-stored-scores %d' % args.max_stored_scores) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
68 if len(args.motifs) > 0: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
69 for motif in args.motifs: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
70 fimo_cmd_list.append('--motif "%s"' % motif) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
71 fimo_cmd_list.append('--motif-pseudo %4f' % args.motif_pseudo) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
72 if args.no_qvalue: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
73 fimo_cmd_list.append('--no-qvalue') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
74 if args.norc: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
75 fimo_cmd_list.append('--norc') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
76 if args.parse_genomic_coord: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
77 fimo_cmd_list.append('--parse-genomic-coord') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
78 if args.qv_thresh: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
79 fimo_cmd_list.append('--qv-thresh') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
80 fimo_cmd_list.append('--thresh %4f' % args.thresh) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
81 if args.input_psp is not None: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
82 fimo_cmd_list.append('--psp "%s"' % args.input_psp) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
83 if args.input_prior_dist is not None: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
84 fimo_cmd_list.append('--prior-dist "%s"' % args.input_prior_dist) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
85 fimo_cmd_list.append('--o "%s"' % (args.output_path)) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
86 fimo_cmd_list.append('--verbosity 1') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
87 fimo_cmd_list.append(args.input_motifs) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
88 fimo_cmd_list.append(args.input_fasta) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
89 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
90 fimo_cmd = ' '.join(fimo_cmd_list) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
91 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
92 try: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
93 tmp_stderr = tempfile.NamedTemporaryFile() |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
94 proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
95 returncode = proc.wait() |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
96 tmp_stderr.seek(0) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
97 stderr = '' |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
98 try: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
99 while True: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
100 stderr += tmp_stderr.read(BUFFSIZE) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
101 if not stderr or len(stderr) % BUFFSIZE != 0: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
102 break |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
103 except OverflowError: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
104 pass |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
105 if returncode != 0: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
106 stop_err(stderr) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
107 except Exception, e: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
108 stop_err('Error running FIMO:\n%s' % str(e)) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
109 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
110 shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
111 shutil.move(os.path.join(args.output_path, 'fimo.gff'), args.gff_output) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
112 shutil.move(os.path.join(args.output_path, 'fimo.xml'), args.xml_output) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
113 shutil.move(os.path.join(args.output_path, 'fimo.html'), args.html_output) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
114 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
115 out_file = open(args.interval_output, 'wb') |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
116 out_file.write("#%s\n" % "\t".join(("chr", "start", "end", "pattern name", "score", "strand", "matched sequence", "p-value", "q-value"))) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
117 for line in open(args.txt_output): |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
118 if line.startswith('#'): |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
119 continue |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
120 fields = line.rstrip("\n\r").split("\t") |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
121 start, end = int(fields[2]), int(fields[3]) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
122 sequence = fields[7] |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
123 if start > end: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
124 # Flip start and end and set strand. |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
125 start, end = end, start |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
126 strand = "-" |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
127 # We want sequences relative to strand; FIMO always provides + stranded sequence. |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
128 sequence = dna_reverse_complement(sequence) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
129 else: |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
130 strand = "+" |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
131 # Make 0-based start position. |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
132 start -= 1 |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
133 out_file.write("%s\n" % "\t".join([fields[1], str(start), str(end), fields[0], fields[4], strand, sequence, fields[5], fields[6]])) |
d20e391eb22f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
iuc
parents:
diff
changeset
|
134 out_file.close() |