Mercurial > repos > iuc > meme_meme
changeset 6:62d1fae3b7d3 draft
Uploaded
| author | iuc |
|---|---|
| date | Fri, 17 Jun 2016 13:16:52 -0400 |
| parents | 34c794383f81 |
| children | 487ce3fa1822 |
| files | fimo_wrapper.py test-data/fimo_output_almost-gff_1.txt test-data/fimo_output_almost-gff_2.txt test-data/fimo_output_html_1.html test-data/fimo_output_html_2.html test-data/fimo_output_interval_1.txt test-data/fimo_output_interval_2.txt test-data/fimo_output_txt_1.txt test-data/fimo_output_txt_2.txt test-data/fimo_output_xml_1.xml test-data/fimo_output_xml_2.xml test-data/meme_output_html_1.html test-data/meme_output_html_2.html test-data/meme_output_txt_1.txt test-data/meme_output_txt_2.txt test-data/motif1.gff tool_dependencies.xml |
| diffstat | 17 files changed, 109 insertions(+), 1103 deletions(-) [+] |
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--- a/fimo_wrapper.py Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,134 +0,0 @@ -#!/usr/bin/env python -import argparse -import os -import shutil -import string -import subprocess -import sys -import tempfile - -BUFFSIZE = 1048576 -# Translation table for reverse Complement, with ambiguity codes. -DNA_COMPLEMENT = string.maketrans("ACGTRYKMBDHVacgtrykmbdhv", "TGCAYRMKVHDBtgcayrmkvhdb") - - -def reverse(sequence): - # Reverse sequence string. - return sequence[::-1] - - -def dna_complement(sequence): - # Complement DNA sequence string. - return sequence.translate(DNA_COMPLEMENT) - - -def dna_reverse_complement(sequence): - # Returns the reverse complement of the sequence. - sequence = reverse(sequence) - return dna_complement(sequence) - - -def stop_err(msg): - sys.stderr.write(msg) - sys.exit(1) - -parser = argparse.ArgumentParser() -parser.add_argument('--input_motifs', dest='input_motifs', help='MEME output formatted files for input to fimo') -parser.add_argument('--input_fasta', dest='input_fasta', help='Fassta sequence file') -parser.add_argument('--options_type', dest='options_type', help='Basic or Advance options') -parser.add_argument('--input_psp', dest='input_psp', default=None, help='File containing position specific priors') -parser.add_argument('--input_prior_dist', dest='input_prior_dist', default=None, help='File containing binned distribution of priors') -parser.add_argument('--alpha', dest='alpha', type=float, default=1.0, help='The alpha parameter for calculating position specific priors') -parser.add_argument('--bgfile', dest='bgfile', default=None, help='Background file type, used only if not "default"') -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') -parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store') -parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id') -parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix') -parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value') -parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand') -parser.add_argument('--output_path', dest='output_path', help='Output files directory') -parser.add_argument('--parse_genomic_coord', action='store_true', help='Check each sequence header for UCSC style genomic coordinates') -parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold') -parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold') -parser.add_argument('--gff_output', dest='gff_output', help='Gff output file') -parser.add_argument('--html_output', dest='html_output', help='HTML output file') -parser.add_argument('--interval_output', dest='interval_output', help='Interval output file') -parser.add_argument('--txt_output', dest='txt_output', help='Text output file') -parser.add_argument('--xml_output', dest='xml_output', help='XML output file') -args = parser.parse_args() - -fimo_cmd_list = ['fimo'] -if args.options_type == 'advanced': - fimo_cmd_list.append('--alpha %4f' % args.alpha) - if args.bgfile is not None: - fimo_cmd_list.append('--bgfile "%s"' % args.bgfile) - if args.max_strand: - fimo_cmd_list.append('--max-strand') - fimo_cmd_list.append('--max-stored-scores %d' % args.max_stored_scores) - if len(args.motifs) > 0: - for motif in args.motifs: - fimo_cmd_list.append('--motif "%s"' % motif) - fimo_cmd_list.append('--motif-pseudo %4f' % args.motif_pseudo) - if args.no_qvalue: - fimo_cmd_list.append('--no-qvalue') - if args.norc: - fimo_cmd_list.append('--norc') - if args.parse_genomic_coord: - fimo_cmd_list.append('--parse-genomic-coord') - if args.qv_thresh: - fimo_cmd_list.append('--qv-thresh') - fimo_cmd_list.append('--thresh %4f' % args.thresh) - if args.input_psp is not None: - fimo_cmd_list.append('--psp "%s"' % args.input_psp) - if args.input_prior_dist is not None: - fimo_cmd_list.append('--prior-dist "%s"' % args.input_prior_dist) -fimo_cmd_list.append('--o "%s"' % (args.output_path)) -fimo_cmd_list.append('--verbosity 1') -fimo_cmd_list.append(args.input_motifs) -fimo_cmd_list.append(args.input_fasta) - -fimo_cmd = ' '.join(fimo_cmd_list) - -try: - tmp_stderr = tempfile.NamedTemporaryFile() - proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr) - returncode = proc.wait() - tmp_stderr.seek(0) - stderr = '' - try: - while True: - stderr += tmp_stderr.read(BUFFSIZE) - if not stderr or len(stderr) % BUFFSIZE != 0: - break - except OverflowError: - pass - if returncode != 0: - stop_err(stderr) -except Exception, e: - stop_err('Error running FIMO:\n%s' % str(e)) - -shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output) -shutil.move(os.path.join(args.output_path, 'fimo.gff'), args.gff_output) -shutil.move(os.path.join(args.output_path, 'fimo.xml'), args.xml_output) -shutil.move(os.path.join(args.output_path, 'fimo.html'), args.html_output) - -out_file = open(args.interval_output, 'wb') -out_file.write("#%s\n" % "\t".join(("chr", "start", "end", "pattern name", "score", "strand", "matched sequence", "p-value", "q-value"))) -for line in open(args.txt_output): - if line.startswith('#'): - continue - fields = line.rstrip("\n\r").split("\t") - start, end = int(fields[2]), int(fields[3]) - sequence = fields[7] - if start > end: - # Flip start and end and set strand. - start, end = end, start - strand = "-" - # We want sequences relative to strand; FIMO always provides + stranded sequence. - sequence = dna_reverse_complement(sequence) - else: - strand = "+" - # Make 0-based start position. - start -= 1 - out_file.write("%s\n" % "\t".join([fields[1], str(start), str(end), fields[0], fields[4], strand, sequence, fields[5], fields[6]])) -out_file.close()
--- a/test-data/fimo_output_almost-gff_1.txt Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -##gff-version 3 -phiX174 fimo polypeptide_motif 1388 1398 102 + . Name=1;ID=1-1-phiX174;pvalue=6.36e-11;qvalue= 1.25e-09;sequence=AATATCTATAA; -phiX174 fimo polypeptide_motif 847 857 102 + . Name=1;ID=1-2-phiX174;pvalue=7.02e-11;qvalue= 1.25e-09;sequence=AATGTCTAAAG; -phiX174 fimo polypeptide_motif 2301 2311 99.6 + . Name=1;ID=1-3-phiX174;pvalue=1.08e-10;qvalue= 1.29e-09;sequence=AGGTTATAACG; -phiX174 fimo polypeptide_motif 5063 5073 95.6 + . Name=1;ID=1-4-phiX174;pvalue=2.73e-10;qvalue= 2.25e-09;sequence=AGGAGCTAAAG; -phiX174 fimo polypeptide_motif 989 999 95 + . Name=1;ID=1-5-phiX174;pvalue=3.15e-10;qvalue= 2.25e-09;sequence=TGAGGATAAAT; -phiX174 fimo polypeptide_motif 4713 4723 91.1 + . Name=1;ID=1-6-phiX174;pvalue=7.74e-10;qvalue= 3.48e-09;sequence=GACTGCTATCA; -phiX174 fimo polypeptide_motif 5048 5058 90.7 + . Name=1;ID=1-7-phiX174;pvalue=8.51e-10;qvalue= 3.48e-09;sequence=TGCTGCTAAAG; -phiX174 fimo polypeptide_motif 855 865 90.6 + . Name=1;ID=1-8-phiX174;pvalue=8.64e-10;qvalue= 3.48e-09;sequence=AAGGTAAAAAA; -phiX174 fimo polypeptide_motif 3155 3165 90.1 + . Name=1;ID=1-9-phiX174;pvalue=9.76e-10;qvalue= 3.48e-09;sequence=TATGGCTAAAG; -phiX174 fimo polypeptide_motif 5009 5019 90.1 + . Name=1;ID=1-10-phiX174;pvalue=9.76e-10;qvalue= 3.48e-09;sequence=TGTGGCTAAAT; -phiX174 fimo polypeptide_motif 814 824 88.9 + . Name=1;ID=1-11-phiX174;pvalue=1.28e-09;qvalue= 4.14e-09;sequence=TGCGTCAAAAA; -phiX174 fimo polypeptide_motif 2832 2842 88.5 + . Name=1;ID=1-12-phiX174;pvalue=1.42e-09;qvalue= 4.23e-09;sequence=TTGGTCTAACT; -phiX174 fimo polypeptide_motif 3830 3840 87.7 + . Name=1;ID=1-13-phiX174;pvalue=1.7e-09;qvalue= 4.68e-09;sequence=TATTGATAAAG; -phiX174 fimo polypeptide_motif 3560 3570 87.2 + . Name=1;ID=1-14-phiX174;pvalue=1.89e-09;qvalue= 4.82e-09;sequence=TGCGTCTATTA; -phiX174 fimo polypeptide_motif 2882 2892 86.4 + . Name=1;ID=1-15-phiX174;pvalue=2.29e-09;qvalue= 5.46e-09;sequence=AGGTTATTAAA; -phiX174 fimo polypeptide_motif 4453 4463 85.9 + . Name=1;ID=1-16-phiX174;pvalue=2.58e-09;qvalue= 5.75e-09;sequence=AAGGTATTAAG; -phiX174 fimo polypeptide_motif 2493 2503 85.1 + . Name=1;ID=1-17-phiX174;pvalue=3.06e-09;qvalue= 5.79e-09;sequence=GACACCTAAAG; -phiX174 fimo polypeptide_motif 4104 4114 85.1 + . Name=1;ID=1-18-phiX174;pvalue=3.08e-09;qvalue= 5.79e-09;sequence=GGCTTCCATAA; -phiX174 fimo polypeptide_motif 4955 4965 85.1 + . Name=1;ID=1-19-phiX174;pvalue=3.08e-09;qvalue= 5.79e-09;sequence=TGATGCTAAAG; -phiX174 fimo polypeptide_motif 1885 1895 84.4 + . Name=1;ID=1-20-phiX174;pvalue=3.61e-09;qvalue= 6.45e-09;sequence=TGCGACTAAAG; -phiX174 fimo polypeptide_motif 3376 3386 84.2 + . Name=1;ID=1-21-phiX174;pvalue=3.81e-09;qvalue= 6.48e-09;sequence=AGAATCAAAAA; -phiX174 fimo polypeptide_motif 52 62 83.9 + . Name=1;ID=1-22-phiX174;pvalue=4.06e-09;qvalue= 6.58e-09;sequence=TGAGTCGAAAA; -phiX174 fimo polypeptide_motif 1390 1400 83.7 + . Name=1;ID=1-23-phiX174;pvalue=4.26e-09;qvalue= 6.61e-09;sequence=TATCTATAACA; -phiX174 fimo polypeptide_motif 2017 2027 83.4 + . Name=1;ID=1-24-phiX174;pvalue=4.6e-09;qvalue= 6.85e-09;sequence=TTCGTCTAAGA; -phiX174 fimo polypeptide_motif 1000 1010 83.1 + . Name=1;ID=1-25-phiX174;pvalue=4.88e-09;qvalue= 6.97e-09;sequence=TATGTCTAATA; -phiX174 fimo polypeptide_motif 1555 1565 82.5 + . Name=1;ID=1-26-phiX174;pvalue=5.58e-09;qvalue= 7.37e-09;sequence=GACTTCTACCA; -phiX174 fimo polypeptide_motif 4430 4440 82.5 + . Name=1;ID=1-27-phiX174;pvalue=5.62e-09;qvalue= 7.37e-09;sequence=TGAGTATAATT; -phiX174 fimo polypeptide_motif 1927 1937 82.3 + . Name=1;ID=1-28-phiX174;pvalue=5.82e-09;qvalue= 7.37e-09;sequence=GACTTATACCG; -phiX174 fimo polypeptide_motif 2981 2991 82.1 + . Name=1;ID=1-29-phiX174;pvalue=6.13e-09;qvalue= 7.37e-09;sequence=CATGTCTAAAT; -phiX174 fimo polypeptide_motif 4203 4213 82 + . Name=1;ID=1-30-phiX174;pvalue=6.34e-09;qvalue= 7.37e-09;sequence=GACGGCCATAA; -phiX174 fimo polypeptide_motif 1669 1679 81.9 + . Name=1;ID=1-31-phiX174;pvalue=6.4e-09;qvalue= 7.37e-09;sequence=TGGAGGTAAAA; -phiX174 fimo polypeptide_motif 3260 3270 81.5 + . Name=1;ID=1-32-phiX174;pvalue=7.01e-09;qvalue= 7.82e-09;sequence=CGCTGATAAAG; -phiX174 fimo polypeptide_motif 3047 3057 81.3 + . Name=1;ID=1-33-phiX174;pvalue=7.4e-09;qvalue= 7.85e-09;sequence=TACCGATAACA; -phiX174 fimo polypeptide_motif 4176 4186 81.2 + . Name=1;ID=1-34-phiX174;pvalue=7.6e-09;qvalue= 7.85e-09;sequence=GAGTTCGATAA; -phiX174 fimo polypeptide_motif 4118 4128 81.1 + . Name=1;ID=1-35-phiX174;pvalue=7.7e-09;qvalue= 7.85e-09;sequence=GATGGATAACC; -phiX174 fimo polypeptide_motif 5370 5380 80.9 + . Name=1;ID=1-36-phiX174;pvalue=8.03e-09;qvalue= 7.87e-09;sequence=GGCGTATCCAA; -phiX174 fimo polypeptide_motif 1242 1252 80.5 + . Name=1;ID=1-37-phiX174;pvalue=8.94e-09;qvalue= 7.87e-09;sequence=AGTGGATTAAG; -phiX174 fimo polypeptide_motif 2583 2593 80.5 + . Name=1;ID=1-38-phiX174;pvalue=8.94e-09;qvalue= 7.87e-09;sequence=TACATCTGTCA; -phiX174 fimo polypeptide_motif 698 708 80.4 + . Name=1;ID=1-39-phiX174;pvalue=9.13e-09;qvalue= 7.87e-09;sequence=TACGGAAAACA; -phiX174 fimo polypeptide_motif 2299 2309 80.3 + . Name=1;ID=1-40-phiX174;pvalue=9.26e-09;qvalue= 7.87e-09;sequence=TGAGGTTATAA; -phiX174 fimo polypeptide_motif 4189 4199 80.1 + . Name=1;ID=1-41-phiX174;pvalue=9.69e-09;qvalue= 7.87e-09;sequence=GTGATATGTAT; -phiX174 fimo polypeptide_motif 275 285 80.1 + . Name=1;ID=1-42-phiX174;pvalue=9.85e-09;qvalue= 7.87e-09;sequence=GGTTTAGATAT; -phiX174 fimo polypeptide_motif 1801 1811 80 + . Name=1;ID=1-43-phiX174;pvalue=1e-08;qvalue= 7.87e-09;sequence=GACCTATAAAC; -phiX174 fimo polypeptide_motif 1386 1396 79.9 + . Name=1;ID=1-44-phiX174;pvalue=1.03e-08;qvalue= 7.87e-09;sequence=TGAATATCTAT; -phiX174 fimo polypeptide_motif 1303 1313 79.8 + . Name=1;ID=1-45-phiX174;pvalue=1.03e-08;qvalue= 7.87e-09;sequence=TGGTTATATTG; -phiX174 fimo polypeptide_motif 3772 3782 79.8 + . Name=1;ID=1-46-phiX174;pvalue=1.04e-08;qvalue= 7.87e-09;sequence=AGGATATTTCT; -phiX174 fimo polypeptide_motif 1288 1298 79.8 + . Name=1;ID=1-47-phiX174;pvalue=1.04e-08;qvalue= 7.87e-09;sequence=GACTGTTAACA; -phiX174 fimo polypeptide_motif 2577 2587 79.7 + . Name=1;ID=1-48-phiX174;pvalue=1.08e-08;qvalue= 7.87e-09;sequence=GATGGATACAT; -phiX174 fimo polypeptide_motif 937 947 79.6 + . Name=1;ID=1-49-phiX174;pvalue=1.08e-08;qvalue= 7.87e-09;sequence=TTGGTATGTAG; -phiX174 fimo polypeptide_motif 904 914 79.5 + . Name=1;ID=1-50-phiX174;pvalue=1.11e-08;qvalue= 7.93e-09;sequence=AGGTACTAAAG; -phiX174 fimo polypeptide_motif 2279 2289 79.4 + . Name=1;ID=1-51-phiX174;pvalue=1.13e-08;qvalue= 7.93e-09;sequence=TCGTGATAAAA; -phiX174 fimo polypeptide_motif 3164 3174 79.3 + . Name=1;ID=1-52-phiX174;pvalue=1.16e-08;qvalue= 7.98e-09;sequence=AGCTGGTAAAG; -phiX174 fimo polypeptide_motif 24 34 79.1 + . Name=1;ID=1-53-phiX174;pvalue=1.23e-08;qvalue= 8.24e-09;sequence=AGAAGTTAACA; -phiX174 fimo polypeptide_motif 838 848 78.9 + . Name=1;ID=1-54-phiX174;pvalue=1.27e-08;qvalue= 8.24e-09;sequence=GAGTGATGTAA; -phiX174 fimo polypeptide_motif 853 863 78.9 + . Name=1;ID=1-55-phiX174;pvalue=1.27e-08;qvalue= 8.24e-09;sequence=TAAAGGTAAAA; -phiX174 fimo polypeptide_motif 1984 1994 78.6 + . Name=1;ID=1-56-phiX174;pvalue=1.36e-08;qvalue= 8.68e-09;sequence=AATTTCTATGA; -phiX174 fimo polypeptide_motif 1 11 78.3 + . Name=1;ID=1-57-phiX174;pvalue=1.46e-08;qvalue= 9.05e-09;sequence=GAGTTTTATCG; -phiX174 fimo polypeptide_motif 4307 4317 78.3 + . Name=1;ID=1-58-phiX174;pvalue=1.47e-08;qvalue= 9.05e-09;sequence=TATTAATAACA; -phiX174 fimo polypeptide_motif 4303 4313 78.2 + . Name=1;ID=1-59-phiX174;pvalue=1.52e-08;qvalue= 9.19e-09;sequence=TTGATATTAAT; -phiX174 fimo polypeptide_motif 5033 5043 78 + . Name=1;ID=1-60-phiX174;pvalue=1.58e-08;qvalue= 9.41e-09;sequence=GTCAGATATGG; -phiX174 fimo polypeptide_motif 2579 2589 77.6 + . Name=1;ID=1-61-phiX174;pvalue=1.73e-08;qvalue= 1.01e-08;sequence=TGGATACATCT; -phiX174 fimo polypeptide_motif 322 332 77.4 + . Name=1;ID=1-62-phiX174;pvalue=1.82e-08;qvalue= 1.05e-08;sequence=GACATTTTAAA; -phiX174 fimo polypeptide_motif 5001 5011 76.8 + . Name=1;ID=1-63-phiX174;pvalue=2.09e-08;qvalue= 1.19e-08;sequence=GGTTTCTATGT; -phiX174 fimo polypeptide_motif 4217 4227 76.7 + . Name=1;ID=1-64-phiX174;pvalue=2.15e-08;qvalue= 1.2e-08;sequence=TGCTTCTGACG; -phiX174 fimo polypeptide_motif 4262 4272 76.6 + . Name=1;ID=1-65-phiX174;pvalue=2.18e-08;qvalue= 1.2e-08;sequence=AATGGATGAAT; -phiX174 fimo polypeptide_motif 3569 3579 76.5 + . Name=1;ID=1-66-phiX174;pvalue=2.26e-08;qvalue= 1.22e-08;sequence=TATGGAAAACA; -phiX174 fimo polypeptide_motif 194 204 76.4 + . Name=1;ID=1-67-phiX174;pvalue=2.29e-08;qvalue= 1.22e-08;sequence=ATCAACTAACG; -phiX174 fimo polypeptide_motif 131 141 76 + . Name=1;ID=1-68-phiX174;pvalue=2.49e-08;qvalue= 1.31e-08;sequence=AAATGAGAAAA; -phiX174 fimo polypeptide_motif 1491 1501 75.9 + . Name=1;ID=1-69-phiX174;pvalue=2.55e-08;qvalue= 1.32e-08;sequence=GCCATCTCAAA; -phiX174 fimo polypeptide_motif 434 444 75.7 + . Name=1;ID=1-70-phiX174;pvalue=2.67e-08;qvalue= 1.36e-08;sequence=GGCCTCTATTA; -phiX174 fimo polypeptide_motif 4565 4575 75.6 + . Name=1;ID=1-71-phiX174;pvalue=2.73e-08;qvalue= 1.36e-08;sequence=TTGGTTTATCG; -phiX174 fimo polypeptide_motif 102 112 75.6 + . Name=1;ID=1-72-phiX174;pvalue=2.75e-08;qvalue= 1.36e-08;sequence=GAATTAAATCG; -phiX174 fimo polypeptide_motif 903 913 75.5 + . Name=1;ID=1-73-phiX174;pvalue=2.82e-08;qvalue= 1.38e-08;sequence=GAGGTACTAAA; -phiX174 fimo polypeptide_motif 4748 4758 75.2 + . Name=1;ID=1-74-phiX174;pvalue=3.01e-08;qvalue= 1.45e-08;sequence=TACAGCTAATG; -phiX174 fimo polypeptide_motif 2622 2632 75 + . Name=1;ID=1-75-phiX174;pvalue=3.16e-08;qvalue= 1.5e-08;sequence=TGCTGATATTG; -phiX174 fimo polypeptide_motif 467 477 74.7 + . Name=1;ID=1-76-phiX174;pvalue=3.35e-08;qvalue= 1.57e-08;sequence=TTTGGATTTAA; -phiX174 fimo polypeptide_motif 4033 4043 74.6 + . Name=1;ID=1-77-phiX174;pvalue=3.44e-08;qvalue= 1.58e-08;sequence=AGCGTATCGAG; -phiX174 fimo polypeptide_motif 1348 1358 74.6 + . Name=1;ID=1-78-phiX174;pvalue=3.46e-08;qvalue= 1.58e-08;sequence=TACCAATAAAA; -phiX174 fimo polypeptide_motif 239 249 74.4 + . Name=1;ID=1-79-phiX174;pvalue=3.62e-08;qvalue= 1.64e-08;sequence=AGTGGCTTAAT; -phiX174 fimo polypeptide_motif 500 510 74.1 + . Name=1;ID=1-80-phiX174;pvalue=3.84e-08;qvalue= 1.71e-08;sequence=GACGAGTAACA; -phiX174 fimo polypeptide_motif 3001 3011 74 + . Name=1;ID=1-81-phiX174;pvalue=3.93e-08;qvalue= 1.73e-08;sequence=GCGGTCAAAAA; -phiX174 fimo polypeptide_motif 3776 3786 74 + . Name=1;ID=1-82-phiX174;pvalue=3.98e-08;qvalue= 1.73e-08;sequence=TATTTCTAATG; -phiX174 fimo polypeptide_motif 2026 2036 73.9 + . Name=1;ID=1-83-phiX174;pvalue=4.06e-08;qvalue= 1.75e-08;sequence=GAAGTTTAAGA; -phiX174 fimo polypeptide_motif 4237 4247 73.8 + . Name=1;ID=1-84-phiX174;pvalue=4.12e-08;qvalue= 1.75e-08;sequence=AGTTTGTATCT; -phiX174 fimo polypeptide_motif 803 813 73.7 + . Name=1;ID=1-85-phiX174;pvalue=4.24e-08;qvalue= 1.78e-08;sequence=AGAAGAAAACG; -phiX174 fimo polypeptide_motif 3770 3780 73.6 + . Name=1;ID=1-86-phiX174;pvalue=4.35e-08;qvalue= 1.81e-08;sequence=AAAGGATATTT; -phiX174 fimo polypeptide_motif 3429 3439 73.5 + . Name=1;ID=1-87-phiX174;pvalue=4.45e-08;qvalue= 1.82e-08;sequence=GAGATGCAAAA; -phiX174 fimo polypeptide_motif 99 109 73.5 + . Name=1;ID=1-88-phiX174;pvalue=4.48e-08;qvalue= 1.82e-08;sequence=TACGAATTAAA; -phiX174 fimo polypeptide_motif 67 77 73.2 + . Name=1;ID=1-89-phiX174;pvalue=4.78e-08;qvalue= 1.92e-08;sequence=TCTTGATAAAG; -phiX174 fimo polypeptide_motif 5332 5342 72.9 + . Name=1;ID=1-90-phiX174;pvalue=5.13e-08;qvalue= 2.01e-08;sequence=ATCTGCTCAAA; -phiX174 fimo polypeptide_motif 277 287 72.9 + . Name=1;ID=1-91-phiX174;pvalue=5.14e-08;qvalue= 2.01e-08;sequence=TTTAGATATGA; -phiX174 fimo polypeptide_motif 4338 4348 72.8 + . Name=1;ID=1-92-phiX174;pvalue=5.18e-08;qvalue= 2.01e-08;sequence=GGGGACGAAAA; -phiX174 fimo polypeptide_motif 3812 3822 72.8 + . Name=1;ID=1-93-phiX174;pvalue=5.28e-08;qvalue= 2.03e-08;sequence=GGTTGATATTT; -phiX174 fimo polypeptide_motif 1909 1919 72.6 + . Name=1;ID=1-94-phiX174;pvalue=5.51e-08;qvalue= 2.08e-08;sequence=TAACGCTAAAG; -phiX174 fimo polypeptide_motif 3000 3010 72.6 + . Name=1;ID=1-95-phiX174;pvalue=5.54e-08;qvalue= 2.08e-08;sequence=GGCGGTCAAAA; -phiX174 fimo polypeptide_motif 3891 3901 72.4 + . Name=1;ID=1-96-phiX174;pvalue=5.75e-08;qvalue= 2.11e-08;sequence=ATTGGCTCTAA; -phiX174 fimo polypeptide_motif 3079 3089 72.4 + . Name=1;ID=1-97-phiX174;pvalue=5.76e-08;qvalue= 2.11e-08;sequence=CTGGTATTAAA; -phiX174 fimo polypeptide_motif 37 47 72.4 + . Name=1;ID=1-98-phiX174;pvalue=5.79e-08;qvalue= 2.11e-08;sequence=TTCGGATATTT; -phiX174 fimo polypeptide_motif 380 390 72.2 + . Name=1;ID=1-99-phiX174;pvalue=6.01e-08;qvalue= 2.17e-08;sequence=GTAAGAAATCA;
--- a/test-data/fimo_output_almost-gff_2.txt Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -##gff-version 3 -phiX174 fimo polypeptide_motif 1388 1398 102 + . Name=1;ID=1-1-phiX174;pvalue=6.36e-11;sequence=AATATCTATAA; -phiX174 fimo polypeptide_motif 847 857 102 + . Name=1;ID=1-2-phiX174;pvalue=7.02e-11;sequence=AATGTCTAAAG; -phiX174 fimo polypeptide_motif 2301 2311 99.6 + . Name=1;ID=1-3-phiX174;pvalue=1.08e-10;sequence=AGGTTATAACG; -phiX174 fimo polypeptide_motif 5063 5073 95.6 + . Name=1;ID=1-4-phiX174;pvalue=2.73e-10;sequence=AGGAGCTAAAG; -phiX174 fimo polypeptide_motif 989 999 95 + . Name=1;ID=1-5-phiX174;pvalue=3.15e-10;sequence=TGAGGATAAAT; -phiX174 fimo polypeptide_motif 4713 4723 91.1 + . Name=1;ID=1-6-phiX174;pvalue=7.74e-10;sequence=GACTGCTATCA; -phiX174 fimo polypeptide_motif 5048 5058 90.7 + . Name=1;ID=1-7-phiX174;pvalue=8.51e-10;sequence=TGCTGCTAAAG; -phiX174 fimo polypeptide_motif 855 865 90.6 + . Name=1;ID=1-8-phiX174;pvalue=8.64e-10;sequence=AAGGTAAAAAA; -phiX174 fimo polypeptide_motif 3155 3165 90.1 + . Name=1;ID=1-9-phiX174;pvalue=9.76e-10;sequence=TATGGCTAAAG; -phiX174 fimo polypeptide_motif 5009 5019 90.1 + . Name=1;ID=1-10-phiX174;pvalue=9.76e-10;sequence=TGTGGCTAAAT; -phiX174 fimo polypeptide_motif 814 824 88.9 + . Name=1;ID=1-11-phiX174;pvalue=1.28e-09;sequence=TGCGTCAAAAA; -phiX174 fimo polypeptide_motif 2832 2842 88.5 + . Name=1;ID=1-12-phiX174;pvalue=1.42e-09;sequence=TTGGTCTAACT; -phiX174 fimo polypeptide_motif 3830 3840 87.7 + . Name=1;ID=1-13-phiX174;pvalue=1.7e-09;sequence=TATTGATAAAG; -phiX174 fimo polypeptide_motif 3560 3570 87.2 + . Name=1;ID=1-14-phiX174;pvalue=1.89e-09;sequence=TGCGTCTATTA; -phiX174 fimo polypeptide_motif 2882 2892 86.4 + . Name=1;ID=1-15-phiX174;pvalue=2.29e-09;sequence=AGGTTATTAAA; -phiX174 fimo polypeptide_motif 4453 4463 85.9 + . Name=1;ID=1-16-phiX174;pvalue=2.58e-09;sequence=AAGGTATTAAG; -phiX174 fimo polypeptide_motif 2493 2503 85.1 + . Name=1;ID=1-17-phiX174;pvalue=3.06e-09;sequence=GACACCTAAAG; -phiX174 fimo polypeptide_motif 4104 4114 85.1 + . Name=1;ID=1-18-phiX174;pvalue=3.08e-09;sequence=GGCTTCCATAA; -phiX174 fimo polypeptide_motif 4955 4965 85.1 + . Name=1;ID=1-19-phiX174;pvalue=3.08e-09;sequence=TGATGCTAAAG; -phiX174 fimo polypeptide_motif 1885 1895 84.4 + . Name=1;ID=1-20-phiX174;pvalue=3.61e-09;sequence=TGCGACTAAAG; -phiX174 fimo polypeptide_motif 3376 3386 84.2 + . Name=1;ID=1-21-phiX174;pvalue=3.81e-09;sequence=AGAATCAAAAA; -phiX174 fimo polypeptide_motif 52 62 83.9 + . Name=1;ID=1-22-phiX174;pvalue=4.06e-09;sequence=TGAGTCGAAAA; -phiX174 fimo polypeptide_motif 1390 1400 83.7 + . Name=1;ID=1-23-phiX174;pvalue=4.26e-09;sequence=TATCTATAACA; -phiX174 fimo polypeptide_motif 2017 2027 83.4 + . Name=1;ID=1-24-phiX174;pvalue=4.6e-09;sequence=TTCGTCTAAGA; -phiX174 fimo polypeptide_motif 1000 1010 83.1 + . Name=1;ID=1-25-phiX174;pvalue=4.88e-09;sequence=TATGTCTAATA; -phiX174 fimo polypeptide_motif 1555 1565 82.5 + . Name=1;ID=1-26-phiX174;pvalue=5.58e-09;sequence=GACTTCTACCA; -phiX174 fimo polypeptide_motif 4430 4440 82.5 + . Name=1;ID=1-27-phiX174;pvalue=5.62e-09;sequence=TGAGTATAATT; -phiX174 fimo polypeptide_motif 1927 1937 82.3 + . Name=1;ID=1-28-phiX174;pvalue=5.82e-09;sequence=GACTTATACCG; -phiX174 fimo polypeptide_motif 2981 2991 82.1 + . Name=1;ID=1-29-phiX174;pvalue=6.13e-09;sequence=CATGTCTAAAT; -phiX174 fimo polypeptide_motif 4203 4213 82 + . Name=1;ID=1-30-phiX174;pvalue=6.34e-09;sequence=GACGGCCATAA; -phiX174 fimo polypeptide_motif 1669 1679 81.9 + . Name=1;ID=1-31-phiX174;pvalue=6.4e-09;sequence=TGGAGGTAAAA; -phiX174 fimo polypeptide_motif 3260 3270 81.5 + . Name=1;ID=1-32-phiX174;pvalue=7.01e-09;sequence=CGCTGATAAAG; -phiX174 fimo polypeptide_motif 3047 3057 81.3 + . Name=1;ID=1-33-phiX174;pvalue=7.4e-09;sequence=TACCGATAACA; -phiX174 fimo polypeptide_motif 4176 4186 81.2 + . Name=1;ID=1-34-phiX174;pvalue=7.6e-09;sequence=GAGTTCGATAA; -phiX174 fimo polypeptide_motif 4118 4128 81.1 + . Name=1;ID=1-35-phiX174;pvalue=7.7e-09;sequence=GATGGATAACC; -phiX174 fimo polypeptide_motif 5370 5380 80.9 + . Name=1;ID=1-36-phiX174;pvalue=8.03e-09;sequence=GGCGTATCCAA; -phiX174 fimo polypeptide_motif 1242 1252 80.5 + . Name=1;ID=1-37-phiX174;pvalue=8.94e-09;sequence=AGTGGATTAAG; -phiX174 fimo polypeptide_motif 2583 2593 80.5 + . Name=1;ID=1-38-phiX174;pvalue=8.94e-09;sequence=TACATCTGTCA; -phiX174 fimo polypeptide_motif 698 708 80.4 + . Name=1;ID=1-39-phiX174;pvalue=9.13e-09;sequence=TACGGAAAACA; -phiX174 fimo polypeptide_motif 2299 2309 80.3 + . Name=1;ID=1-40-phiX174;pvalue=9.26e-09;sequence=TGAGGTTATAA; -phiX174 fimo polypeptide_motif 4189 4199 80.1 + . Name=1;ID=1-41-phiX174;pvalue=9.69e-09;sequence=GTGATATGTAT; -phiX174 fimo polypeptide_motif 275 285 80.1 + . Name=1;ID=1-42-phiX174;pvalue=9.85e-09;sequence=GGTTTAGATAT; -phiX174 fimo polypeptide_motif 1801 1811 80 + . Name=1;ID=1-43-phiX174;pvalue=1e-08;sequence=GACCTATAAAC; -phiX174 fimo polypeptide_motif 1386 1396 79.9 + . Name=1;ID=1-44-phiX174;pvalue=1.03e-08;sequence=TGAATATCTAT; -phiX174 fimo polypeptide_motif 1303 1313 79.8 + . Name=1;ID=1-45-phiX174;pvalue=1.03e-08;sequence=TGGTTATATTG; -phiX174 fimo polypeptide_motif 3772 3782 79.8 + . Name=1;ID=1-46-phiX174;pvalue=1.04e-08;sequence=AGGATATTTCT; -phiX174 fimo polypeptide_motif 1288 1298 79.8 + . Name=1;ID=1-47-phiX174;pvalue=1.04e-08;sequence=GACTGTTAACA; -phiX174 fimo polypeptide_motif 2577 2587 79.7 + . Name=1;ID=1-48-phiX174;pvalue=1.08e-08;sequence=GATGGATACAT; -phiX174 fimo polypeptide_motif 937 947 79.6 + . Name=1;ID=1-49-phiX174;pvalue=1.08e-08;sequence=TTGGTATGTAG; -phiX174 fimo polypeptide_motif 904 914 79.5 + . Name=1;ID=1-50-phiX174;pvalue=1.11e-08;sequence=AGGTACTAAAG; -phiX174 fimo polypeptide_motif 2279 2289 79.4 + . Name=1;ID=1-51-phiX174;pvalue=1.13e-08;sequence=TCGTGATAAAA; -phiX174 fimo polypeptide_motif 3164 3174 79.3 + . Name=1;ID=1-52-phiX174;pvalue=1.16e-08;sequence=AGCTGGTAAAG; -phiX174 fimo polypeptide_motif 24 34 79.1 + . Name=1;ID=1-53-phiX174;pvalue=1.23e-08;sequence=AGAAGTTAACA; -phiX174 fimo polypeptide_motif 838 848 78.9 + . Name=1;ID=1-54-phiX174;pvalue=1.27e-08;sequence=GAGTGATGTAA; -phiX174 fimo polypeptide_motif 853 863 78.9 + . Name=1;ID=1-55-phiX174;pvalue=1.27e-08;sequence=TAAAGGTAAAA; -phiX174 fimo polypeptide_motif 1984 1994 78.6 + . Name=1;ID=1-56-phiX174;pvalue=1.36e-08;sequence=AATTTCTATGA; -phiX174 fimo polypeptide_motif 1 11 78.3 + . Name=1;ID=1-57-phiX174;pvalue=1.46e-08;sequence=GAGTTTTATCG; -phiX174 fimo polypeptide_motif 4307 4317 78.3 + . Name=1;ID=1-58-phiX174;pvalue=1.47e-08;sequence=TATTAATAACA; -phiX174 fimo polypeptide_motif 4303 4313 78.2 + . Name=1;ID=1-59-phiX174;pvalue=1.52e-08;sequence=TTGATATTAAT; -phiX174 fimo polypeptide_motif 5033 5043 78 + . Name=1;ID=1-60-phiX174;pvalue=1.58e-08;sequence=GTCAGATATGG; -phiX174 fimo polypeptide_motif 2579 2589 77.6 + . Name=1;ID=1-61-phiX174;pvalue=1.73e-08;sequence=TGGATACATCT; -phiX174 fimo polypeptide_motif 322 332 77.4 + . Name=1;ID=1-62-phiX174;pvalue=1.82e-08;sequence=GACATTTTAAA; -phiX174 fimo polypeptide_motif 5001 5011 76.8 + . Name=1;ID=1-63-phiX174;pvalue=2.09e-08;sequence=GGTTTCTATGT; -phiX174 fimo polypeptide_motif 4217 4227 76.7 + . Name=1;ID=1-64-phiX174;pvalue=2.15e-08;sequence=TGCTTCTGACG; -phiX174 fimo polypeptide_motif 4262 4272 76.6 + . Name=1;ID=1-65-phiX174;pvalue=2.18e-08;sequence=AATGGATGAAT; -phiX174 fimo polypeptide_motif 3569 3579 76.5 + . Name=1;ID=1-66-phiX174;pvalue=2.26e-08;sequence=TATGGAAAACA; -phiX174 fimo polypeptide_motif 194 204 76.4 + . Name=1;ID=1-67-phiX174;pvalue=2.29e-08;sequence=ATCAACTAACG; -phiX174 fimo polypeptide_motif 131 141 76 + . Name=1;ID=1-68-phiX174;pvalue=2.49e-08;sequence=AAATGAGAAAA; -phiX174 fimo polypeptide_motif 1491 1501 75.9 + . Name=1;ID=1-69-phiX174;pvalue=2.55e-08;sequence=GCCATCTCAAA; -phiX174 fimo polypeptide_motif 434 444 75.7 + . Name=1;ID=1-70-phiX174;pvalue=2.67e-08;sequence=GGCCTCTATTA; -phiX174 fimo polypeptide_motif 4565 4575 75.6 + . Name=1;ID=1-71-phiX174;pvalue=2.73e-08;sequence=TTGGTTTATCG; -phiX174 fimo polypeptide_motif 102 112 75.6 + . Name=1;ID=1-72-phiX174;pvalue=2.75e-08;sequence=GAATTAAATCG; -phiX174 fimo polypeptide_motif 903 913 75.5 + . Name=1;ID=1-73-phiX174;pvalue=2.82e-08;sequence=GAGGTACTAAA; -phiX174 fimo polypeptide_motif 4748 4758 75.2 + . Name=1;ID=1-74-phiX174;pvalue=3.01e-08;sequence=TACAGCTAATG; -phiX174 fimo polypeptide_motif 2622 2632 75 + . Name=1;ID=1-75-phiX174;pvalue=3.16e-08;sequence=TGCTGATATTG; -phiX174 fimo polypeptide_motif 467 477 74.7 + . Name=1;ID=1-76-phiX174;pvalue=3.35e-08;sequence=TTTGGATTTAA; -phiX174 fimo polypeptide_motif 4033 4043 74.6 + . Name=1;ID=1-77-phiX174;pvalue=3.44e-08;sequence=AGCGTATCGAG; -phiX174 fimo polypeptide_motif 1348 1358 74.6 + . Name=1;ID=1-78-phiX174;pvalue=3.46e-08;sequence=TACCAATAAAA; -phiX174 fimo polypeptide_motif 239 249 74.4 + . Name=1;ID=1-79-phiX174;pvalue=3.62e-08;sequence=AGTGGCTTAAT; -phiX174 fimo polypeptide_motif 500 510 74.1 + . Name=1;ID=1-80-phiX174;pvalue=3.84e-08;sequence=GACGAGTAACA; -phiX174 fimo polypeptide_motif 3001 3011 74 + . Name=1;ID=1-81-phiX174;pvalue=3.93e-08;sequence=GCGGTCAAAAA; -phiX174 fimo polypeptide_motif 3776 3786 74 + . Name=1;ID=1-82-phiX174;pvalue=3.98e-08;sequence=TATTTCTAATG; -phiX174 fimo polypeptide_motif 2026 2036 73.9 + . Name=1;ID=1-83-phiX174;pvalue=4.06e-08;sequence=GAAGTTTAAGA; -phiX174 fimo polypeptide_motif 4237 4247 73.8 + . Name=1;ID=1-84-phiX174;pvalue=4.12e-08;sequence=AGTTTGTATCT; -phiX174 fimo polypeptide_motif 803 813 73.7 + . Name=1;ID=1-85-phiX174;pvalue=4.24e-08;sequence=AGAAGAAAACG; -phiX174 fimo polypeptide_motif 3770 3780 73.6 + . Name=1;ID=1-86-phiX174;pvalue=4.35e-08;sequence=AAAGGATATTT; -phiX174 fimo polypeptide_motif 3429 3439 73.5 + . Name=1;ID=1-87-phiX174;pvalue=4.45e-08;sequence=GAGATGCAAAA; -phiX174 fimo polypeptide_motif 99 109 73.5 + . Name=1;ID=1-88-phiX174;pvalue=4.48e-08;sequence=TACGAATTAAA; -phiX174 fimo polypeptide_motif 67 77 73.2 + . Name=1;ID=1-89-phiX174;pvalue=4.78e-08;sequence=TCTTGATAAAG; -phiX174 fimo polypeptide_motif 5332 5342 72.9 + . Name=1;ID=1-90-phiX174;pvalue=5.13e-08;sequence=ATCTGCTCAAA; -phiX174 fimo polypeptide_motif 277 287 72.9 + . Name=1;ID=1-91-phiX174;pvalue=5.14e-08;sequence=TTTAGATATGA; -phiX174 fimo polypeptide_motif 4338 4348 72.8 + . Name=1;ID=1-92-phiX174;pvalue=5.18e-08;sequence=GGGGACGAAAA; -phiX174 fimo polypeptide_motif 3812 3822 72.8 + . Name=1;ID=1-93-phiX174;pvalue=5.28e-08;sequence=GGTTGATATTT; -phiX174 fimo polypeptide_motif 1909 1919 72.6 + . Name=1;ID=1-94-phiX174;pvalue=5.51e-08;sequence=TAACGCTAAAG; -phiX174 fimo polypeptide_motif 3000 3010 72.6 + . Name=1;ID=1-95-phiX174;pvalue=5.54e-08;sequence=GGCGGTCAAAA; -phiX174 fimo polypeptide_motif 3891 3901 72.4 + . Name=1;ID=1-96-phiX174;pvalue=5.75e-08;sequence=ATTGGCTCTAA; -phiX174 fimo polypeptide_motif 3079 3089 72.4 + . Name=1;ID=1-97-phiX174;pvalue=5.76e-08;sequence=CTGGTATTAAA; -phiX174 fimo polypeptide_motif 37 47 72.4 + . Name=1;ID=1-98-phiX174;pvalue=5.79e-08;sequence=TTCGGATATTT; -phiX174 fimo polypeptide_motif 380 390 72.2 + . Name=1;ID=1-99-phiX174;pvalue=6.01e-08;sequence=GTAAGAAATCA;
--- a/test-data/fimo_output_html_1.html Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme"> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> -<meta charset="UTF-8"> -<title>FIMO Results</title> -<style type="text/css"> -td.left {text-align: left;} -td.right {text-align: right; padding-right: 1cm;} -</style> -</head> -<body bgcolor="#D5F0FF"> -<a name="top_buttons"></a> -<hr> -<table summary="buttons" align="left" cellspacing="0"> -<tr> -<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td> -<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td> -<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td> -</tr> -</table> -<br/> -<br/> -<hr/> -<center><big><b>FIMO - Motif search tool</b></big></center> -<hr> -<p> -FIMO version 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000) -</p> -<p> -For further information on how to interpret these results -or to get a copy of the FIMO software please access -<a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p> -<p>If you use FIMO in your research, please cite the following paper:<br> -Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, -"FIMO: Scanning for occurrences of a given motif", -<i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011. -<a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p> -<hr> -<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center> -<hr> -<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;"> -<p> - DATABASE /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat - <br /> - Database contains 1 sequences, 5386 residues -</p> -<p> - MOTIFS /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat (Protein) - <table> - <thead> - <tr> - <th style="border-bottom: 1px dashed;">MOTIF</th> - <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th> - <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" > - BEST POSSIBLE MATCH - </th> - </tr> - </thead> - <tbody> - <tr> - <td style="text-align:right;">1</td> - <td style="text-align:right;padding-left: 1em;">11</td> - <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td> - </tr> - </tbody> - </table> -</p> -<p> -Random model letter frequencies (from non-redundant database): -<br/> - -A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 -L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 -W 0.013 Y 0.033 </p> -</div> -<hr> -<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center> -<hr> -<ul> -<li> -There were 1937 motif occurences with a p-value less than 0.0001. -<b>Only the most significant 1000 matches are shown here.</b> - -The full set of motif occurences can be seen in the -tab-delimited plain text output file -<a href="fimo.txt">fimo.txt</a>, -the GFF file -<a href="fimo.gff">fimo.gff</a> -which may be suitable for uploading to the -<a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a> -(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), -or the XML file -<a href="fimo.xml">fimo.xml</a>. -</li> -<li> -The p-value of a motif occurrence is defined as the -probability of a random sequence of the same length as the motif -matching that position of the sequence with as good or better a score. -</li>
--- a/test-data/fimo_output_html_2.html Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd"> -<html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme"> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> -<meta charset="UTF-8"> -<title>FIMO Results</title> -<style type="text/css"> -td.left {text-align: left;} -td.right {text-align: right; padding-right: 1cm;} -</style> -</head> -<body bgcolor="#D5F0FF"> -<a name="top_buttons"></a> -<hr> -<table summary="buttons" align="left" cellspacing="0"> -<tr> -<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td> -<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td> -<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td> -</tr> -</table> -<br/> -<br/> -<hr/> -<center><big><b>FIMO - Motif search tool</b></big></center> -<hr> -<p> -FIMO version 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000) -</p> -<p> -For further information on how to interpret these results -or to get a copy of the FIMO software please access -<a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p> -<p>If you use FIMO in your research, please cite the following paper:<br> -Charles E. Grant, Timothy L. Bailey, and William Stafford Noble, -"FIMO: Scanning for occurrences of a given motif", -<i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011. -<a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p> -<hr> -<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center> -<hr> -<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;"> -<p> - DATABASE /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat - <br /> - Database contains 1 sequences, 5386 residues -</p> -<p> - MOTIFS /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat (Protein) - <table> - <thead> - <tr> - <th style="border-bottom: 1px dashed;">MOTIF</th> - <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th> - <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" > - BEST POSSIBLE MATCH - </th> - </tr> - </thead> - <tbody> - <tr> - <td style="text-align:right;">1</td> - <td style="text-align:right;padding-left: 1em;">11</td> - <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td> - </tr> - </tbody> - </table> -</p> -<p> -Random model letter frequencies (from non-redundant database): -<br/> - -A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058 -L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064 -W 0.013 Y 0.033 </p> -</div> -<hr> -<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center> -<hr> -<ul> -<li> -There were 1937 motif occurences with a p-value less than 0.0001. -<b>Only the most significant 1000 matches are shown here.</b> - -The full set of motif occurences can be seen in the -tab-delimited plain text output file -<a href="fimo.txt">fimo.txt</a>, -the GFF file -<a href="fimo.gff">fimo.gff</a> -which may be suitable for uploading to the -<a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a> -(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), -or the XML file -<a href="fimo.xml">fimo.xml</a>. -</li> -<li> -The p-value of a motif occurrence is defined as the -probability of a random sequence of the same length as the motif -matching that position of the sequence with as good or better a score. -</li>
--- a/test-data/fimo_output_interval_1.txt Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#chr start end pattern name score strand matched sequence p-value q-value -phiX174 1387 1398 1 + + 1.25e-09 29.4024 6.36e-11 -phiX174 846 857 1 + + 1.25e-09 29.122 7.02e-11 -phiX174 2300 2311 1 + + 1.29e-09 27.6463 1.08e-10 -phiX174 5062 5073 1 + + 2.25e-09 25.5366 2.73e-10 -phiX174 988 999 1 + + 2.25e-09 25.3049 3.15e-10 -phiX174 4712 4723 1 + + 3.48e-09 23.622 7.74e-10 -phiX174 5047 5058 1 + + 3.48e-09 23.3293 8.51e-10 -phiX174 854 865 1 + + 3.48e-09 23.3049 8.64e-10 -phiX174 3154 3165 1 + + 3.48e-09 23.0366 9.76e-10 -phiX174 5008 5019 1 + + 3.48e-09 23.0366 9.76e-10 -phiX174 813 824 1 + + 4.14e-09 22.5854 1.28e-09 -phiX174 2831 2842 1 + + 4.23e-09 22.3415 1.42e-09 -phiX174 3829 3840 1 + + 4.68e-09 21.8293 1.7e-09 -phiX174 3559 3570 1 + + 4.82e-09 21.5976 1.89e-09 -phiX174 2881 2892 1 + + 5.46e-09 21.1951 2.29e-09 -phiX174 4452 4463 1 + + 5.75e-09 20.8902 2.58e-09 -phiX174 2492 2503 1 + + 5.79e-09 20.3415 3.06e-09 -phiX174 4103 4114 1 + + 5.79e-09 20.3171 3.08e-09 -phiX174 4954 4965 1 + + 5.79e-09 20.3171 3.08e-09 -phiX174 1884 1895 1 + + 6.45e-09 19.9268 3.61e-09 -phiX174 3375 3386 1 + + 6.48e-09 19.7683 3.81e-09 -phiX174 51 62 1 + + 6.58e-09 19.5732 4.06e-09 -phiX174 1389 1400 1 + + 6.61e-09 19.378 4.26e-09 -phiX174 2016 2027 1 + + 6.85e-09 19.0854 4.6e-09 -phiX174 999 1010 1 + + 6.97e-09 18.878 4.88e-09 -phiX174 1554 1565 1 + + 7.37e-09 18.439 5.58e-09 -phiX174 4429 4440 1 + + 7.37e-09 18.4268 5.62e-09 -phiX174 1926 1937 1 + + 7.37e-09 18.2927 5.82e-09 -phiX174 2980 2991 1 + + 7.37e-09 18.0732 6.13e-09 -phiX174 4202 4213 1 + + 7.37e-09 17.9268 6.34e-09 -phiX174 1668 1679 1 + + 7.37e-09 17.8659 6.4e-09 -phiX174 3259 3270 1 + + 7.82e-09 17.5 7.01e-09 -phiX174 3046 3057 1 + + 7.85e-09 17.2805 7.4e-09 -phiX174 4175 4186 1 + + 7.85e-09 17.1829 7.6e-09 -phiX174 4117 4128 1 + + 7.85e-09 17.1341 7.7e-09 -phiX174 5369 5380 1 + + 7.87e-09 16.9878 8.03e-09 -phiX174 1241 1252 1 + + 7.87e-09 16.5122 8.94e-09 -phiX174 2582 2593 1 + + 7.87e-09 16.5122 8.94e-09 -phiX174 697 708 1 + + 7.87e-09 16.4146 9.13e-09 -phiX174 2298 2309 1 + + 7.87e-09 16.3537 9.26e-09 -phiX174 4188 4199 1 + + 7.87e-09 16.1707 9.69e-09 -phiX174 274 285 1 + + 7.87e-09 16.0976 9.85e-09 -phiX174 1800 1811 1 + + 7.87e-09 16.0366 1e-08 -phiX174 1385 1396 1 + + 7.87e-09 15.9268 1.03e-08 -phiX174 1302 1313 1 + + 7.87e-09 15.9024 1.03e-08 -phiX174 3771 3782 1 + + 7.87e-09 15.878 1.04e-08 -phiX174 1287 1298 1 + + 7.87e-09 15.8659 1.04e-08 -phiX174 2576 2587 1 + + 7.87e-09 15.7683 1.08e-08 -phiX174 936 947 1 + + 7.87e-09 15.7561 1.08e-08 -phiX174 903 914 1 + + 7.93e-09 15.6585 1.11e-08 -phiX174 2278 2289 1 + + 7.93e-09 15.5854 1.13e-08 -phiX174 3163 3174 1 + + 7.98e-09 15.5 1.16e-08 -phiX174 23 34 1 + + 8.24e-09 15.3293 1.23e-08 -phiX174 837 848 1 + + 8.24e-09 15.2561 1.27e-08 -phiX174 852 863 1 + + 8.24e-09 15.2561 1.27e-08 -phiX174 1983 1994 1 + + 8.68e-09 15.0244 1.36e-08 -phiX174 0 11 1 + + 9.05e-09 14.8293 1.46e-08 -phiX174 4306 4317 1 + + 9.05e-09 14.7927 1.47e-08 -phiX174 4302 4313 1 + + 9.19e-09 14.6585 1.52e-08 -phiX174 5032 5043 1 + + 9.41e-09 14.561 1.58e-08 -phiX174 2578 2589 1 + + 1.01e-08 14.2927 1.73e-08 -phiX174 321 332 1 + + 1.05e-08 14.1951 1.82e-08 -phiX174 5000 5011 1 + + 1.19e-08 13.8902 2.09e-08 -phiX174 4216 4227 1 + + 1.2e-08 13.8171 2.15e-08 -phiX174 4261 4272 1 + + 1.2e-08 13.7805 2.18e-08 -phiX174 3568 3579 1 + + 1.22e-08 13.7073 2.26e-08 -phiX174 193 204 1 + + 1.22e-08 13.6829 2.29e-08 -phiX174 130 141 1 + + 1.31e-08 13.4756 2.49e-08 -phiX174 1490 1501 1 + + 1.32e-08 13.4024 2.55e-08 -phiX174 433 444 1 + + 1.36e-08 13.2805 2.67e-08 -phiX174 4564 4575 1 + + 1.36e-08 13.2439 2.73e-08 -phiX174 101 112 1 + + 1.36e-08 13.2195 2.75e-08 -phiX174 902 913 1 + + 1.38e-08 13.1463 2.82e-08 -phiX174 4747 4758 1 + + 1.45e-08 12.9756 3.01e-08 -phiX174 2621 2632 1 + + 1.5e-08 12.8659 3.16e-08 -phiX174 466 477 1 + + 1.57e-08 12.7317 3.35e-08 -phiX174 4032 4043 1 + + 1.58e-08 12.6829 3.44e-08 -phiX174 1347 1358 1 + + 1.58e-08 12.6707 3.46e-08 -phiX174 238 249 1 + + 1.64e-08 12.5732 3.62e-08 -phiX174 499 510 1 + + 1.71e-08 12.4634 3.84e-08 -phiX174 3000 3011 1 + + 1.73e-08 12.4146 3.93e-08 -phiX174 3775 3786 1 + + 1.73e-08 12.378 3.98e-08 -phiX174 2025 2036 1 + + 1.75e-08 12.3293 4.06e-08 -phiX174 4236 4247 1 + + 1.75e-08 12.3049 4.12e-08 -phiX174 802 813 1 + + 1.78e-08 12.2439 4.24e-08 -phiX174 3769 3780 1 + + 1.81e-08 12.1829 4.35e-08 -phiX174 3428 3439 1 + + 1.82e-08 12.122 4.45e-08 -phiX174 98 109 1 + + 1.82e-08 12.1098 4.48e-08 -phiX174 66 77 1 + + 1.92e-08 11.9268 4.78e-08 -phiX174 5331 5342 1 + + 2.01e-08 11.7195 5.13e-08 -phiX174 276 287 1 + + 2.01e-08 11.7073 5.14e-08 -phiX174 4337 4348 1 + + 2.01e-08 11.6951 5.18e-08 -phiX174 3811 3822 1 + + 2.03e-08 11.6585 5.28e-08 -phiX174 1908 1919 1 + + 2.08e-08 11.5488 5.51e-08 -phiX174 2999 3010 1 + + 2.08e-08 11.5366 5.54e-08 -phiX174 3890 3901 1 + + 2.11e-08 11.439 5.75e-08 -phiX174 3078 3089 1 + + 2.11e-08 11.4268 5.76e-08 -phiX174 36 47 1 + + 2.11e-08 11.4146 5.79e-08 -phiX174 379 390 1 + + 2.17e-08 11.3293 6.01e-08
--- a/test-data/fimo_output_interval_2.txt Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#chr start end pattern name score strand matched sequence p-value q-value -phiX174 1387 1398 1 + + 0 29.4024 6.36e-11 -phiX174 846 857 1 + + 0 29.122 7.02e-11 -phiX174 2300 2311 1 + + 0 27.6463 1.08e-10 -phiX174 5062 5073 1 + + 0 25.5366 2.73e-10 -phiX174 988 999 1 + + 0 25.3049 3.15e-10 -phiX174 4712 4723 1 + + 0 23.622 7.74e-10 -phiX174 5047 5058 1 + + 0 23.3293 8.51e-10 -phiX174 854 865 1 + + 0 23.3049 8.64e-10 -phiX174 3154 3165 1 + + 0 23.0366 9.76e-10 -phiX174 5008 5019 1 + + 0 23.0366 9.76e-10 -phiX174 813 824 1 + + 0 22.5854 1.28e-09 -phiX174 2831 2842 1 + + 0 22.3415 1.42e-09 -phiX174 3829 3840 1 + + 0 21.8293 1.7e-09 -phiX174 3559 3570 1 + + 0 21.5976 1.89e-09 -phiX174 2881 2892 1 + + 0 21.1951 2.29e-09 -phiX174 4452 4463 1 + + 0 20.8902 2.58e-09 -phiX174 2492 2503 1 + + 0 20.3415 3.06e-09 -phiX174 4103 4114 1 + + 0 20.3171 3.08e-09 -phiX174 4954 4965 1 + + 0 20.3171 3.08e-09 -phiX174 1884 1895 1 + + 0 19.9268 3.61e-09 -phiX174 3375 3386 1 + + 0 19.7683 3.81e-09 -phiX174 51 62 1 + + 0 19.5732 4.06e-09 -phiX174 1389 1400 1 + + 0 19.378 4.26e-09 -phiX174 2016 2027 1 + + 0 19.0854 4.6e-09 -phiX174 999 1010 1 + + 0 18.878 4.88e-09 -phiX174 1554 1565 1 + + 0 18.439 5.58e-09 -phiX174 4429 4440 1 + + 0 18.4268 5.62e-09 -phiX174 1926 1937 1 + + 0 18.2927 5.82e-09 -phiX174 2980 2991 1 + + 0 18.0732 6.13e-09 -phiX174 4202 4213 1 + + 0 17.9268 6.34e-09 -phiX174 1668 1679 1 + + 0 17.8659 6.4e-09 -phiX174 3259 3270 1 + + 0 17.5 7.01e-09 -phiX174 3046 3057 1 + + 0 17.2805 7.4e-09 -phiX174 4175 4186 1 + + 0 17.1829 7.6e-09 -phiX174 4117 4128 1 + + 0 17.1341 7.7e-09 -phiX174 5369 5380 1 + + 0 16.9878 8.03e-09 -phiX174 1241 1252 1 + + 0 16.5122 8.94e-09 -phiX174 2582 2593 1 + + 0 16.5122 8.94e-09 -phiX174 697 708 1 + + 0 16.4146 9.13e-09 -phiX174 2298 2309 1 + + 0 16.3537 9.26e-09 -phiX174 4188 4199 1 + + 0 16.1707 9.69e-09 -phiX174 274 285 1 + + 0 16.0976 9.85e-09 -phiX174 1800 1811 1 + + 0 16.0366 1e-08 -phiX174 1385 1396 1 + + 0 15.9268 1.03e-08 -phiX174 1302 1313 1 + + 0 15.9024 1.03e-08 -phiX174 3771 3782 1 + + 0 15.878 1.04e-08 -phiX174 1287 1298 1 + + 0 15.8659 1.04e-08 -phiX174 2576 2587 1 + + 0 15.7683 1.08e-08 -phiX174 936 947 1 + + 0 15.7561 1.08e-08 -phiX174 903 914 1 + + 0 15.6585 1.11e-08 -phiX174 2278 2289 1 + + 0 15.5854 1.13e-08 -phiX174 3163 3174 1 + + 0 15.5 1.16e-08 -phiX174 23 34 1 + + 0 15.3293 1.23e-08 -phiX174 837 848 1 + + 0 15.2561 1.27e-08 -phiX174 852 863 1 + + 0 15.2561 1.27e-08 -phiX174 1983 1994 1 + + 0 15.0244 1.36e-08 -phiX174 0 11 1 + + 0 14.8293 1.46e-08 -phiX174 4306 4317 1 + + 0 14.7927 1.47e-08 -phiX174 4302 4313 1 + + 0 14.6585 1.52e-08 -phiX174 5032 5043 1 + + 0 14.561 1.58e-08 -phiX174 2578 2589 1 + + 0 14.2927 1.73e-08 -phiX174 321 332 1 + + 0 14.1951 1.82e-08 -phiX174 5000 5011 1 + + 0 13.8902 2.09e-08 -phiX174 4216 4227 1 + + 0 13.8171 2.15e-08 -phiX174 4261 4272 1 + + 0 13.7805 2.18e-08 -phiX174 3568 3579 1 + + 0 13.7073 2.26e-08 -phiX174 193 204 1 + + 0 13.6829 2.29e-08 -phiX174 130 141 1 + + 0 13.4756 2.49e-08 -phiX174 1490 1501 1 + + 0 13.4024 2.55e-08 -phiX174 433 444 1 + + 0 13.2805 2.67e-08 -phiX174 4564 4575 1 + + 0 13.2439 2.73e-08 -phiX174 101 112 1 + + 0 13.2195 2.75e-08 -phiX174 902 913 1 + + 0 13.1463 2.82e-08 -phiX174 4747 4758 1 + + 0 12.9756 3.01e-08 -phiX174 2621 2632 1 + + 0 12.8659 3.16e-08 -phiX174 466 477 1 + + 0 12.7317 3.35e-08 -phiX174 4032 4043 1 + + 0 12.6829 3.44e-08 -phiX174 1347 1358 1 + + 0 12.6707 3.46e-08 -phiX174 238 249 1 + + 0 12.5732 3.62e-08 -phiX174 499 510 1 + + 0 12.4634 3.84e-08 -phiX174 3000 3011 1 + + 0 12.4146 3.93e-08 -phiX174 3775 3786 1 + + 0 12.378 3.98e-08 -phiX174 2025 2036 1 + + 0 12.3293 4.06e-08 -phiX174 4236 4247 1 + + 0 12.3049 4.12e-08 -phiX174 802 813 1 + + 0 12.2439 4.24e-08 -phiX174 3769 3780 1 + + 0 12.1829 4.35e-08 -phiX174 3428 3439 1 + + 0 12.122 4.45e-08 -phiX174 98 109 1 + + 0 12.1098 4.48e-08 -phiX174 66 77 1 + + 0 11.9268 4.78e-08 -phiX174 5331 5342 1 + + 0 11.7195 5.13e-08 -phiX174 276 287 1 + + 0 11.7073 5.14e-08 -phiX174 4337 4348 1 + + 0 11.6951 5.18e-08 -phiX174 3811 3822 1 + + 0 11.6585 5.28e-08 -phiX174 1908 1919 1 + + 0 11.5488 5.51e-08 -phiX174 2999 3010 1 + + 0 11.5366 5.54e-08 -phiX174 3890 3901 1 + + 0 11.439 5.75e-08 -phiX174 3078 3089 1 + + 0 11.4268 5.76e-08 -phiX174 36 47 1 + + 0 11.4146 5.79e-08 -phiX174 379 390 1 + + 0 11.3293 6.01e-08
--- a/test-data/fimo_output_txt_1.txt Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#pattern name sequence name start stop strand score p-value q-value matched sequence -1 phiX174 1388 1398 + 29.4024 6.36e-11 1.25e-09 AATATCTATAA -1 phiX174 847 857 + 29.122 7.02e-11 1.25e-09 AATGTCTAAAG -1 phiX174 2301 2311 + 27.6463 1.08e-10 1.29e-09 AGGTTATAACG -1 phiX174 5063 5073 + 25.5366 2.73e-10 2.25e-09 AGGAGCTAAAG -1 phiX174 989 999 + 25.3049 3.15e-10 2.25e-09 TGAGGATAAAT -1 phiX174 4713 4723 + 23.622 7.74e-10 3.48e-09 GACTGCTATCA -1 phiX174 5048 5058 + 23.3293 8.51e-10 3.48e-09 TGCTGCTAAAG -1 phiX174 855 865 + 23.3049 8.64e-10 3.48e-09 AAGGTAAAAAA -1 phiX174 3155 3165 + 23.0366 9.76e-10 3.48e-09 TATGGCTAAAG -1 phiX174 5009 5019 + 23.0366 9.76e-10 3.48e-09 TGTGGCTAAAT -1 phiX174 814 824 + 22.5854 1.28e-09 4.14e-09 TGCGTCAAAAA -1 phiX174 2832 2842 + 22.3415 1.42e-09 4.23e-09 TTGGTCTAACT -1 phiX174 3830 3840 + 21.8293 1.7e-09 4.68e-09 TATTGATAAAG -1 phiX174 3560 3570 + 21.5976 1.89e-09 4.82e-09 TGCGTCTATTA -1 phiX174 2882 2892 + 21.1951 2.29e-09 5.46e-09 AGGTTATTAAA -1 phiX174 4453 4463 + 20.8902 2.58e-09 5.75e-09 AAGGTATTAAG -1 phiX174 2493 2503 + 20.3415 3.06e-09 5.79e-09 GACACCTAAAG -1 phiX174 4104 4114 + 20.3171 3.08e-09 5.79e-09 GGCTTCCATAA -1 phiX174 4955 4965 + 20.3171 3.08e-09 5.79e-09 TGATGCTAAAG -1 phiX174 1885 1895 + 19.9268 3.61e-09 6.45e-09 TGCGACTAAAG -1 phiX174 3376 3386 + 19.7683 3.81e-09 6.48e-09 AGAATCAAAAA -1 phiX174 52 62 + 19.5732 4.06e-09 6.58e-09 TGAGTCGAAAA -1 phiX174 1390 1400 + 19.378 4.26e-09 6.61e-09 TATCTATAACA -1 phiX174 2017 2027 + 19.0854 4.6e-09 6.85e-09 TTCGTCTAAGA -1 phiX174 1000 1010 + 18.878 4.88e-09 6.97e-09 TATGTCTAATA -1 phiX174 1555 1565 + 18.439 5.58e-09 7.37e-09 GACTTCTACCA -1 phiX174 4430 4440 + 18.4268 5.62e-09 7.37e-09 TGAGTATAATT -1 phiX174 1927 1937 + 18.2927 5.82e-09 7.37e-09 GACTTATACCG -1 phiX174 2981 2991 + 18.0732 6.13e-09 7.37e-09 CATGTCTAAAT -1 phiX174 4203 4213 + 17.9268 6.34e-09 7.37e-09 GACGGCCATAA -1 phiX174 1669 1679 + 17.8659 6.4e-09 7.37e-09 TGGAGGTAAAA -1 phiX174 3260 3270 + 17.5 7.01e-09 7.82e-09 CGCTGATAAAG -1 phiX174 3047 3057 + 17.2805 7.4e-09 7.85e-09 TACCGATAACA -1 phiX174 4176 4186 + 17.1829 7.6e-09 7.85e-09 GAGTTCGATAA -1 phiX174 4118 4128 + 17.1341 7.7e-09 7.85e-09 GATGGATAACC -1 phiX174 5370 5380 + 16.9878 8.03e-09 7.87e-09 GGCGTATCCAA -1 phiX174 1242 1252 + 16.5122 8.94e-09 7.87e-09 AGTGGATTAAG -1 phiX174 2583 2593 + 16.5122 8.94e-09 7.87e-09 TACATCTGTCA -1 phiX174 698 708 + 16.4146 9.13e-09 7.87e-09 TACGGAAAACA -1 phiX174 2299 2309 + 16.3537 9.26e-09 7.87e-09 TGAGGTTATAA -1 phiX174 4189 4199 + 16.1707 9.69e-09 7.87e-09 GTGATATGTAT -1 phiX174 275 285 + 16.0976 9.85e-09 7.87e-09 GGTTTAGATAT -1 phiX174 1801 1811 + 16.0366 1e-08 7.87e-09 GACCTATAAAC -1 phiX174 1386 1396 + 15.9268 1.03e-08 7.87e-09 TGAATATCTAT -1 phiX174 1303 1313 + 15.9024 1.03e-08 7.87e-09 TGGTTATATTG -1 phiX174 3772 3782 + 15.878 1.04e-08 7.87e-09 AGGATATTTCT -1 phiX174 1288 1298 + 15.8659 1.04e-08 7.87e-09 GACTGTTAACA -1 phiX174 2577 2587 + 15.7683 1.08e-08 7.87e-09 GATGGATACAT -1 phiX174 937 947 + 15.7561 1.08e-08 7.87e-09 TTGGTATGTAG -1 phiX174 904 914 + 15.6585 1.11e-08 7.93e-09 AGGTACTAAAG -1 phiX174 2279 2289 + 15.5854 1.13e-08 7.93e-09 TCGTGATAAAA -1 phiX174 3164 3174 + 15.5 1.16e-08 7.98e-09 AGCTGGTAAAG -1 phiX174 24 34 + 15.3293 1.23e-08 8.24e-09 AGAAGTTAACA -1 phiX174 838 848 + 15.2561 1.27e-08 8.24e-09 GAGTGATGTAA -1 phiX174 853 863 + 15.2561 1.27e-08 8.24e-09 TAAAGGTAAAA -1 phiX174 1984 1994 + 15.0244 1.36e-08 8.68e-09 AATTTCTATGA -1 phiX174 1 11 + 14.8293 1.46e-08 9.05e-09 GAGTTTTATCG -1 phiX174 4307 4317 + 14.7927 1.47e-08 9.05e-09 TATTAATAACA -1 phiX174 4303 4313 + 14.6585 1.52e-08 9.19e-09 TTGATATTAAT -1 phiX174 5033 5043 + 14.561 1.58e-08 9.41e-09 GTCAGATATGG -1 phiX174 2579 2589 + 14.2927 1.73e-08 1.01e-08 TGGATACATCT -1 phiX174 322 332 + 14.1951 1.82e-08 1.05e-08 GACATTTTAAA -1 phiX174 5001 5011 + 13.8902 2.09e-08 1.19e-08 GGTTTCTATGT -1 phiX174 4217 4227 + 13.8171 2.15e-08 1.2e-08 TGCTTCTGACG -1 phiX174 4262 4272 + 13.7805 2.18e-08 1.2e-08 AATGGATGAAT -1 phiX174 3569 3579 + 13.7073 2.26e-08 1.22e-08 TATGGAAAACA -1 phiX174 194 204 + 13.6829 2.29e-08 1.22e-08 ATCAACTAACG -1 phiX174 131 141 + 13.4756 2.49e-08 1.31e-08 AAATGAGAAAA -1 phiX174 1491 1501 + 13.4024 2.55e-08 1.32e-08 GCCATCTCAAA -1 phiX174 434 444 + 13.2805 2.67e-08 1.36e-08 GGCCTCTATTA -1 phiX174 4565 4575 + 13.2439 2.73e-08 1.36e-08 TTGGTTTATCG -1 phiX174 102 112 + 13.2195 2.75e-08 1.36e-08 GAATTAAATCG -1 phiX174 903 913 + 13.1463 2.82e-08 1.38e-08 GAGGTACTAAA -1 phiX174 4748 4758 + 12.9756 3.01e-08 1.45e-08 TACAGCTAATG -1 phiX174 2622 2632 + 12.8659 3.16e-08 1.5e-08 TGCTGATATTG -1 phiX174 467 477 + 12.7317 3.35e-08 1.57e-08 TTTGGATTTAA -1 phiX174 4033 4043 + 12.6829 3.44e-08 1.58e-08 AGCGTATCGAG -1 phiX174 1348 1358 + 12.6707 3.46e-08 1.58e-08 TACCAATAAAA -1 phiX174 239 249 + 12.5732 3.62e-08 1.64e-08 AGTGGCTTAAT -1 phiX174 500 510 + 12.4634 3.84e-08 1.71e-08 GACGAGTAACA -1 phiX174 3001 3011 + 12.4146 3.93e-08 1.73e-08 GCGGTCAAAAA -1 phiX174 3776 3786 + 12.378 3.98e-08 1.73e-08 TATTTCTAATG -1 phiX174 2026 2036 + 12.3293 4.06e-08 1.75e-08 GAAGTTTAAGA -1 phiX174 4237 4247 + 12.3049 4.12e-08 1.75e-08 AGTTTGTATCT -1 phiX174 803 813 + 12.2439 4.24e-08 1.78e-08 AGAAGAAAACG -1 phiX174 3770 3780 + 12.1829 4.35e-08 1.81e-08 AAAGGATATTT -1 phiX174 3429 3439 + 12.122 4.45e-08 1.82e-08 GAGATGCAAAA -1 phiX174 99 109 + 12.1098 4.48e-08 1.82e-08 TACGAATTAAA -1 phiX174 67 77 + 11.9268 4.78e-08 1.92e-08 TCTTGATAAAG -1 phiX174 5332 5342 + 11.7195 5.13e-08 2.01e-08 ATCTGCTCAAA -1 phiX174 277 287 + 11.7073 5.14e-08 2.01e-08 TTTAGATATGA -1 phiX174 4338 4348 + 11.6951 5.18e-08 2.01e-08 GGGGACGAAAA -1 phiX174 3812 3822 + 11.6585 5.28e-08 2.03e-08 GGTTGATATTT -1 phiX174 1909 1919 + 11.5488 5.51e-08 2.08e-08 TAACGCTAAAG -1 phiX174 3000 3010 + 11.5366 5.54e-08 2.08e-08 GGCGGTCAAAA -1 phiX174 3891 3901 + 11.439 5.75e-08 2.11e-08 ATTGGCTCTAA -1 phiX174 3079 3089 + 11.4268 5.76e-08 2.11e-08 CTGGTATTAAA -1 phiX174 37 47 + 11.4146 5.79e-08 2.11e-08 TTCGGATATTT -1 phiX174 380 390 + 11.3293 6.01e-08 2.17e-08 GTAAGAAATCA
--- a/test-data/fimo_output_txt_2.txt Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -#pattern name sequence name start stop strand score p-value q-value matched sequence -1 phiX174 1388 1398 + 29.4024 6.36e-11 0 AATATCTATAA -1 phiX174 847 857 + 29.122 7.02e-11 0 AATGTCTAAAG -1 phiX174 2301 2311 + 27.6463 1.08e-10 0 AGGTTATAACG -1 phiX174 5063 5073 + 25.5366 2.73e-10 0 AGGAGCTAAAG -1 phiX174 989 999 + 25.3049 3.15e-10 0 TGAGGATAAAT -1 phiX174 4713 4723 + 23.622 7.74e-10 0 GACTGCTATCA -1 phiX174 5048 5058 + 23.3293 8.51e-10 0 TGCTGCTAAAG -1 phiX174 855 865 + 23.3049 8.64e-10 0 AAGGTAAAAAA -1 phiX174 3155 3165 + 23.0366 9.76e-10 0 TATGGCTAAAG -1 phiX174 5009 5019 + 23.0366 9.76e-10 0 TGTGGCTAAAT -1 phiX174 814 824 + 22.5854 1.28e-09 0 TGCGTCAAAAA -1 phiX174 2832 2842 + 22.3415 1.42e-09 0 TTGGTCTAACT -1 phiX174 3830 3840 + 21.8293 1.7e-09 0 TATTGATAAAG -1 phiX174 3560 3570 + 21.5976 1.89e-09 0 TGCGTCTATTA -1 phiX174 2882 2892 + 21.1951 2.29e-09 0 AGGTTATTAAA -1 phiX174 4453 4463 + 20.8902 2.58e-09 0 AAGGTATTAAG -1 phiX174 2493 2503 + 20.3415 3.06e-09 0 GACACCTAAAG -1 phiX174 4104 4114 + 20.3171 3.08e-09 0 GGCTTCCATAA -1 phiX174 4955 4965 + 20.3171 3.08e-09 0 TGATGCTAAAG -1 phiX174 1885 1895 + 19.9268 3.61e-09 0 TGCGACTAAAG -1 phiX174 3376 3386 + 19.7683 3.81e-09 0 AGAATCAAAAA -1 phiX174 52 62 + 19.5732 4.06e-09 0 TGAGTCGAAAA -1 phiX174 1390 1400 + 19.378 4.26e-09 0 TATCTATAACA -1 phiX174 2017 2027 + 19.0854 4.6e-09 0 TTCGTCTAAGA -1 phiX174 1000 1010 + 18.878 4.88e-09 0 TATGTCTAATA -1 phiX174 1555 1565 + 18.439 5.58e-09 0 GACTTCTACCA -1 phiX174 4430 4440 + 18.4268 5.62e-09 0 TGAGTATAATT -1 phiX174 1927 1937 + 18.2927 5.82e-09 0 GACTTATACCG -1 phiX174 2981 2991 + 18.0732 6.13e-09 0 CATGTCTAAAT -1 phiX174 4203 4213 + 17.9268 6.34e-09 0 GACGGCCATAA -1 phiX174 1669 1679 + 17.8659 6.4e-09 0 TGGAGGTAAAA -1 phiX174 3260 3270 + 17.5 7.01e-09 0 CGCTGATAAAG -1 phiX174 3047 3057 + 17.2805 7.4e-09 0 TACCGATAACA -1 phiX174 4176 4186 + 17.1829 7.6e-09 0 GAGTTCGATAA -1 phiX174 4118 4128 + 17.1341 7.7e-09 0 GATGGATAACC -1 phiX174 5370 5380 + 16.9878 8.03e-09 0 GGCGTATCCAA -1 phiX174 1242 1252 + 16.5122 8.94e-09 0 AGTGGATTAAG -1 phiX174 2583 2593 + 16.5122 8.94e-09 0 TACATCTGTCA -1 phiX174 698 708 + 16.4146 9.13e-09 0 TACGGAAAACA -1 phiX174 2299 2309 + 16.3537 9.26e-09 0 TGAGGTTATAA -1 phiX174 4189 4199 + 16.1707 9.69e-09 0 GTGATATGTAT -1 phiX174 275 285 + 16.0976 9.85e-09 0 GGTTTAGATAT -1 phiX174 1801 1811 + 16.0366 1e-08 0 GACCTATAAAC -1 phiX174 1386 1396 + 15.9268 1.03e-08 0 TGAATATCTAT -1 phiX174 1303 1313 + 15.9024 1.03e-08 0 TGGTTATATTG -1 phiX174 3772 3782 + 15.878 1.04e-08 0 AGGATATTTCT -1 phiX174 1288 1298 + 15.8659 1.04e-08 0 GACTGTTAACA -1 phiX174 2577 2587 + 15.7683 1.08e-08 0 GATGGATACAT -1 phiX174 937 947 + 15.7561 1.08e-08 0 TTGGTATGTAG -1 phiX174 904 914 + 15.6585 1.11e-08 0 AGGTACTAAAG -1 phiX174 2279 2289 + 15.5854 1.13e-08 0 TCGTGATAAAA -1 phiX174 3164 3174 + 15.5 1.16e-08 0 AGCTGGTAAAG -1 phiX174 24 34 + 15.3293 1.23e-08 0 AGAAGTTAACA -1 phiX174 838 848 + 15.2561 1.27e-08 0 GAGTGATGTAA -1 phiX174 853 863 + 15.2561 1.27e-08 0 TAAAGGTAAAA -1 phiX174 1984 1994 + 15.0244 1.36e-08 0 AATTTCTATGA -1 phiX174 1 11 + 14.8293 1.46e-08 0 GAGTTTTATCG -1 phiX174 4307 4317 + 14.7927 1.47e-08 0 TATTAATAACA -1 phiX174 4303 4313 + 14.6585 1.52e-08 0 TTGATATTAAT -1 phiX174 5033 5043 + 14.561 1.58e-08 0 GTCAGATATGG -1 phiX174 2579 2589 + 14.2927 1.73e-08 0 TGGATACATCT -1 phiX174 322 332 + 14.1951 1.82e-08 0 GACATTTTAAA -1 phiX174 5001 5011 + 13.8902 2.09e-08 0 GGTTTCTATGT -1 phiX174 4217 4227 + 13.8171 2.15e-08 0 TGCTTCTGACG -1 phiX174 4262 4272 + 13.7805 2.18e-08 0 AATGGATGAAT -1 phiX174 3569 3579 + 13.7073 2.26e-08 0 TATGGAAAACA -1 phiX174 194 204 + 13.6829 2.29e-08 0 ATCAACTAACG -1 phiX174 131 141 + 13.4756 2.49e-08 0 AAATGAGAAAA -1 phiX174 1491 1501 + 13.4024 2.55e-08 0 GCCATCTCAAA -1 phiX174 434 444 + 13.2805 2.67e-08 0 GGCCTCTATTA -1 phiX174 4565 4575 + 13.2439 2.73e-08 0 TTGGTTTATCG -1 phiX174 102 112 + 13.2195 2.75e-08 0 GAATTAAATCG -1 phiX174 903 913 + 13.1463 2.82e-08 0 GAGGTACTAAA -1 phiX174 4748 4758 + 12.9756 3.01e-08 0 TACAGCTAATG -1 phiX174 2622 2632 + 12.8659 3.16e-08 0 TGCTGATATTG -1 phiX174 467 477 + 12.7317 3.35e-08 0 TTTGGATTTAA -1 phiX174 4033 4043 + 12.6829 3.44e-08 0 AGCGTATCGAG -1 phiX174 1348 1358 + 12.6707 3.46e-08 0 TACCAATAAAA -1 phiX174 239 249 + 12.5732 3.62e-08 0 AGTGGCTTAAT -1 phiX174 500 510 + 12.4634 3.84e-08 0 GACGAGTAACA -1 phiX174 3001 3011 + 12.4146 3.93e-08 0 GCGGTCAAAAA -1 phiX174 3776 3786 + 12.378 3.98e-08 0 TATTTCTAATG -1 phiX174 2026 2036 + 12.3293 4.06e-08 0 GAAGTTTAAGA -1 phiX174 4237 4247 + 12.3049 4.12e-08 0 AGTTTGTATCT -1 phiX174 803 813 + 12.2439 4.24e-08 0 AGAAGAAAACG -1 phiX174 3770 3780 + 12.1829 4.35e-08 0 AAAGGATATTT -1 phiX174 3429 3439 + 12.122 4.45e-08 0 GAGATGCAAAA -1 phiX174 99 109 + 12.1098 4.48e-08 0 TACGAATTAAA -1 phiX174 67 77 + 11.9268 4.78e-08 0 TCTTGATAAAG -1 phiX174 5332 5342 + 11.7195 5.13e-08 0 ATCTGCTCAAA -1 phiX174 277 287 + 11.7073 5.14e-08 0 TTTAGATATGA -1 phiX174 4338 4348 + 11.6951 5.18e-08 0 GGGGACGAAAA -1 phiX174 3812 3822 + 11.6585 5.28e-08 0 GGTTGATATTT -1 phiX174 1909 1919 + 11.5488 5.51e-08 0 TAACGCTAAAG -1 phiX174 3000 3010 + 11.5366 5.54e-08 0 GGCGGTCAAAA -1 phiX174 3891 3901 + 11.439 5.75e-08 0 ATTGGCTCTAA -1 phiX174 3079 3089 + 11.4268 5.76e-08 0 CTGGTATTAAA -1 phiX174 37 47 + 11.4146 5.79e-08 0 TTCGGATATTT -1 phiX174 380 390 + 11.3293 6.01e-08 0 GTAAGAAATCA
--- a/test-data/fimo_output_xml_1.xml Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -<?xml version="1.0" encoding="UTF-8" standalone="no"?> -<!-- Begin document body --> -<fimo version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000"> - xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" -> -<command-line>fimo --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1973/dataset_2713_files --verbosity 1 /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</command-line> -<settings> -<setting name="output directory">/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1973/dataset_2713_files</setting> -<setting name="MEME file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat</setting> -<setting name="sequence file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</setting> -<setting name="allow clobber">false</setting> -<setting name="compute q-values">true</setting> -<setting name="parse genomic coord.">false</setting> -<setting name="text only">false</setting> -<setting name="scan both strands">false</setting> -<setting name="output threshold">0.0001</setting> -<setting name="threshold type">p-value</setting> -<setting name="max stored scores">100000</setting> -<setting name="pseudocount">0.1</setting> -<setting name="verbosity">1</setting> -</settings> -<sequence-data num-sequences="1" num-residues="5386" /> -<alphabet name="Protein" like="protein"> -<letter id="A" symbol="A" name="Alanine" colour="0000CC"/> -<letter id="C" symbol="C" name="Cysteine" colour="0000CC"/> -<letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/> -<letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/> -<letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/> -<letter id="G" symbol="G" name="Glycine" colour="FFB300"/> -<letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/> -<letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/> -<letter id="K" symbol="K" name="Lysine" colour="CC0000"/> -<letter id="L" symbol="L" name="Leucine" colour="0000CC"/> -<letter id="M" symbol="M" name="Methionine" colour="0000CC"/> -<letter id="N" symbol="N" name="Asparagine" colour="008000"/> -<letter id="P" symbol="P" name="Proline" colour="FFFF00"/> -<letter id="Q" symbol="Q" name="Glutamine" colour="008000"/> -<letter id="R" symbol="R" name="Arginine" colour="CC0000"/> -<letter id="S" symbol="S" name="Serine" colour="008000"/> -<letter id="T" symbol="T" name="Threonine" colour="008000"/> -<letter id="V" symbol="V" name="Valine" colour="0000CC"/> -<letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/> -<letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/> -<letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/> -<letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/> -<letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/> -<letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/> -</alphabet> -<motif name="1" width="11" best-possible-match="GGGGTATAAAA"/> -<background source="non-redundant database"> -<value letter="A">0.073</value> -<value letter="C">0.018</value> -<value letter="D">0.052</value> -<value letter="E">0.062</value> -<value letter="F">0.040</value> -<value letter="G">0.069</value> -<value letter="H">0.022</value> -<value letter="I">0.056</value> -<value letter="K">0.058</value> -<value letter="L">0.092</value> -<value letter="M">0.023</value> -<value letter="N">0.046</value> -<value letter="P">0.051</value> -<value letter="Q">0.041</value> -<value letter="R">0.052</value> -<value letter="S">0.074</value> -<value letter="T">0.059</value> -<value letter="V">0.064</value> -<value letter="W">0.013</value> -<value letter="Y">0.033</value> -</background> -<cisml-file>cisml.xml</cisml-file> -</fimo>
--- a/test-data/fimo_output_xml_2.xml Fri Mar 18 08:23:54 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,74 +0,0 @@ -<?xml version="1.0" encoding="UTF-8" standalone="no"?> -<!-- Begin document body --> -<fimo version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000"> - xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" - xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo" -> -<command-line>fimo --alpha 1.000000 --max-stored-scores 100000 --motif-pseudo 0.100000 --no-qvalue --thresh 0.000100 --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files --verbosity 1 /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</command-line> -<settings> -<setting name="output directory">/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files</setting> -<setting name="MEME file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat</setting> -<setting name="sequence file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</setting> -<setting name="allow clobber">false</setting> -<setting name="compute q-values">false</setting> -<setting name="parse genomic coord.">false</setting> -<setting name="text only">false</setting> -<setting name="scan both strands">false</setting> -<setting name="output threshold">0.0001</setting> -<setting name="threshold type">p-value</setting> -<setting name="max stored scores">100000</setting> -<setting name="pseudocount">0.1</setting> -<setting name="verbosity">1</setting> -</settings> -<sequence-data num-sequences="1" num-residues="5386" /> -<alphabet name="Protein" like="protein"> -<letter id="A" symbol="A" name="Alanine" colour="0000CC"/> -<letter id="C" symbol="C" name="Cysteine" colour="0000CC"/> -<letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/> -<letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/> -<letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/> -<letter id="G" symbol="G" name="Glycine" colour="FFB300"/> -<letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/> -<letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/> -<letter id="K" symbol="K" name="Lysine" colour="CC0000"/> -<letter id="L" symbol="L" name="Leucine" colour="0000CC"/> -<letter id="M" symbol="M" name="Methionine" colour="0000CC"/> -<letter id="N" symbol="N" name="Asparagine" colour="008000"/> -<letter id="P" symbol="P" name="Proline" colour="FFFF00"/> -<letter id="Q" symbol="Q" name="Glutamine" colour="008000"/> -<letter id="R" symbol="R" name="Arginine" colour="CC0000"/> -<letter id="S" symbol="S" name="Serine" colour="008000"/> -<letter id="T" symbol="T" name="Threonine" colour="008000"/> -<letter id="V" symbol="V" name="Valine" colour="0000CC"/> -<letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/> -<letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/> -<letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/> -<letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/> -<letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/> -<letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/> -</alphabet> -<motif name="1" width="11" best-possible-match="GGGGTATAAAA"/> -<background source="non-redundant database"> -<value letter="A">0.073</value> -<value letter="C">0.018</value> -<value letter="D">0.052</value> -<value letter="E">0.062</value> -<value letter="F">0.040</value> -<value letter="G">0.069</value> -<value letter="H">0.022</value> -<value letter="I">0.056</value> -<value letter="K">0.058</value> -<value letter="L">0.092</value> -<value letter="M">0.023</value> -<value letter="N">0.046</value> -<value letter="P">0.051</value> -<value letter="Q">0.041</value> -<value letter="R">0.052</value> -<value letter="S">0.074</value> -<value letter="T">0.059</value> -<value letter="V">0.064</value> -<value letter="W">0.013</value> -<value letter="Y">0.033</value> -</background> -<cisml-file>cisml.xml</cisml-file> -</fimo>
--- a/test-data/meme_output_html_1.html Fri Mar 18 08:23:54 2016 -0400 +++ b/test-data/meme_output_html_1.html Fri Jun 17 13:16:52 2016 -0400 @@ -12,9 +12,6 @@ "stop_reason": "Stopped because requested number of motifs (1) found.", "cmd": [ "meme", - "/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat", - "-o", - "/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1912/dataset_2530_files", "-nostatus" ], "options": {
--- a/test-data/meme_output_html_2.html Fri Mar 18 08:23:54 2016 -0400 +++ b/test-data/meme_output_html_2.html Fri Jun 17 13:16:52 2016 -0400 @@ -12,15 +12,6 @@ "stop_reason": "Stopped because requested number of motifs (1) found.", "cmd": [ "meme", - "/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat", - "-o", - "/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1929/dataset_2578_files", - "-nostatus", "-sf", "Galaxy_FASTA_Input", "-dna", "-mod", "zoops", - "-nmotifs", "1", "-wnsites", "0.8", "-minw", "8", "-maxw", "50", - "-wg", "11", "-ws", "1", "-maxiter", "50", "-distance", "0.001", - "-prior", "dirichlet", "-b", "0.01", "-plib", - "/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2577.dat", - "-spmap", "uni", "-spfuzz", "0.5" ], "options": { "mod": "zoops",
--- a/test-data/meme_output_txt_1.txt Fri Mar 18 08:23:54 2016 -0400 +++ b/test-data/meme_output_txt_1.txt Fri Jun 17 13:16:52 2016 -0400 @@ -28,7 +28,7 @@ ******************************************************************************** TRAINING SET ******************************************************************************** -DATAFILE= /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat +DATAFILE= ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ @@ -55,7 +55,7 @@ This information can also be useful in the event you wish to report a problem with the MEME software. -command: meme /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat -o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1912/dataset_2530_files -nostatus +command: meme model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values @@ -267,7 +267,7 @@ -Time 0.53 secs. +Time ******************************************************************************** @@ -320,6 +320,6 @@ Stopped because requested number of motifs (1) found. ******************************************************************************** -CPU: MacBook-Pro-2.local +CPU: ********************************************************************************
--- a/test-data/meme_output_txt_2.txt Fri Mar 18 08:23:54 2016 -0400 +++ b/test-data/meme_output_txt_2.txt Fri Jun 17 13:16:52 2016 -0400 @@ -55,7 +55,7 @@ This information can also be useful in the event you wish to report a problem with the MEME software. -command: meme /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat -o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1929/dataset_2578_files -nostatus -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2577.dat -spmap uni -spfuzz 0.5 +command: meme model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values @@ -69,7 +69,7 @@ data: n= 1500 N= 30 shuffle= -1 strands: + sample: seed= 0 ctfrac= -1 maxwords= -1 -Dirichlet mixture priors file: dataset_2577.dat +Dirichlet mixture priors file: Letter frequencies in dataset: A 0.294 C 0.231 G 0.257 T 0.217 Background letter frequencies (from dataset with add-one prior applied): @@ -261,7 +261,7 @@ -Time 0.17 secs. +Time ******************************************************************************** @@ -314,6 +314,6 @@ Stopped because requested number of motifs (1) found. ******************************************************************************** -CPU: dot1x-cb-51.aset.psu.edu +CPU: ********************************************************************************
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif1.gff Fri Jun 17 13:16:52 2016 -0400 @@ -0,0 +1,100 @@ +##gff-version 3 +phiX174 fimo polypeptide_motif 1 11 78.3 + . Name=1;ID=1-57-phiX174;pvalue=1.46e-08;sequence=GAGTTTTATCG; +phiX174 fimo polypeptide_motif 3 13 57.5 + . Name=1;ID=1-471-phiX174;pvalue=1.79e-06;sequence=GTTTTATCGCT; +phiX174 fimo polypeptide_motif 7 17 45 + . Name=1;ID=1-1378-phiX174;pvalue=3.18e-05;sequence=TATCGCTTCCA; +phiX174 fimo polypeptide_motif 10 20 53.9 + . Name=1;ID=1-605-phiX174;pvalue=4.1e-06;sequence=CGCTTCCATGA; +phiX174 fimo polypeptide_motif 17 27 40.2 + . Name=1;ID=1-1887-phiX174;pvalue=9.55e-05;sequence=ATGACGCAGAA; +phiX174 fimo polypeptide_motif 18 28 45.3 + . Name=1;ID=1-1349-phiX174;pvalue=2.98e-05;sequence=TGACGCAGAAG; +phiX174 fimo polypeptide_motif 19 29 55.8 + . Name=1;ID=1-527-phiX174;pvalue=2.6e-06;sequence=GACGCAGAAGT; +phiX174 fimo polypeptide_motif 21 31 41.5 + . Name=1;ID=1-1705-phiX174;pvalue=7.07e-05;sequence=CGCAGAAGTTA; +phiX174 fimo polypeptide_motif 22 32 44.6 + . Name=1;ID=1-1404-phiX174;pvalue=3.44e-05;sequence=GCAGAAGTTAA; +phiX174 fimo polypeptide_motif 24 34 79.1 + . Name=1;ID=1-53-phiX174;pvalue=1.23e-08;sequence=AGAAGTTAACA; +phiX174 fimo polypeptide_motif 25 35 45.3 + . Name=1;ID=1-1347-phiX174;pvalue=2.97e-05;sequence=GAAGTTAACAC; +phiX174 fimo polypeptide_motif 26 36 59.2 + . Name=1;ID=1-417-phiX174;pvalue=1.19e-06;sequence=AAGTTAACACT; +phiX174 fimo polypeptide_motif 30 40 44.7 + . Name=1;ID=1-1399-phiX174;pvalue=3.4e-05;sequence=TAACACTTTCG; +phiX174 fimo polypeptide_motif 37 47 72.4 + . Name=1;ID=1-98-phiX174;pvalue=5.79e-08;sequence=TTCGGATATTT; +phiX174 fimo polypeptide_motif 39 49 65.3 + . Name=1;ID=1-213-phiX174;pvalue=2.92e-07;sequence=CGGATATTTCT; +phiX174 fimo polypeptide_motif 41 51 55.3 + . Name=1;ID=1-548-phiX174;pvalue=2.97e-06;sequence=GATATTTCTGA; +phiX174 fimo polypeptide_motif 43 53 58.4 + . Name=1;ID=1-442-phiX174;pvalue=1.43e-06;sequence=TATTTCTGATG; +phiX174 fimo polypeptide_motif 46 56 53.7 + . Name=1;ID=1-617-phiX174;pvalue=4.23e-06;sequence=TTCTGATGAGT; +phiX174 fimo polypeptide_motif 50 60 45.4 + . Name=1;ID=1-1333-phiX174;pvalue=2.86e-05;sequence=GATGAGTCGAA; +phiX174 fimo polypeptide_motif 51 61 48.4 + . Name=1;ID=1-1094-phiX174;pvalue=1.44e-05;sequence=ATGAGTCGAAA; +phiX174 fimo polypeptide_motif 52 62 83.9 + . Name=1;ID=1-22-phiX174;pvalue=4.06e-09;sequence=TGAGTCGAAAA; +phiX174 fimo polypeptide_motif 53 63 53.9 + . Name=1;ID=1-601-phiX174;pvalue=4.03e-06;sequence=GAGTCGAAAAA; +phiX174 fimo polypeptide_motif 54 64 62.9 + . Name=1;ID=1-297-phiX174;pvalue=5.16e-07;sequence=AGTCGAAAAAT; +phiX174 fimo polypeptide_motif 55 65 52.8 + . Name=1;ID=1-675-phiX174;pvalue=5.26e-06;sequence=GTCGAAAAATT; +phiX174 fimo polypeptide_motif 56 66 41.4 + . Name=1;ID=1-1713-phiX174;pvalue=7.2e-05;sequence=TCGAAAAATTA; +phiX174 fimo polypeptide_motif 58 68 43.4 + . Name=1;ID=1-1500-phiX174;pvalue=4.56e-05;sequence=GAAAAATTATC; +phiX174 fimo polypeptide_motif 59 69 59.6 + . Name=1;ID=1-409-phiX174;pvalue=1.1e-06;sequence=AAAAATTATCT; +phiX174 fimo polypeptide_motif 61 71 61.8 + . Name=1;ID=1-329-phiX174;pvalue=6.52e-07;sequence=AAATTATCTTG; +phiX174 fimo polypeptide_motif 63 73 59.2 + . Name=1;ID=1-419-phiX174;pvalue=1.2e-06;sequence=ATTATCTTGAT; +phiX174 fimo polypeptide_motif 65 75 53.3 + . Name=1;ID=1-643-phiX174;pvalue=4.66e-06;sequence=TATCTTGATAA; +phiX174 fimo polypeptide_motif 66 76 51.8 + . Name=1;ID=1-737-phiX174;pvalue=6.54e-06;sequence=ATCTTGATAAA; +phiX174 fimo polypeptide_motif 67 77 73.2 + . Name=1;ID=1-89-phiX174;pvalue=4.78e-08;sequence=TCTTGATAAAG; +phiX174 fimo polypeptide_motif 69 79 63.8 + . Name=1;ID=1-268-phiX174;pvalue=4.15e-07;sequence=TTGATAAAGCA; +phiX174 fimo polypeptide_motif 71 81 40.2 + . Name=1;ID=1-1882-phiX174;pvalue=9.49e-05;sequence=GATAAAGCAGG; +phiX174 fimo polypeptide_motif 73 83 45.4 + . Name=1;ID=1-1334-phiX174;pvalue=2.87e-05;sequence=TAAAGCAGGAA; +phiX174 fimo polypeptide_motif 74 84 50.9 + . Name=1;ID=1-832-phiX174;pvalue=8.05e-06;sequence=AAAGCAGGAAT; +phiX174 fimo polypeptide_motif 76 86 52.2 + . Name=1;ID=1-710-phiX174;pvalue=5.96e-06;sequence=AGCAGGAATTA; +phiX174 fimo polypeptide_motif 78 88 51.8 + . Name=1;ID=1-741-phiX174;pvalue=6.65e-06;sequence=CAGGAATTACT; +phiX174 fimo polypeptide_motif 79 89 45 + . Name=1;ID=1-1369-phiX174;pvalue=3.16e-05;sequence=AGGAATTACTA; +phiX174 fimo polypeptide_motif 80 90 43.3 + . Name=1;ID=1-1511-phiX174;pvalue=4.63e-05;sequence=GGAATTACTAC; +phiX174 fimo polypeptide_motif 81 91 59.8 + . Name=1;ID=1-402-phiX174;pvalue=1.05e-06;sequence=GAATTACTACT; +phiX174 fimo polypeptide_motif 82 92 46.9 + . Name=1;ID=1-1205-phiX174;pvalue=2.03e-05;sequence=AATTACTACTG; +phiX174 fimo polypeptide_motif 88 98 41.2 + . Name=1;ID=1-1744-phiX174;pvalue=7.51e-05;sequence=TACTGCTTGTT; +phiX174 fimo polypeptide_motif 91 101 53.6 + . Name=1;ID=1-621-phiX174;pvalue=4.33e-06;sequence=TGCTTGTTTAC; +phiX174 fimo polypeptide_motif 92 102 44.8 + . Name=1;ID=1-1388-phiX174;pvalue=3.31e-05;sequence=GCTTGTTTACG; +phiX174 fimo polypeptide_motif 93 103 43.2 + . Name=1;ID=1-1525-phiX174;pvalue=4.82e-05;sequence=CTTGTTTACGA; +phiX174 fimo polypeptide_motif 95 105 61.9 + . Name=1;ID=1-327-phiX174;pvalue=6.5e-07;sequence=TGTTTACGAAT; +phiX174 fimo polypeptide_motif 96 106 42.9 + . Name=1;ID=1-1553-phiX174;pvalue=5.08e-05;sequence=GTTTACGAATT; +phiX174 fimo polypeptide_motif 98 108 45.4 + . Name=1;ID=1-1340-phiX174;pvalue=2.9e-05;sequence=TTACGAATTAA; +phiX174 fimo polypeptide_motif 99 109 73.5 + . Name=1;ID=1-88-phiX174;pvalue=4.48e-08;sequence=TACGAATTAAA; +phiX174 fimo polypeptide_motif 100 110 53 + . Name=1;ID=1-661-phiX174;pvalue=4.99e-06;sequence=ACGAATTAAAT; +phiX174 fimo polypeptide_motif 102 112 75.6 + . Name=1;ID=1-72-phiX174;pvalue=2.75e-08;sequence=GAATTAAATCG; +phiX174 fimo polypeptide_motif 104 114 52.2 + . Name=1;ID=1-713-phiX174;pvalue=6.05e-06;sequence=ATTAAATCGAA; +phiX174 fimo polypeptide_motif 106 116 59.6 + . Name=1;ID=1-407-phiX174;pvalue=1.09e-06;sequence=TAAATCGAAGT; +phiX174 fimo polypeptide_motif 112 122 41.6 + . Name=1;ID=1-1683-phiX174;pvalue=6.85e-05;sequence=GAAGTGGACTG; +phiX174 fimo polypeptide_motif 114 124 45.3 + . Name=1;ID=1-1342-phiX174;pvalue=2.92e-05;sequence=AGTGGACTGCT; +phiX174 fimo polypeptide_motif 118 128 56.2 + . Name=1;ID=1-512-phiX174;pvalue=2.38e-06;sequence=GACTGCTGGCG; +phiX174 fimo polypeptide_motif 122 132 51.4 + . Name=1;ID=1-774-phiX174;pvalue=7.15e-06;sequence=GCTGGCGGAAA; +phiX174 fimo polypeptide_motif 123 133 43.1 + . Name=1;ID=1-1533-phiX174;pvalue=4.93e-05;sequence=CTGGCGGAAAA; +phiX174 fimo polypeptide_motif 124 134 48.6 + . Name=1;ID=1-1085-phiX174;pvalue=1.38e-05;sequence=TGGCGGAAAAT; +phiX174 fimo polypeptide_motif 125 135 68.3 + . Name=1;ID=1-146-phiX174;pvalue=1.49e-07;sequence=GGCGGAAAATG; +phiX174 fimo polypeptide_motif 126 136 46.4 + . Name=1;ID=1-1243-phiX174;pvalue=2.27e-05;sequence=GCGGAAAATGA; +phiX174 fimo polypeptide_motif 128 138 58.3 + . Name=1;ID=1-446-phiX174;pvalue=1.48e-06;sequence=GGAAAATGAGA; +phiX174 fimo polypeptide_motif 129 139 43.2 + . Name=1;ID=1-1522-phiX174;pvalue=4.78e-05;sequence=GAAAATGAGAA; +phiX174 fimo polypeptide_motif 130 140 54.1 + . Name=1;ID=1-595-phiX174;pvalue=3.92e-06;sequence=AAAATGAGAAA; +phiX174 fimo polypeptide_motif 131 141 76 + . Name=1;ID=1-68-phiX174;pvalue=2.49e-08;sequence=AAATGAGAAAA; +phiX174 fimo polypeptide_motif 132 142 51.2 + . Name=1;ID=1-800-phiX174;pvalue=7.57e-06;sequence=AATGAGAAAAT; +phiX174 fimo polypeptide_motif 133 143 56.2 + . Name=1;ID=1-513-phiX174;pvalue=2.41e-06;sequence=ATGAGAAAATT; +phiX174 fimo polypeptide_motif 134 144 41.1 + . Name=1;ID=1-1761-phiX174;pvalue=7.83e-05;sequence=TGAGAAAATTC; +phiX174 fimo polypeptide_motif 135 145 50.3 + . Name=1;ID=1-910-phiX174;pvalue=9.39e-06;sequence=GAGAAAATTCG; +phiX174 fimo polypeptide_motif 136 146 43.3 + . Name=1;ID=1-1517-phiX174;pvalue=4.66e-05;sequence=AGAAAATTCGA; +phiX174 fimo polypeptide_motif 139 149 54.2 + . Name=1;ID=1-588-phiX174;pvalue=3.75e-06;sequence=AAATTCGACCT; +phiX174 fimo polypeptide_motif 141 151 42.2 + . Name=1;ID=1-1625-phiX174;pvalue=6.01e-05;sequence=ATTCGACCTAT; +phiX174 fimo polypeptide_motif 143 153 50 + . Name=1;ID=1-938-phiX174;pvalue=9.94e-06;sequence=TCGACCTATCC; +phiX174 fimo polypeptide_motif 145 155 44.6 + . Name=1;ID=1-1403-phiX174;pvalue=3.42e-05;sequence=GACCTATCCTT; +phiX174 fimo polypeptide_motif 155 165 51.3 + . Name=1;ID=1-787-phiX174;pvalue=7.35e-06;sequence=TGCGCAGCTCG; +phiX174 fimo polypeptide_motif 157 167 51.1 + . Name=1;ID=1-807-phiX174;pvalue=7.68e-06;sequence=CGCAGCTCGAG; +phiX174 fimo polypeptide_motif 159 169 44.5 + . Name=1;ID=1-1420-phiX174;pvalue=3.56e-05;sequence=CAGCTCGAGAA; +phiX174 fimo polypeptide_motif 160 170 40 + . Name=1;ID=1-1921-phiX174;pvalue=9.89e-05;sequence=AGCTCGAGAAG; +phiX174 fimo polypeptide_motif 166 176 60.9 + . Name=1;ID=1-365-phiX174;pvalue=8.02e-07;sequence=AGAAGCTCTTA; +phiX174 fimo polypeptide_motif 168 178 62.3 + . Name=1;ID=1-311-phiX174;pvalue=5.87e-07;sequence=AAGCTCTTACT; +phiX174 fimo polypeptide_motif 181 191 49.9 + . Name=1;ID=1-946-phiX174;pvalue=1.01e-05;sequence=GCGACCTTTCG; +phiX174 fimo polypeptide_motif 187 197 52.5 + . Name=1;ID=1-694-phiX174;pvalue=5.64e-06;sequence=TTTCGCCATCA; +phiX174 fimo polypeptide_motif 191 201 46.6 + . Name=1;ID=1-1232-phiX174;pvalue=2.2e-05;sequence=GCCATCAACTA; +phiX174 fimo polypeptide_motif 194 204 76.4 + . Name=1;ID=1-67-phiX174;pvalue=2.29e-08;sequence=ATCAACTAACG; +phiX174 fimo polypeptide_motif 201 211 40.1 + . Name=1;ID=1-1908-phiX174;pvalue=9.77e-05;sequence=AACGATTCTGT; +phiX174 fimo polypeptide_motif 203 213 63 + . Name=1;ID=1-291-phiX174;pvalue=5e-07;sequence=CGATTCTGTCA; +phiX174 fimo polypeptide_motif 205 215 53.8 + . Name=1;ID=1-610-phiX174;pvalue=4.16e-06;sequence=ATTCTGTCAAA; +phiX174 fimo polypeptide_motif 206 216 59.1 + . Name=1;ID=1-421-phiX174;pvalue=1.23e-06;sequence=TTCTGTCAAAA; +phiX174 fimo polypeptide_motif 207 217 68 + . Name=1;ID=1-153-phiX174;pvalue=1.58e-07;sequence=TCTGTCAAAAA; +phiX174 fimo polypeptide_motif 209 219 49.6 + . Name=1;ID=1-988-phiX174;pvalue=1.09e-05;sequence=TGTCAAAAACT; +phiX174 fimo polypeptide_motif 210 220 40.8 + . Name=1;ID=1-1810-phiX174;pvalue=8.33e-05;sequence=GTCAAAAACTG; +phiX174 fimo polypeptide_motif 213 223 59.7 + . Name=1;ID=1-404-phiX174;pvalue=1.06e-06;sequence=AAAAACTGACG; +phiX174 fimo polypeptide_motif 223 233 42 + . Name=1;ID=1-1654-phiX174;pvalue=6.36e-05;sequence=GCGTTGGATGA; +phiX174 fimo polypeptide_motif 225 235 61.4 + . Name=1;ID=1-349-phiX174;pvalue=7.16e-07;sequence=GTTGGATGAGG; +phiX174 fimo polypeptide_motif 227 237 40.3 + . Name=1;ID=1-1874-phiX174;pvalue=9.32e-05;sequence=TGGATGAGGAG; +phiX174 fimo polypeptide_motif 228 238 49.9 + . Name=1;ID=1-947-phiX174;pvalue=1.01e-05;sequence=GGATGAGGAGA; +phiX174 fimo polypeptide_motif 229 239 45 + . Name=1;ID=1-1370-phiX174;pvalue=3.16e-05;sequence=GATGAGGAGAA; +phiX174 fimo polypeptide_motif 230 240 44.8 + . Name=1;ID=1-1395-phiX174;pvalue=3.33e-05;sequence=ATGAGGAGAAG;
--- a/tool_dependencies.xml Fri Mar 18 08:23:54 2016 -0400 +++ b/tool_dependencies.xml Fri Jun 17 13:16:52 2016 -0400 @@ -4,6 +4,6 @@ <repository changeset_revision="942ae5bafee3" name="package_imagemagick_6_9_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="meme" version="4.11.0"> - <repository changeset_revision="738dc831aeac" name="package_meme_4_11_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="5774a0e96d6f" name="package_meme_4_11_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>