Mercurial > repos > iuc > meme_psp_gen

annotate fimo_wrapper.py @ 1:793225b11202 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 42fa6e319cf1a97330818dc8c869871a32f0e7aa
author iuc
date Wed, 25 Apr 2018 12:13:08 -0400
parents a0fa4efeeee3
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a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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1 #!/usr/bin/env python
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2 import argparse
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3 import os
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4 import shutil
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5 import string
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6 import subprocess
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7 import sys
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8 import tempfile
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9
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10 BUFFSIZE = 1048576
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11 # Translation table for reverse Complement, with ambiguity codes.
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12 DNA_COMPLEMENT = string.maketrans("ACGTRYKMBDHVacgtrykmbdhv", "TGCAYRMKVHDBtgcayrmkvhdb")
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13
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14
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15 def get_stderr(tmp_stderr):
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16 tmp_stderr.seek(0)
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17 stderr = ''
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18 try:
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19 while True:
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20 stderr += tmp_stderr.read(BUFFSIZE)
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21 if not stderr or len(stderr) % BUFFSIZE != 0:
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22 break
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23 except OverflowError:
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24 pass
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25 return stderr
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27
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28 def reverse(sequence):
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29 # Reverse sequence string.
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30 return sequence[::-1]
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32
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33 def dna_complement(sequence):
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34 # Complement DNA sequence string.
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35 return sequence.translate(DNA_COMPLEMENT)
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36
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37
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38 def dna_reverse_complement(sequence):
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39 # Returns the reverse complement of the sequence.
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40 sequence = reverse(sequence)
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41 return dna_complement(sequence)
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42
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43
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44 def stop_err(msg):
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45 sys.stderr.write(msg)
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46 sys.exit(1)
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47
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48
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49 parser = argparse.ArgumentParser()
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50 parser.add_argument('--input_motifs', dest='input_motifs', help='MEME output formatted files for input to fimo')
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51 parser.add_argument('--input_fasta', dest='input_fasta', help='Fassta sequence file')
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52 parser.add_argument('--options_type', dest='options_type', help='Basic or Advance options')
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53 parser.add_argument('--input_psp', dest='input_psp', default=None, help='File containing position specific priors')
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54 parser.add_argument('--input_prior_dist', dest='input_prior_dist', default=None, help='File containing binned distribution of priors')
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55 parser.add_argument('--alpha', dest='alpha', type=float, default=1.0, help='The alpha parameter for calculating position specific priors')
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56 parser.add_argument('--bgfile', dest='bgfile', default=None, help='Background file type, used only if not "default"')
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57 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')
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58 parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store')
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59 parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id')
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60 parser.add_argument('--output_separate_motifs', dest='output_separate_motifs', default='no', help='Output one dataset per motif')
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61 parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix')
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62 parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value')
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63 parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand')
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64 parser.add_argument('--output_path', dest='output_path', help='Output files directory')
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65 parser.add_argument('--parse_genomic_coord', dest='parse_genomic_coord', default='no', help='Check each sequence header for UCSC style genomic coordinates')
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66 parser.add_argument('--remove_duplicate_coords', dest='remove_duplicate_coords', default='no', help='Remove duplicate entries in unique GFF coordinates')
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67 parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold')
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68 parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold')
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69 parser.add_argument('--gff_output', dest='gff_output', help='Gff output file')
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70 parser.add_argument('--html_output', dest='html_output', help='HTML output file')
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71 parser.add_argument('--interval_output', dest='interval_output', help='Interval output file')
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72 parser.add_argument('--txt_output', dest='txt_output', help='Text output file')
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73 parser.add_argument('--xml_output', dest='xml_output', help='XML output file')
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74 args = parser.parse_args()
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75
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76 fimo_cmd_list = ['fimo']
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77 if args.options_type == 'advanced':
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78 fimo_cmd_list.append('--alpha %4f' % args.alpha)
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79 if args.bgfile is not None:
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80 fimo_cmd_list.append('--bgfile "%s"' % args.bgfile)
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81 if args.max_strand:
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82 fimo_cmd_list.append('--max-strand')
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83 fimo_cmd_list.append('--max-stored-scores %d' % args.max_stored_scores)
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84 if len(args.motifs) > 0:
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85 for motif in args.motifs:
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86 fimo_cmd_list.append('--motif "%s"' % motif)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
87 fimo_cmd_list.append('--motif-pseudo %4f' % args.motif_pseudo)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
88 if args.no_qvalue:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
89 fimo_cmd_list.append('--no-qvalue')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
90 if args.norc:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
91 fimo_cmd_list.append('--norc')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
92 if args.parse_genomic_coord == 'yes':
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
93 fimo_cmd_list.append('--parse-genomic-coord')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
94 if args.qv_thresh:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
95 fimo_cmd_list.append('--qv-thresh')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
96 fimo_cmd_list.append('--thresh %4f' % args.thresh)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
97 if args.input_psp is not None:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
98 fimo_cmd_list.append('--psp "%s"' % args.input_psp)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
99 if args.input_prior_dist is not None:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
100 fimo_cmd_list.append('--prior-dist "%s"' % args.input_prior_dist)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
101 fimo_cmd_list.append('--o "%s"' % (args.output_path))
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
102 fimo_cmd_list.append('--verbosity 1')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
103 fimo_cmd_list.append(args.input_motifs)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
104 fimo_cmd_list.append(args.input_fasta)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
105
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
106 fimo_cmd = ' '.join(fimo_cmd_list)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
107
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
108 try:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
109 tmp_stderr = tempfile.NamedTemporaryFile()
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
110 proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
111 returncode = proc.wait()
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
112 if returncode != 0:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
113 stderr = get_stderr(tmp_stderr)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
114 stop_err(stderr)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
115 except Exception as e:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
116 stop_err('Error running FIMO:\n%s' % e)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
117
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
118 shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
119
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
120 gff_file = os.path.join(args.output_path, 'fimo.gff')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
121 if args.remove_duplicate_coords == 'yes':
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
122 tmp_stderr = tempfile.NamedTemporaryFile()
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
123 # Identify and eliminating identical motif occurrences. These
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
124 # are identical if the combination of chrom, start, end and
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
125 # motif id are identical.
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
126 cmd = 'sort -k1,1 -k4,4n -k5,5n -k9.1,9.6 -u -o %s %s' % (gff_file, gff_file)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
127 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
128 returncode = proc.wait()
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
129 if returncode != 0:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
130 stderr = get_stderr(tmp_stderr)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
131 stop_err(stderr)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
132 # Sort GFF output by a combination of chrom, score, start.
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
133 cmd = 'sort -k1,1 -k4,4n -k6,6n -o %s %s' % (gff_file, gff_file)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
134 proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, shell=True)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
135 returncode = proc.wait()
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
136 if returncode != 0:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
137 stderr = get_stderr(tmp_stderr)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
138 stop_err(stderr)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
139 if args.output_separate_motifs == 'yes':
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
140 # Create the collection output directory.
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
141 collection_path = (os.path.join(os.getcwd(), 'output'))
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
142 # Keep track of motif occurrences.
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
143 header_line = None
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
144 motif_ids = []
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
145 file_handles = []
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
146 for line in open(gff_file, 'r'):
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
147 if line.startswith('#'):
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
148 if header_line is None:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
149 header_line = line
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
150 continue
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
151 items = line.split('\t')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
152 attribute = items[8]
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
153 attributes = attribute.split(';')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
154 name = attributes[0]
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
155 motif_id = name.split('=')[1]
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
156 file_name = os.path.join(collection_path, 'MOTIF%s.gff' % motif_id)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
157 if motif_id in motif_ids:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
158 i = motif_ids.index(motif_id)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
159 fh = file_handles[i]
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
160 fh.write(line)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
161 else:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
162 fh = open(file_name, 'wb')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
163 if header_line is not None:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
164 fh.write(header_line)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
165 fh.write(line)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
166 motif_ids.append(motif_id)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
167 file_handles.append(fh)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
168 for file_handle in file_handles:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
169 file_handle.close()
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
170 else:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
171 shutil.move(gff_file, args.gff_output)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
172 shutil.move(os.path.join(args.output_path, 'fimo.xml'), args.xml_output)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
173 shutil.move(os.path.join(args.output_path, 'fimo.html'), args.html_output)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
diff changeset
174
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
iuc
parents:
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175 out_file = open(args.interval_output, 'wb')
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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176 out_file.write("#%s\n" % "\t".join(("chr", "start", "end", "pattern name", "score", "strand", "matched sequence", "p-value", "q-value")))
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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177 for line in open(args.txt_output):
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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178 if line.startswith('#'):
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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179 continue
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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180 fields = line.rstrip("\n\r").split("\t")
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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181 start, end = int(fields[2]), int(fields[3])
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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182 sequence = fields[7]
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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183 if start > end:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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184 # Flip start and end and set strand.
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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185 start, end = end, start
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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186 strand = "-"
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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187 # We want sequences relative to strand; FIMO always provides + stranded sequence.
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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188 sequence = dna_reverse_complement(sequence)
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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189 else:
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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190 strand = "+"
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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191 # Make 0-based start position.
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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192 start -= 1
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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193 out_file.write("%s\n" % "\t".join([fields[1], str(start), str(end), fields[0], fields[4], strand, sequence, fields[5], fields[6]]))
a0fa4efeeee3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 3f116ddc83447056068573320c148a9bfca9aa2e
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194 out_file.close()