Mercurial > repos > iuc > meme_fimo
changeset 0:fd522a964017 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +#
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fimo.xml Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,250 @@ +<tool id="meme_fimo" name="FIMO" version="4.11.0.0"> + <description>- Scan a set of sequences for motifs.</description> + <requirements> + <requirement type="package" version="4.11.0.0">meme</requirement> + </requirements> + <command> + <![CDATA[ + python $__tool_directory__/fimo_wrapper.py + --input_motifs "${input_motifs}" + #if str($fasta_type.fasta_type_selector) == 'history': + --input_fasta "${fasta_type.input_database}" + #else: + --input_fasta "${fasta_type.input_database.fields.path}" + #end if + --options_type $options_type.options_type_selector + #if str($options_type.options_type_selector) == 'advanced': + --alpha "${options_type.alpha}" + #if str($options_type.bgfile_type.bgfile_type_selector) == 'motif_file': + --bgfile "motif-file" + #elif str($options_type.bgfile_type.bgfile_type_selector) == 'bgfile': + --bgfile "${options_type.bgfile_type.bgfile}" + #end if + ${options_type.max_strand} + --max_stored_scores "${options_type.max_stored_scores}" + #if str($options_type.motifs_cond.motifs_selector) == 'no': + #for $motif in $options_type.motifs: + --motif "${motif.motif}" + #end for + #end if + --motif_pseudo "${options_type.motif_pseudo}" + ${options_type.no_qvalue} + ${options_type.norc} + ${options_type.parse_genomic_coord} + #if str($options_type.psp_cond.psp_selector) == 'yes': + --input_psp "${input_psp}" + #end if + #if str($options_type.prior_dist_cond.prior_dist_selector) == 'yes': + --input_prior_dist "${input_prior_dist}" + #end if + ${options_type.qv_thresh} + --thresh ${options_type.thresh} + #end if + --output_path '${html_outfile.files_path}' + --html_output "${html_outfile}" + --interval_output '${interval_outfile}' + --txt_output "${txt_outfile}" + --xml_output "${xml_outfile}" + --gff_output "${gff_outfile}" + ]]> + </command> + <inputs> + <param name="input_motifs" type="data" format="memexml" label="'MEME output' formatted file"/> + <conditional name="fasta_type"> + <param name="fasta_type_selector" type="select" label="Source for sequence to search"> + <option value="cached">Locally Cached sequences</option> + <option value="history" selected="true">Sequences from your history</option> + </param> + <when value="cached"> + <param name="input_database" type="select" label="Genome to search"> + <options from_data_table="all_fasta" /> + </param> + </when> + <when value="history"> + <param format="fasta" name="input_database" type="data" label="Sequences"/> + </when> + </conditional> + <conditional name="options_type"> + <param name="options_type_selector" type="select" label="Options configuration"> + <option value="basic" selected="true">Basic</option> + <option value="advanced">Advanced</option> + </param> + <when value="basic" /> + <when value="advanced"> + <param name="alpha" type="float" value="1.0" min="0" max="1.0" label="Alpha parameter for calculating position specific priors" help="Represents the fraction of all transcription factor binding sites that are binding sites for the TF of interest (must be between 0 and 1)."/> + <conditional name="bgfile_type"> + <param name="bgfile_type_selector" type="select" label="Background file type"> + <option value="default" selected="true">Use frequencies embedded in the application from the non-redundant database</option> + <option value="motif_file">Use frequencies from motif file</option> + <option value="bgfile">Use frequencies from background file</option> + </param> + <when value="motif_file" /> + <when value="default" /> + <when value="bgfile"> + <param name="bgfile" type="data" format="txt" optional="True" label="Background Model" help="File must be in MEME background file format."/> + </when> + </conditional> + <param name="max_strand" label="If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score" type="boolean" truevalue="--max_strand" falsevalue="" checked="False" help="If the scores are tied, the matching strand is chosen at random. Leave unchecked to report both matches."/> + <param name="max_stored_scores" type="integer" value="100000" label="Maximum number of scores that will be stored" /> + <conditional name="motifs_cond"> + <param name="motifs_selector" type="select" label="Use all motifs in input?"> + <option value="yes" selected="true">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"/> + <when value="no"> + <repeat name="motifs" title="Limit to specified motif"> + <param name="motif" type="text" value="" label="Specify motif by id" /> + </repeat> + </when> + </conditional> + <param name="motif_pseudo" type="float" value="0.1" label="Pseudocount to add to counts in motif matrix" help="A pseudocount to be added to each count in the motif matrix, after first multiplying by the corresponding background frequency"/> + <param name="no_qvalue" label="Do not compute a q-value for each p-value" type="boolean" truevalue="--no_qvalue" falsevalue="" checked="True" help="The q-value calculation is that of Benjamini and Hochberg (1995)."/> + <param name="norc" label="Do not score the reverse complement DNA strand" type="boolean" truevalue="--norc" falsevalue="" checked="False" /> + <param name="parse_genomic_coord" label="Check each sequence header for UCSC style genomic coordinates" type="boolean" truevalue="--parse_genomic_coord" falsevalue="" checked="False" /> + <conditional name="psp_cond"> + <param name="psp_selector" type="select" label="Use position-specific priors?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="input_psp" type="data" format="txt" label="Select dataset containing position specific priors" help="Format must be meme psp or wiggle."/> + </when> + </conditional> + <conditional name="prior_dist_cond"> + <param name="prior_dist_selector" type="select" label="Use binned distribution of priors?"> + <option value="no" selected="true">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"/> + <when value="yes"> + <param name="input_prior_dist" type="data" format="txt" label="Select dataset containing binned distribution of priors"/> + </when> + </conditional> + <param name="qv_thresh" label="Use q-values for the output threshold" type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" help="Leave unchecked to use p-values for the output threshold."/> + <param name="thresh" type="float" value="1e-4" label="Output threshold for displaying search results" help="Only search results with a p-value less than the threshold will be output. The threshold can be set to use q-values rather than p-values via the option above."/> + </when> + </conditional> + <param name="non_commercial_use" label="I certify that I am not using this tool for commercial purposes." type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False"> + <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> + </param> + </inputs> + <outputs> + <data format="html" name="html_outfile" label="${tool.name} on ${on_string} (html)"> + <actions> + <conditional name="fasta_type.fasta_type_selector"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="all_fasta" column="1" offset="0"> + <filter type="param_value" column="0" value="seq" keep="True"/> + <filter type="param_value" ref="fasta_type.input_database" column="1"/> + </option> + </action> + </when> + </conditional> + </actions> + </data> + <data format="tabular" name="txt_outfile" label="${tool.name} on ${on_string} (text)"> + <actions> + <conditional name="fasta_type.fasta_type_selector"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="all_fasta" column="1" offset="0"> + <filter type="param_value" ref="fasta_type.input_database" column="0"/> + </option> + </action> + </when> + </conditional> + </actions> + </data> + <data format="tabular" name="gff_outfile" label="${tool.name} on ${on_string} (almost-gff)"> + <actions> + <conditional name="fasta_type.fasta_type_selector"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="all_fasta" column="1" offset="0"> + <filter type="param_value" ref="fasta_type.input_database" column="0"/> + </option> + </action> + </when> + </conditional> + </actions> + </data> + <data format="cisml" name="xml_outfile" label="${tool.name} on ${on_string} (xml)"> + <actions> + <conditional name="fasta_type.fasta_type_selector"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="all_fasta" column="1" offset="0"> + <filter type="param_value" ref="fasta_type.input_database" column="0"/> + </option> + </action> + </when> + </conditional> + </actions> + </data> + <data format="interval" name="interval_outfile" label="${tool.name} on ${on_string} (interval)"> + <actions> + <conditional name="fasta_type.fasta_type_selector"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="all_fasta" column="1" offset="0"> + <filter type="param_value" ref="fasta_type.input_database" column="0"/> + </option> + </action> + </when> + </conditional> + </actions> + </data> + </outputs> + <tests> + <test> + <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> + <param name="fasta_type_selector" value="history"/> + <param name="input_database" value="phiX.fasta" ftype="fasta"/> + <param name="options_type_selector" value="basic"/> + <param name="non_commercial_use" value="True"/> + <output name="html_outfile" file="fimo_output_html_1.html" compare="contains"/> + <output name="txt_outfile" file="fimo_output_txt_1.txt" compare="contains"/> + <output name="gff_outfile" file="fimo_output_almost-gff_1.txt" compare="contains"/> + <output name="xml_outfile" file="fimo_output_xml_1.xml" lines_diff="8"/> + <output name="interval_outfile" file="fimo_output_interval_1.txt" compare="contains"/> + </test> + <test> + <param name="input_motifs" value="meme_output_xml_1.xml" ftype="memexml"/> + <param name="fasta_type_selector" value="history"/> + <param name="input_database" value="phiX.fasta" ftype="fasta"/> + <param name="options_type_selector" value="advanced"/> + <param name="non_commercial_use" value="True"/> + <output name="html_outfile" file="fimo_output_html_2.html" compare="contains"/> + <output name="txt_outfile" file="fimo_output_txt_2.txt" compare="contains"/> + <output name="gff_outfile" file="fimo_output_almost-gff_2.txt" compare="contains"/> + <output name="xml_outfile" file="fimo_output_xml_2.xml" lines_diff="8"/> + <output name="interval_outfile" file="fimo_output_interval_2.txt" compare="contains"/> + </test> + </tests> + <help> + +.. class:: warningmark + +**WARNING: This tool is only available for non-commercial use. Use for educational, research and non-profit purposes is permitted. +Before using, be sure to review, agree, and comply with the license.** + +FIMO scans a sequence database for individual matches to each of the motifs you provide (sample output for motifs and sequences). +The name FIMO stands for 'Find Individual Motif Occurrences'. The program searches a database of sequences for occurrences of +known motifs, treating each motif independently. Motifs must be in MEME Motif Format. You can define the statistical threshold +(p-value) for motifs and whether FIMO scans just the given sequences or their reverse complements (where applicable), too. + +.. class:: infomark + +For detailed information on FIMO, click here_, or view the license_. + +.. _here: http://meme-suite.org/doc/fimo.html?man_type=web +.. _license: http://meme-suite.org/doc/copyright.html?man_type=web + + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btr064</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fimo_wrapper.py Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,134 @@ +#!/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()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_almost-gff_1.txt Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +##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;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_almost-gff_2.txt Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +##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;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_html_1.html Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +<!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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_html_2.html Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +<!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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_interval_1.txt Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_interval_2.txt Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_txt_1.txt Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_txt_2.txt Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +#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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_xml_1.xml Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,74 @@ +<?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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fimo_output_xml_2.xml Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,74 @@ +<?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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_input_1.fasta Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,66 @@ +>chr21_19617074_19617124_+ +AAAAATTATTACTAGGGAGGGGGCCGGAACCTCGGGACGTGGGTATATAA +>chr21_26934381_26934431_+ +GCGCCTGGTCGGTTATGAGTCACAAGTGAGTTATAAAAGGGTCGCACGTT +>chr21_28217753_28217803_- +CAAAGGGGAGGAGTGGGGTGGGGGTGGGGGTTTCACTGGTCCACTATAAA +>chr21_31710037_31710087_- +AACACCCAGGTTTCTGAGTATATAATCGCCGCACCAAAGAATTTAATTTT +>chr21_31744582_31744632_- +CCCAGGTCTAAGAGCATATATAACTTGGAGTCCAGACTATGACATTCAAA +>chr21_31768316_31768366_+ +AACGTATATAAATGGTCCTGTCCAGATGTGGCATGCAAACTCAGAATCTT +>chr21_31914206_31914256_- +TGACACCCACTACTTAGAGTATAAAATCATTCTGAGAAGTTAGAGACACC +>chr21_31933633_31933683_- +TCAGAGTATATATAAATGTTCCTGTCCAGTCACAGTCACCAAACTGACCT +>chr21_31962741_31962791_- +ACATATAACTCAGGTTGGATAAAATAATTTGTACAAATCAGGAGAGTCAA +>chr21_31964683_31964733_+ +TCTGATTCACTGAGGCATATAAAAGGCCCTCTGCGGAGAAGTGTCCATAC +>chr21_31973364_31973414_+ +aaacttaaaactctataaacttaaaactCTAGAATCTGATCCTGCTATAC +>chr21_31992870_31992920_+ +CTCATACACTATTGAAGATGTATAAAATTTCATTTGCAGATGGTGACATT +>chr21_32185595_32185645_- +TCACCACCCACCAGAGCTGGGATATATAAAGAAGGTTCTGAGACTAGGAA +>chr21_32202076_32202126_- +TGCCCACCAGCTTGAGGTATAAAAAGCCCTGTACGGGAAGAGACCTTCAT +>chr21_32253899_32253949_- +AGCCCCACCCACCAGCAAGGATATATAAAAGCTCAGGAGTCTGGAGTGAC +>chr21_32410820_32410870_- +TCTACCCCACTAATCACTGAGGATGTATAAAAGTCCCAGGGAAGCTGGTG +>chr21_36411748_36411798_- +ATAGTTCTGTATAGTTTCAGTTGGCATCtaaaaattatataactttattt +>chr21_37838750_37838800_- +gatggttttataaggggcctcaccctcggctcagccctcattcttctcct +>chr21_45705687_45705737_+ +CCGGGGCGGAGCGGCCTTTGCTCTTTGCGTGGTCGCGGGGGTATAACAGC +>chr21_45971413_45971463_- +CAGGCCCTGGGCATATAAAAGCCCCAGCAGCCAACAGGctcacacacaca +>chr21_45978668_45978718_- +CAGAGGGGTATAAAGGTTCCGACCACTCAGAGGCCTGGCACGAtcactca +>chr21_45993530_45993580_+ +CCAAGGAGGAGTATAAAAGCCCCACAAACCCGAGCACCTCACTCACTCGC +>chr21_46020421_46020471_+ +GAGACATATAAAAGCCAACATCCCTGAGCACCTAACACACGGactcactc +>chr21_46031920_46031970_+ +GGAAAATACCCAGGGAGGGTATAAAACCTCAGCAGCCAGGGCACACAAAC +>chr21_46046964_46047014_+ +ACAAGGCCAGGAGGGGTATAAAAGCCTGAGAGCCCCAAGAACctcacaca +>chr21_46057197_46057247_+ +ATTGCTGAGTCTCCTGCTGGGAAAACACAGGCCCTGGGCATATAAAAGCC +>chr21_46086869_46086919_- +GACAGGTGTGCTTCTGTGCTGTGGGGATGCCTGGGCCCAGGTATAAAGGC +>chr21_46102103_46102153_- +AGGTGTGTGCTTCTGTGCTGTGGGGATGCCTGGGTCCAGGTATAAAGGCT +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47517957_47518007_+ +CCTGGCGGCGGGGCGGGTCAGGCCGGCGGGGCGGGGTATAAAGGGGGCGG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG +>chr21_47575506_47575556_- +TGAGAAGCCGGTGGGGAGGTGCTGCCGGTGAGCGTATAAAGGCCCTGGCG
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_html_1.html Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +<!DOCTYPE HTML> +<html> + <head> + <meta charset="UTF-8"> + <title>MEME</title> + <script> + // @JSON_VAR data + var data = { + "program": "MEME", + "version": "4.11.0", + "release": "Thu Nov 26 17:48:49 2015 +1000", + "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": { + "mod": "zoops", + "revcomp": false, + "nmotifs": 1, + "minw": 8, + "maxw": 50, + "minsites": 2, + "maxsites": 30, + "wnsites": 0.8, + "spmap": "pam", + "spfuzz": 120, + "maxwords": -1, + "prior": "megap", + "b": 7500, + "maxiter": 50, + "distance": 1e-05, + "wg": 11, + "ws": 1, + "noendgaps": false, + "substring": true + }, + "alphabet": { + "name": "Protein", + "like": "protein", + "ncore": 20, + "symbols": [ + { + "symbol": "A", + "name": "Alanine", + "colour": "0000CC" + }, { + "symbol": "C", + "name": "Cysteine", + "colour": "0000CC" + }, { + "symbol": "D", + "name": "Aspartic acid", + "colour": "FF00FF" + }, { + "symbol": "E", + "name": "Glutamic acid", + "colour": "FF00FF" + }, { + "symbol": "F", + "name": "Phenylalanine", + "colour": "0000CC" + }, { + "symbol": "G", + "name": "Glycine", + "colour": "FFB300" + }, { + "symbol": "H", + "name": "Histidine", + "colour": "FFCCCC" + }, { + "symbol": "I", + "name": "Isoleucine", + "colour": "0000CC" + }, { + "symbol": "K", + "name": "Lysine", + "colour": "CC0000" + }, { + "symbol": "L", + "name": "Leucine", + "colour": "0000CC" + }, { + "symbol": "M", + "name": "Methionine", + "colour": "0000CC" + }, { + "symbol": "N", + "name": "Asparagine", + "colour": "008000" + }, { + "symbol": "P", + "name": "Proline", + "colour": "FFFF00" + }, { + "symbol": "Q", + "name": "Glutamine",
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_html_2.html Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,100 @@ +<!DOCTYPE HTML> +<html> + <head> + <meta charset="UTF-8"> + <title>MEME</title> + <script> + // @JSON_VAR data + var data = { + "program": "MEME", + "version": "4.11.0", + "release": "Thu Nov 26 17:48:49 2015 +1000", + "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", + "revcomp": false, + "nmotifs": 1, + "minw": 8, + "maxw": 50, + "minsites": 2, + "maxsites": 30, + "wnsites": 0.8, + "spmap": "uni", + "spfuzz": 0.5, + "maxwords": -1, + "prior": "dirichlet", + "b": 0.01, + "maxiter": 50, + "distance": 0.001, + "wg": 11, + "ws": 1, + "noendgaps": false, + "substring": true + }, + "alphabet": { + "name": "DNA", + "like": "dna", + "ncore": 4, + "symbols": [ + { + "symbol": "A", + "name": "Adenine", + "colour": "CC0000", + "complement": "T" + }, { + "symbol": "C", + "name": "Cytosine", + "colour": "0000CC", + "complement": "G" + }, { + "symbol": "G", + "name": "Guanine", + "colour": "FFB300", + "complement": "C" + }, { + "symbol": "T", + "aliases": "U", + "name": "Thymine", + "colour": "008000", + "complement": "A" + }, { + "symbol": "N", + "aliases": "X.", + "name": "Any base", + "equals": "ACGT" + }, { + "symbol": "V", + "name": "Not T", + "equals": "ACG" + }, { + "symbol": "H", + "name": "Not G", + "equals": "ACT" + }, { + "symbol": "D", + "name": "Not C", + "equals": "AGT" + }, { + "symbol": "B", + "name": "Not A", + "equals": "CGT" + }, { + "symbol": "M", + "name": "Amino", + "equals": "AC" + }, { + "symbol": "R", + "name": "Purine", + "equals": "AG"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_txt_1.txt Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,325 @@ +******************************************************************************** +MEME - Motif discovery tool +******************************************************************************** +MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000) + +For further information on how to interpret these results or to get +a copy of the MEME software please access http://meme-suite.org . + +This file may be used as input to the MAST algorithm for searching +sequence databases for matches to groups of motifs. MAST is available +for interactive use and downloading at http://meme-suite.org . +******************************************************************************** + + +******************************************************************************** +REFERENCE +******************************************************************************** +If you use this program in your research, please cite: + +Timothy L. Bailey and Charles Elkan, +"Fitting a mixture model by expectation maximization to discover +motifs in biopolymers", Proceedings of the Second International +Conference on Intelligent Systems for Molecular Biology, pp. 28-36, +AAAI Press, Menlo Park, California, 1994. +******************************************************************************** + + +******************************************************************************** +TRAINING SET +******************************************************************************** +DATAFILE= /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat +ALPHABET= ACDEFGHIKLMNPQRSTVWY +Sequence name Weight Length Sequence name Weight Length +------------- ------ ------ ------------- ------ ------ +chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 +chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 +chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 +chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 +chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 +chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 +chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 +chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 +chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 +chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 +chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 +chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 +chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 +chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 +chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 +******************************************************************************** + +******************************************************************************** +COMMAND LINE SUMMARY +******************************************************************************** +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 + +model: mod= zoops nmotifs= 1 evt= inf +object function= E-value of product of p-values +width: minw= 8 maxw= 50 +width: wg= 11 ws= 1 endgaps= yes +nsites: minsites= 2 maxsites= 30 wnsites= 0.8 +theta: spmap= pam spfuzz= 120 +global: substring= yes branching= no wbranch= no +em: prior= megap b= 7500 maxiter= 50 + distance= 1e-05 +data: n= 1500 N= 30 shuffle= -1 + +sample: seed= 0 ctfrac= -1 maxwords= -1 +Dirichlet mixture priors file: prior30.plib +Letter frequencies in dataset: +A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000 +L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000 +W 0.000 Y 0.000 +Background letter frequencies (from dataset with add-one prior applied): +A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001 +L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001 +W 0.001 Y 0.001 +******************************************************************************** + + +******************************************************************************** +MOTIF 1 MEME width = 11 sites = 25 llr = 239 E-value = 2.4e-011 +******************************************************************************** +-------------------------------------------------------------------------------- + Motif 1 Description +-------------------------------------------------------------------------------- +Simplified A 2323:a:a8a8 +pos.-specific C ::3:::::::: +probability D ::::::::::: +matrix E ::::::::::: + F ::::::::::: + G 7746::::::1 + H ::::::::::: + I ::::::::::: + K ::::::::::: + L ::::::::::: + M ::::::::::: + N ::::::::::: + P ::::::::::: + Q ::::::::::: + R ::::::::::: + S ::::::::::: + T 1:2:a:a:2:: + V ::::::::::: + W ::::::::::: + Y ::::::::::: + + bits 10.6 + 9.5 + 8.5 + 7.4 +Relative 6.3 +Entropy 5.3 +(13.8 bits) 4.2 + 3.2 + 2.1 * ** + 1.1 ** ******** + 0.0 ----------- + +Multilevel GGGGTATAAAA +consensus AACA T +sequence + + +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 sites sorted by position p-value +-------------------------------------------------------------------------------- +Sequence name Start P-value Site +------------- ----- --------- ----------- +chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC +chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC +chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG +chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC +chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA +chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC +chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC +chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA +chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT +chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC +chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC +chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG +chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA +chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG +chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT +chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC +chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA +chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC +chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT +chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG +chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG +chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC +chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCtaaaa attatataac +chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT +chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 block diagrams +-------------------------------------------------------------------------------- +SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM +------------- ---------------- ------------- +chr21_46046964_46047014_ 1.1e-06 12_[1]_27 +chr21_46057197_46057247_ 3.4e-06 36_[1]_3 +chr21_45971413_45971463_ 3.4e-06 9_[1]_30 +chr21_31964683_31964733_ 3.4e-06 13_[1]_26 +chr21_45993530_45993580_ 4e-06 7_[1]_32 +chr21_32202076_32202126_ 5e-06 13_[1]_26 +chr21_46031920_46031970_ 6.1e-06 15_[1]_24 +chr21_32410820_32410870_ 8.7e-06 21_[1]_18 +chr21_32185595_32185645_ 8.7e-06 18_[1]_21 +chr21_31992870_31992920_ 8.7e-06 16_[1]_23 +chr21_46020421_46020471_ 1.2e-05 2_[1]_37 +chr21_47517957_47518007_ 1.6e-05 32_[1]_7 +chr21_45978668_45978718_ 1.6e-05 4_[1]_35 +chr21_31914206_31914256_ 1.7e-05 15_[1]_24 +chr21_32253899_32253949_ 2e-05 19_[1]_20 +chr21_31744582_31744632_ 3.1e-05 12_[1]_27 +chr21_19617074_19617124_ 3.1e-05 39_[1] +chr21_45705687_45705737_ 3.8e-05 37_[1]_2 +chr21_31768316_31768366_ 3.8e-05 [1]_39 +chr21_47575506_47575556_ 4e-05 30_[1]_9 +chr21_26934381_26934431_ 5.5e-05 27_[1]_12 +chr21_31710037_31710087_ 5.9e-05 14_[1]_25 +chr21_36411748_36411798_ 6.8e-05 22_[1]_17 +chr21_31933633_31933683_ 0.00021 2_[1]_37 +chr21_31962741_31962791_ 0.0004 13_[1]_26 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 in BLOCKS format +-------------------------------------------------------------------------------- +BL MOTIF 1 width=11 seqs=25 +chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 +chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 +chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 +chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 +chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 +chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 +chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 +chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 +chr21_32185595_32185645_ ( 19) GGGATATATAA 1 +chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 +chr21_46020421_46020471_ ( 3) GACATATAAAA 1 +chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 +chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 +chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 +chr21_32253899_32253949_ ( 20) GATATATAAAA 1 +chr21_31744582_31744632_ ( 13) AGCATATATAA 1 +chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 +chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 +chr21_31768316_31768366_ ( 1) AACGTATATAA 1 +chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 +chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 +chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 +chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 +chr21_31933633_31933683_ ( 3) AGAGTATATAT 1 +chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 +// + +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 position-specific scoring matrix +-------------------------------------------------------------------------------- +log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 + -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36 + -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36 + -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68 + 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55 + -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95 + 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 + -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173 + 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153 + 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71 + 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 + 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 position-specific probability matrix +-------------------------------------------------------------------------------- +letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 + 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000 + 0.280000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 + 0.160000 0.320000 0.000000 0.000000 0.000000 0.360000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.160000 0.000000 0.000000 0.000000 + 0.320000 0.000000 0.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.960000 0.000000 0.000000 0.000000 + 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 + 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000 + 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 + 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 regular expression +-------------------------------------------------------------------------------- +[GA][GA][GC][GA]TATA[AT]AA +-------------------------------------------------------------------------------- + + + + +Time 0.53 secs. + +******************************************************************************** + + +******************************************************************************** +SUMMARY OF MOTIFS +******************************************************************************** + +-------------------------------------------------------------------------------- + Combined block diagrams: non-overlapping sites with p-value < 0.0001 +-------------------------------------------------------------------------------- +SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM +------------- ---------------- ------------- +chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)] +chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12 +chr21_28217753_28217803_ 7.29e-01 50 +chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25 +chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27 +chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39 +chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24 +chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35 +chr21_31962741_31962791_ 1.61e-02 50 +chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26 +chr21_31973364_31973414_ 1.99e-01 50 +chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23 +chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21 +chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26 +chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20 +chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18 +chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17 +chr21_37838750_37838800_ 8.23e-02 50 +chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2 +chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30 +chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35 +chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32 +chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37 +chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24 +chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27 +chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3 +chr21_46086869_46086919_ 4.30e-02 50 +chr21_46102103_46102153_ 4.30e-02 50 +chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7 +chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9 +-------------------------------------------------------------------------------- + +******************************************************************************** + + +******************************************************************************** +Stopped because requested number of motifs (1) found. +******************************************************************************** + +CPU: MacBook-Pro-2.local + +********************************************************************************
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_txt_2.txt Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,319 @@ +******************************************************************************** +MEME - Motif discovery tool +******************************************************************************** +MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000) + +For further information on how to interpret these results or to get +a copy of the MEME software please access http://meme-suite.org . + +This file may be used as input to the MAST algorithm for searching +sequence databases for matches to groups of motifs. MAST is available +for interactive use and downloading at http://meme-suite.org . +******************************************************************************** + + +******************************************************************************** +REFERENCE +******************************************************************************** +If you use this program in your research, please cite: + +Timothy L. Bailey and Charles Elkan, +"Fitting a mixture model by expectation maximization to discover +motifs in biopolymers", Proceedings of the Second International +Conference on Intelligent Systems for Molecular Biology, pp. 28-36, +AAAI Press, Menlo Park, California, 1994. +******************************************************************************** + + +******************************************************************************** +TRAINING SET +******************************************************************************** +DATAFILE= Galaxy_FASTA_Input +ALPHABET= ACGT +Sequence name Weight Length Sequence name Weight Length +------------- ------ ------ ------------- ------ ------ +chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 +chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 +chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 +chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 +chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 +chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 +chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 +chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 +chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 +chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 +chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 +chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 +chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 +chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 +chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 +******************************************************************************** + +******************************************************************************** +COMMAND LINE SUMMARY +******************************************************************************** +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 + +model: mod= zoops nmotifs= 1 evt= inf +object function= E-value of product of p-values +width: minw= 8 maxw= 50 +width: wg= 11 ws= 1 endgaps= yes +nsites: minsites= 2 maxsites= 30 wnsites= 0.8 +theta: spmap= uni spfuzz= 0.5 +global: substring= yes branching= no wbranch= no +em: prior= dirichlet b= 0.01 maxiter= 50 + distance= 0.001 +data: n= 1500 N= 30 shuffle= -1 +strands: + +sample: seed= 0 ctfrac= -1 maxwords= -1 +Dirichlet mixture priors file: dataset_2577.dat +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): +A 0.294 C 0.231 G 0.257 T 0.217 +******************************************************************************** + + +******************************************************************************** +MOTIF 1 MEME width = 11 sites = 30 llr = 254 E-value = 5.1e-040 +******************************************************************************** +-------------------------------------------------------------------------------- + Motif 1 Description +-------------------------------------------------------------------------------- +Simplified A 3313:9:a798 +pos.-specific C 1:3::1:::1: +probability G 6756::::::2 +matrix T 1:11a1a:3:: + + bits 2.2 * + 2.0 * * + 1.8 * * + 1.5 * ** * +Relative 1.3 * ** * +Entropy 1.1 ****** +(12.2 bits) 0.9 * ******* + 0.7 * ******* + 0.4 ** ******** + 0.2 *********** + 0.0 ----------- + +Multilevel GGGGTATAAAA +consensus AACA T +sequence + +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 sites sorted by position p-value +-------------------------------------------------------------------------------- +Sequence name Start P-value Site +------------- ----- --------- ----------- +chr21_46046964_46047014_ 13 4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC +chr21_46031920_46031970_ 16 2.22e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC +chr21_32202076_32202126_ 14 2.74e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC +chr21_46057197_46057247_ 37 4.86e-06 ACAGGCCCTG GGCATATAAAA GCC +chr21_45993530_45993580_ 8 4.86e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA +chr21_45971413_45971463_ 10 4.86e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG +chr21_31964683_31964733_ 14 4.86e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC +chr21_47517957_47518007_ 33 6.48e-06 CCGGCGGGGC GGGGTATAAAG GGGGCGG +chr21_45978668_45978718_ 5 6.48e-06 CAGA GGGGTATAAAG GTTCCGACCA +chr21_32185595_32185645_ 19 6.48e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT +chr21_32410820_32410870_ 22 1.38e-05 AATCACTGAG GATGTATAAAA GTCCCAGGGA +chr21_31992870_31992920_ 17 1.38e-05 CACTATTGAA GATGTATAAAA TTTCATTTGC +chr21_19617074_19617124_ 40 1.41e-05 CCTCGGGACG TGGGTATATAA +chr21_31914206_31914256_ 16 1.61e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG +chr21_46020421_46020471_ 3 1.95e-05 GA GACATATAAAA GCCAACATCC +chr21_32253899_32253949_ 18 1.95e-05 CCCACCAGCA AGGATATATAA AAGCTCAGGA +chr21_45705687_45705737_ 38 2.16e-05 CGTGGTCGCG GGGGTATAACA GC +chr21_47575506_47575556_ 31 3.04e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG +chr21_31744582_31744632_ 13 3.04e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC +chr21_31768316_31768366_ 1 3.67e-05 . AACGTATATAA ATGGTCCTGT +chr21_26934381_26934431_ 28 3.93e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG +chr21_31933633_31933683_ 5 5.65e-05 TCAG AGTATATATAA ATGTTCCTGT +chr21_31710037_31710087_ 15 6.24e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC +chr21_36411748_36411798_ 23 7.15e-05 AGTTTCAGTT GGCATCtaaaa attatataac +chr21_46102103_46102153_ 37 1.39e-04 TGCCTGGGTC CAGGTATAAAG GCT +chr21_46086869_46086919_ 38 1.39e-04 TGCCTGGGCC CAGGTATAAAG GC +chr21_37838750_37838800_ 3 4.81e-04 ga tggttttataa ggggcctcac +chr21_31962741_31962791_ 14 8.57e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC +chr21_31973364_31973414_ 8 1.47e-03 aaactta aaactctataa acttaaaact +chr21_28217753_28217803_ 27 2.64e-03 GGTGGGGGTG GGGGTTTCACT GGTCCACTAT +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 block diagrams +-------------------------------------------------------------------------------- +SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM +------------- ---------------- ------------- +chr21_46046964_46047014_ 4.5e-07 12_[+1]_27 +chr21_46031920_46031970_ 2.2e-06 15_[+1]_24 +chr21_32202076_32202126_ 2.7e-06 13_[+1]_26 +chr21_46057197_46057247_ 4.9e-06 36_[+1]_3 +chr21_45993530_45993580_ 4.9e-06 7_[+1]_32 +chr21_45971413_45971463_ 4.9e-06 9_[+1]_30 +chr21_31964683_31964733_ 4.9e-06 13_[+1]_26 +chr21_47517957_47518007_ 6.5e-06 32_[+1]_7 +chr21_45978668_45978718_ 6.5e-06 4_[+1]_35 +chr21_32185595_32185645_ 6.5e-06 18_[+1]_21 +chr21_32410820_32410870_ 1.4e-05 21_[+1]_18 +chr21_31992870_31992920_ 1.4e-05 16_[+1]_23 +chr21_19617074_19617124_ 1.4e-05 39_[+1] +chr21_31914206_31914256_ 1.6e-05 15_[+1]_24 +chr21_46020421_46020471_ 1.9e-05 2_[+1]_37 +chr21_32253899_32253949_ 1.9e-05 17_[+1]_22 +chr21_45705687_45705737_ 2.2e-05 37_[+1]_2 +chr21_47575506_47575556_ 3e-05 30_[+1]_9 +chr21_31744582_31744632_ 3e-05 12_[+1]_27 +chr21_31768316_31768366_ 3.7e-05 [+1]_39 +chr21_26934381_26934431_ 3.9e-05 27_[+1]_12 +chr21_31933633_31933683_ 5.6e-05 4_[+1]_35 +chr21_31710037_31710087_ 6.2e-05 14_[+1]_25 +chr21_36411748_36411798_ 7.1e-05 22_[+1]_17 +chr21_46102103_46102153_ 0.00014 36_[+1]_3 +chr21_46086869_46086919_ 0.00014 37_[+1]_2 +chr21_37838750_37838800_ 0.00048 2_[+1]_37 +chr21_31962741_31962791_ 0.00086 13_[+1]_26 +chr21_31973364_31973414_ 0.0015 7_[+1]_32 +chr21_28217753_28217803_ 0.0026 26_[+1]_13 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 in BLOCKS format +-------------------------------------------------------------------------------- +BL MOTIF 1 width=11 seqs=30 +chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 +chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 +chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 +chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 +chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 +chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 +chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 +chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 +chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 +chr21_32185595_32185645_ ( 19) GGGATATATAA 1 +chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 +chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 +chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 +chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 +chr21_46020421_46020471_ ( 3) GACATATAAAA 1 +chr21_32253899_32253949_ ( 18) AGGATATATAA 1 +chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 +chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 +chr21_31744582_31744632_ ( 13) AGCATATATAA 1 +chr21_31768316_31768366_ ( 1) AACGTATATAA 1 +chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 +chr21_31933633_31933683_ ( 5) AGTATATATAA 1 +chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 +chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 +chr21_46102103_46102153_ ( 37) CAGGTATAAAG 1 +chr21_46086869_46086919_ ( 38) CAGGTATAAAG 1 +chr21_37838750_37838800_ ( 3) TGGTTTTATAA 1 +chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 +chr21_31973364_31973414_ ( 8) AAACTCTATAA 1 +chr21_28217753_28217803_ ( 27) GGGGTTTCACT 1 +// + +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 position-specific scoring matrix +-------------------------------------------------------------------------------- +log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 + -14 -179 114 -112 + 3 -1155 137 -270 + -114 20 86 -71 + 3 -279 122 -170 + -1155 -1155 -295 215 + 156 -179 -1155 -170 + -1155 -1155 -1155 220 + 172 -279 -1155 -1155 + 125 -1155 -1155 46 + 167 -179 -1155 -1155 + 144 -1155 -63 -270 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 position-specific probability matrix +-------------------------------------------------------------------------------- +letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 + 0.266667 0.066667 0.566667 0.100000 + 0.300000 0.000000 0.666667 0.033333 + 0.133333 0.266667 0.466667 0.133333 + 0.300000 0.033333 0.600000 0.066667 + 0.000000 0.000000 0.033333 0.966667 + 0.866667 0.066667 0.000000 0.066667 + 0.000000 0.000000 0.000000 1.000000 + 0.966667 0.033333 0.000000 0.000000 + 0.700000 0.000000 0.000000 0.300000 + 0.933333 0.066667 0.000000 0.000000 + 0.800000 0.000000 0.166667 0.033333 +-------------------------------------------------------------------------------- + +-------------------------------------------------------------------------------- + Motif 1 regular expression +-------------------------------------------------------------------------------- +[GA][GA][GC][GA]TATA[AT]AA +-------------------------------------------------------------------------------- + + + + +Time 0.17 secs. + +******************************************************************************** + + +******************************************************************************** +SUMMARY OF MOTIFS +******************************************************************************** + +-------------------------------------------------------------------------------- + Combined block diagrams: non-overlapping sites with p-value < 0.0001 +-------------------------------------------------------------------------------- +SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM +------------- ---------------- ------------- +chr21_19617074_19617124_ 5.63e-04 39_[+1(1.41e-05)] +chr21_26934381_26934431_ 1.57e-03 27_[+1(3.93e-05)]_12 +chr21_28217753_28217803_ 1.00e-01 50 +chr21_31710037_31710087_ 2.49e-03 14_[+1(6.24e-05)]_25 +chr21_31744582_31744632_ 1.22e-03 12_[+1(3.04e-05)]_27 +chr21_31768316_31768366_ 1.47e-03 [+1(3.67e-05)]_39 +chr21_31914206_31914256_ 6.45e-04 15_[+1(1.61e-05)]_24 +chr21_31933633_31933683_ 2.26e-03 4_[+1(5.65e-05)]_35 +chr21_31962741_31962791_ 3.37e-02 50 +chr21_31964683_31964733_ 1.95e-04 13_[+1(4.86e-06)]_26 +chr21_31973364_31973414_ 5.73e-02 50 +chr21_31992870_31992920_ 5.52e-04 16_[+1(1.38e-05)]_23 +chr21_32185595_32185645_ 2.59e-04 18_[+1(6.48e-06)]_21 +chr21_32202076_32202126_ 1.10e-04 13_[+1(2.74e-06)]_26 +chr21_32253899_32253949_ 7.78e-04 17_[+1(1.95e-05)]_22 +chr21_32410820_32410870_ 5.52e-04 21_[+1(1.38e-05)]_18 +chr21_36411748_36411798_ 2.85e-03 22_[+1(7.15e-05)]_17 +chr21_37838750_37838800_ 1.90e-02 50 +chr21_45705687_45705737_ 8.63e-04 37_[+1(2.16e-05)]_2 +chr21_45971413_45971463_ 1.95e-04 9_[+1(4.86e-06)]_30 +chr21_45978668_45978718_ 2.59e-04 4_[+1(6.48e-06)]_35 +chr21_45993530_45993580_ 1.95e-04 7_[+1(4.86e-06)]_32 +chr21_46020421_46020471_ 7.78e-04 2_[+1(1.95e-05)]_37 +chr21_46031920_46031970_ 8.89e-05 15_[+1(2.22e-06)]_24 +chr21_46046964_46047014_ 1.80e-05 12_[+1(4.51e-07)]_27 +chr21_46057197_46057247_ 1.95e-04 36_[+1(4.86e-06)]_3 +chr21_46086869_46086919_ 5.54e-03 50 +chr21_46102103_46102153_ 5.54e-03 50 +chr21_47517957_47518007_ 2.59e-04 32_[+1(6.48e-06)]_7 +chr21_47575506_47575556_ 1.22e-03 30_[+1(3.04e-05)]_9 +-------------------------------------------------------------------------------- + +******************************************************************************** + + +******************************************************************************** +Stopped because requested number of motifs (1) found. +******************************************************************************** + +CPU: dot1x-cb-51.aset.psu.edu + +********************************************************************************
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_xml_1.xml Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,1285 @@ +<?xml version='1.0' encoding='UTF-8' standalone='yes'?> +<!-- Document definition --> +<!DOCTYPE MEME[ +<!ELEMENT MEME ( + training_set, + model, + motifs, + scanned_sites_summary? +)> +<!ATTLIST MEME + version CDATA #REQUIRED + release CDATA #REQUIRED +> +<!-- Training-set elements --> +<!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)> +<!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED> +<!ELEMENT alphabet (letter*)> +<!ATTLIST alphabet name CDATA #REQUIRED> +<!ELEMENT ambigs (letter*)> +<!ELEMENT letter EMPTY> +<!ATTLIST letter id ID #REQUIRED> +<!ATTLIST letter symbol CDATA #REQUIRED> +<!ATTLIST letter equals CDATA #IMPLIED> +<!ATTLIST letter aliases CDATA #IMPLIED> +<!ATTLIST letter complement CDATA #IMPLIED> +<!ATTLIST letter name CDATA #IMPLIED> +<!ATTLIST letter colour CDATA #IMPLIED> +<!ELEMENT sequence EMPTY> +<!ATTLIST sequence id ID #REQUIRED + name CDATA #REQUIRED + length CDATA #REQUIRED + weight CDATA #REQUIRED +> +<!ELEMENT letter_frequencies (alphabet_array)> + +<!-- Model elements --> +<!ELEMENT model ( + command_line, + host, + type, + nmotifs, + evalue_threshold, + object_function, + min_width, + max_width, + minic, + wg, + ws, + endgaps, + minsites, + maxsites, + wnsites, + prob, + spmap, + spfuzz, + prior, + beta, + maxiter, + distance, + num_sequences, + num_positions, + seed, + seqfrac, + strands, + priors_file, + reason_for_stopping, + background_frequencies +)> +<!ELEMENT command_line (#PCDATA)*> +<!ELEMENT host (#PCDATA)*> +<!ELEMENT type (#PCDATA)*> +<!ELEMENT nmotifs (#PCDATA)*> +<!ELEMENT evalue_threshold (#PCDATA)*> +<!ELEMENT object_function (#PCDATA)*> +<!ELEMENT min_width (#PCDATA)*> +<!ELEMENT max_width (#PCDATA)*> +<!ELEMENT minic (#PCDATA)*> +<!ELEMENT wg (#PCDATA)*> +<!ELEMENT ws (#PCDATA)*> +<!ELEMENT endgaps (#PCDATA)*> +<!ELEMENT minsites (#PCDATA)*> +<!ELEMENT maxsites (#PCDATA)*> +<!ELEMENT wnsites (#PCDATA)*> +<!ELEMENT prob (#PCDATA)*> +<!ELEMENT spmap (#PCDATA)*> +<!ELEMENT spfuzz (#PCDATA)*> +<!ELEMENT prior (#PCDATA)*> +<!ELEMENT beta (#PCDATA)*> +<!ELEMENT maxiter (#PCDATA)*> +<!ELEMENT distance (#PCDATA)*> +<!ELEMENT num_sequences (#PCDATA)*> +<!ELEMENT num_positions (#PCDATA)*> +<!ELEMENT seed (#PCDATA)*> +<!ELEMENT seqfrac (#PCDATA)*> +<!ELEMENT strands (#PCDATA)*> +<!ELEMENT priors_file (#PCDATA)*> +<!ELEMENT reason_for_stopping (#PCDATA)*> +<!ELEMENT background_frequencies (alphabet_array)> +<!ATTLIST background_frequencies source CDATA #REQUIRED> + +<!-- Motif elements --> +<!ELEMENT motifs (motif*)> +<!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)> +<!ATTLIST motif id ID #REQUIRED + name CDATA #REQUIRED + width CDATA #REQUIRED + sites CDATA #REQUIRED + llr CDATA #REQUIRED + ic CDATA #REQUIRED + re CDATA #REQUIRED + bayes_threshold CDATA #REQUIRED + e_value CDATA #REQUIRED + elapsed_time CDATA #REQUIRED + url CDATA "" +> +<!ELEMENT scores (alphabet_matrix)> +<!ELEMENT probabilities (alphabet_matrix)> +<!ELEMENT regular_expression (#PCDATA)*> + +<!-- Contributing site elements --> +<!-- Contributing sites are motif occurences found during the motif discovery phase --> +<!ELEMENT contributing_sites (contributing_site*)> +<!ELEMENT contributing_site (left_flank, site, right_flank)> +<!ATTLIST contributing_site sequence_id IDREF #REQUIRED + position CDATA #REQUIRED + strand (plus|minus|none) 'none' + pvalue CDATA #REQUIRED +> +<!-- The left_flank contains the sequence for 10 bases to the left of the motif start --> +<!ELEMENT left_flank (#PCDATA)> +<!-- The site contains the sequence for the motif instance --> +<!ELEMENT site (letter_ref*)> +<!-- The right_flank contains the sequence for 10 bases to the right of the motif end --> +<!ELEMENT right_flank (#PCDATA)> + +<!-- Scanned site elements --> +<!-- Scanned sites are motif occurences found during the 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letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>TCATTCTGAG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_14" position="19" strand="none" pvalue="2.03e-05" > +<left_flank>CACCAGCAAG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GCTCAGGAGT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_4" position="12" strand="none" pvalue="3.06e-05" > +<left_flank>CAGGTCTAAG</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>CTTGGAGTCC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_0" position="39" strand="none" pvalue="3.06e-05" > +<left_flank>CCTCGGGACG</left_flank> +<site> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank></right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_18" position="37" strand="none" pvalue="3.82e-05" > +<left_flank>CGTGGTCGCG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_5" position="0" strand="none" pvalue="3.82e-05" > +<left_flank></left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>ATGGTCCTGT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_29" position="30" strand="none" pvalue="4.02e-05" > +<left_flank>GCTGCCGGTG</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +</site> +<right_flank>GCCCTGGCG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_1" position="27" strand="none" pvalue="5.52e-05" > +<left_flank>AGTCACAAGT</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GGGTCGCACG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_3" position="14" strand="none" pvalue="5.94e-05" > +<left_flank>CCCAGGTTTC</left_flank> +<site> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>TCGCCGCACC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_16" position="22" strand="none" pvalue="6.78e-05" > +<left_flank>AGTTTCAGTT</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>attatataac</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_7" position="2" strand="none" pvalue="2.08e-04" > +<left_flank>TC</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +</site> +<right_flank>AAATGTTCCT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_8" position="13" strand="none" pvalue="4.05e-04" > +<left_flank>TATAACTCAG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>TAATTTGTAC</right_flank> +</contributing_site> +</contributing_sites> +</motif> +</motifs> +<scanned_sites_summary p_thresh="0.0001"> +<scanned_sites sequence_id="sequence_0" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="39" pvalue="3.06e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_1" pvalue="2.21e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="27" pvalue="5.52e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_2" pvalue="7.29e-01" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_3" pvalue="2.37e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="14" pvalue="5.94e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="3.06e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_5" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="0" pvalue="3.82e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_6" pvalue="6.70e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="1.68e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_7" pvalue="1.81e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="4.54e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_8" pvalue="1.61e-02" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_9" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="3.41e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_10" pvalue="1.99e-01" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_11" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="16" pvalue="8.67e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_12" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="18" pvalue="8.67e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_13" pvalue="2.01e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="13" pvalue="5.01e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_14" pvalue="8.11e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="19" pvalue="2.03e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_15" pvalue="3.47e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="21" pvalue="8.67e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_16" pvalue="2.71e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="22" pvalue="6.78e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_17" pvalue="8.23e-02" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_18" pvalue="1.53e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="37" pvalue="3.82e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_19" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="9" pvalue="3.41e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_20" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="4" pvalue="1.59e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_21" pvalue="1.60e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="7" pvalue="4.00e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_22" pvalue="4.83e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="2" pvalue="1.21e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_23" pvalue="2.43e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="15" pvalue="6.06e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_24" pvalue="4.26e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="12" pvalue="1.06e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_25" pvalue="1.36e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="36" pvalue="3.41e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_26" pvalue="4.30e-02" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_27" pvalue="4.30e-02" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_28" pvalue="6.37e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="32" pvalue="1.59e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_29" pvalue="1.61e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="none" position="30" pvalue="4.02e-05"/> +</scanned_sites> +</scanned_sites_summary> +</MEME>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/meme_output_xml_2.xml Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,977 @@ +<?xml version='1.0' encoding='UTF-8' standalone='yes'?> +<!-- Document definition --> +<!DOCTYPE MEME[ +<!ELEMENT MEME ( + training_set, + model, + motifs, + scanned_sites_summary? +)> +<!ATTLIST MEME + version CDATA #REQUIRED + release CDATA #REQUIRED +> +<!-- Training-set elements --> +<!ELEMENT training_set (alphabet, ambigs, sequence*, letter_frequencies)> +<!ATTLIST training_set datafile CDATA #REQUIRED length CDATA #REQUIRED> +<!ELEMENT alphabet (letter*)> +<!ATTLIST alphabet name CDATA #REQUIRED> +<!ELEMENT ambigs (letter*)> +<!ELEMENT letter EMPTY> +<!ATTLIST letter id ID #REQUIRED> +<!ATTLIST letter symbol CDATA #REQUIRED> +<!ATTLIST letter equals CDATA #IMPLIED> +<!ATTLIST letter aliases CDATA #IMPLIED> +<!ATTLIST letter complement CDATA #IMPLIED> +<!ATTLIST letter name CDATA #IMPLIED> +<!ATTLIST letter colour CDATA #IMPLIED> +<!ELEMENT sequence EMPTY> +<!ATTLIST sequence id ID #REQUIRED + name CDATA #REQUIRED + length CDATA #REQUIRED + weight CDATA #REQUIRED +> +<!ELEMENT letter_frequencies (alphabet_array)> + +<!-- Model elements --> +<!ELEMENT model ( + command_line, + host, + type, + nmotifs, + evalue_threshold, + object_function, + min_width, + max_width, + minic, + wg, + ws, + endgaps, + minsites, + maxsites, + wnsites, + prob, + spmap, + spfuzz, + prior, + beta, + maxiter, + distance, + num_sequences, + num_positions, + seed, + seqfrac, + strands, + priors_file, + reason_for_stopping, + background_frequencies +)> +<!ELEMENT command_line (#PCDATA)*> +<!ELEMENT host (#PCDATA)*> +<!ELEMENT type (#PCDATA)*> +<!ELEMENT nmotifs (#PCDATA)*> +<!ELEMENT evalue_threshold (#PCDATA)*> +<!ELEMENT object_function (#PCDATA)*> +<!ELEMENT min_width (#PCDATA)*> +<!ELEMENT max_width (#PCDATA)*> +<!ELEMENT minic (#PCDATA)*> +<!ELEMENT wg (#PCDATA)*> +<!ELEMENT ws (#PCDATA)*> +<!ELEMENT endgaps (#PCDATA)*> +<!ELEMENT minsites (#PCDATA)*> +<!ELEMENT maxsites (#PCDATA)*> +<!ELEMENT wnsites (#PCDATA)*> +<!ELEMENT prob (#PCDATA)*> +<!ELEMENT spmap (#PCDATA)*> +<!ELEMENT spfuzz (#PCDATA)*> +<!ELEMENT prior (#PCDATA)*> +<!ELEMENT beta (#PCDATA)*> +<!ELEMENT maxiter (#PCDATA)*> +<!ELEMENT distance (#PCDATA)*> +<!ELEMENT num_sequences (#PCDATA)*> +<!ELEMENT num_positions (#PCDATA)*> +<!ELEMENT seed (#PCDATA)*> +<!ELEMENT seqfrac (#PCDATA)*> +<!ELEMENT strands (#PCDATA)*> +<!ELEMENT priors_file (#PCDATA)*> +<!ELEMENT reason_for_stopping (#PCDATA)*> +<!ELEMENT background_frequencies (alphabet_array)> +<!ATTLIST background_frequencies source CDATA #REQUIRED> + +<!-- Motif elements --> +<!ELEMENT motifs (motif*)> +<!ELEMENT motif (scores, probabilities, regular_expression?, contributing_sites)> +<!ATTLIST motif id ID #REQUIRED + name CDATA #REQUIRED + width CDATA #REQUIRED + sites CDATA #REQUIRED + llr CDATA #REQUIRED + ic CDATA #REQUIRED + re CDATA #REQUIRED + bayes_threshold CDATA #REQUIRED + e_value CDATA #REQUIRED + elapsed_time CDATA #REQUIRED + url CDATA "" +> +<!ELEMENT scores (alphabet_matrix)> +<!ELEMENT probabilities (alphabet_matrix)> +<!ELEMENT regular_expression (#PCDATA)*> + +<!-- Contributing site elements --> +<!-- Contributing sites are motif occurences found during the motif discovery phase --> +<!ELEMENT contributing_sites (contributing_site*)> +<!ELEMENT contributing_site (left_flank, site, right_flank)> +<!ATTLIST contributing_site sequence_id IDREF #REQUIRED + position CDATA #REQUIRED + strand (plus|minus|none) 'none' + pvalue CDATA #REQUIRED +> +<!-- The left_flank contains the sequence for 10 bases to the left of the motif start --> +<!ELEMENT left_flank (#PCDATA)> +<!-- The site contains the sequence for the motif instance --> +<!ELEMENT site (letter_ref*)> +<!-- The right_flank contains the sequence for 10 bases to the right of the motif end --> +<!ELEMENT right_flank (#PCDATA)> + +<!-- Scanned site elements --> +<!-- Scanned sites are motif occurences found during the sequence scan phase --> +<!ELEMENT scanned_sites_summary (scanned_sites*)> +<!ATTLIST scanned_sites_summary p_thresh CDATA #REQUIRED> +<!ELEMENT scanned_sites (scanned_site*)> +<!ATTLIST scanned_sites sequence_id IDREF #REQUIRED + pvalue CDATA #REQUIRED + num_sites CDATA #REQUIRED> +<!ELEMENT scanned_site EMPTY> +<!ATTLIST scanned_site motif_id IDREF #REQUIRED + strand (plus|minus|none) 'none' + position CDATA #REQUIRED + pvalue CDATA #REQUIRED> + +<!-- Utility elements --> +<!-- A reference to a letter in the alphabet --> +<!ELEMENT letter_ref EMPTY> +<!ATTLIST letter_ref letter_id IDREF #REQUIRED> +<!-- A alphabet-array contains one floating point value for each letter in an alphabet --> +<!ELEMENT alphabet_array (value*)> +<!ELEMENT value (#PCDATA)> +<!ATTLIST value letter_id IDREF #REQUIRED> + +<!-- A alphabet_matrix contains one alphabet_array for each position in a motif --> +<!ELEMENT alphabet_matrix (alphabet_array*)> + +]> +<!-- Begin document body --> +<MEME version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000"> +<training_set datafile="Galaxy_FASTA_Input" length="30"> +<alphabet name="DNA" like="dna"> +<letter id="A" symbol="A" complement="T" name="Adenine" colour="CC0000"/> +<letter id="C" symbol="C" complement="G" name="Cytosine" colour="0000CC"/> +<letter id="G" symbol="G" complement="C" name="Guanine" colour="FFB300"/> +<letter id="T" symbol="T" aliases="U" complement="A" name="Thymine" colour="008000"/> +<letter id="N" symbol="N" aliases="X." equals="ACGT" name="Any base"/> +<letter id="V" symbol="V" equals="ACG" name="Not T"/> +<letter id="H" symbol="H" equals="ACT" name="Not G"/> +<letter id="D" symbol="D" equals="AGT" name="Not C"/> +<letter id="B" symbol="B" equals="CGT" name="Not A"/> +<letter id="M" symbol="M" equals="AC" name="Amino"/> +<letter id="R" symbol="R" equals="AG" name="Purine"/> +<letter id="W" symbol="W" equals="AT" name="Weak"/> +<letter id="S" symbol="S" equals="CG" name="Strong"/> +<letter id="Y" symbol="Y" equals="CT" name="Pyrimidine"/> +<letter id="K" symbol="K" equals="GT" name="Keto"/> +</alphabet> +<sequence id="sequence_0" name="chr21_19617074_19617124_+" length="50" weight="1.000000" /> +<sequence id="sequence_1" name="chr21_26934381_26934431_+" length="50" weight="1.000000" /> +<sequence id="sequence_2" name="chr21_28217753_28217803_-" length="50" weight="1.000000" /> +<sequence id="sequence_3" name="chr21_31710037_31710087_-" length="50" weight="1.000000" /> +<sequence id="sequence_4" name="chr21_31744582_31744632_-" length="50" weight="1.000000" /> +<sequence id="sequence_5" name="chr21_31768316_31768366_+" length="50" weight="1.000000" /> +<sequence id="sequence_6" name="chr21_31914206_31914256_-" length="50" weight="1.000000" /> +<sequence id="sequence_7" name="chr21_31933633_31933683_-" length="50" weight="1.000000" /> +<sequence id="sequence_8" name="chr21_31962741_31962791_-" length="50" weight="1.000000" /> +<sequence id="sequence_9" name="chr21_31964683_31964733_+" length="50" weight="1.000000" /> +<sequence id="sequence_10" name="chr21_31973364_31973414_+" length="50" weight="1.000000" /> +<sequence id="sequence_11" name="chr21_31992870_31992920_+" length="50" weight="1.000000" /> +<sequence id="sequence_12" name="chr21_32185595_32185645_-" length="50" weight="1.000000" /> +<sequence id="sequence_13" name="chr21_32202076_32202126_-" length="50" weight="1.000000" /> +<sequence id="sequence_14" name="chr21_32253899_32253949_-" length="50" weight="1.000000" /> +<sequence id="sequence_15" name="chr21_32410820_32410870_-" length="50" weight="1.000000" /> +<sequence id="sequence_16" name="chr21_36411748_36411798_-" length="50" weight="1.000000" /> +<sequence id="sequence_17" name="chr21_37838750_37838800_-" length="50" weight="1.000000" /> +<sequence id="sequence_18" name="chr21_45705687_45705737_+" length="50" weight="1.000000" /> +<sequence id="sequence_19" name="chr21_45971413_45971463_-" length="50" weight="1.000000" /> +<sequence id="sequence_20" name="chr21_45978668_45978718_-" length="50" weight="1.000000" /> +<sequence id="sequence_21" name="chr21_45993530_45993580_+" length="50" weight="1.000000" /> +<sequence id="sequence_22" name="chr21_46020421_46020471_+" length="50" weight="1.000000" /> +<sequence id="sequence_23" name="chr21_46031920_46031970_+" length="50" weight="1.000000" /> +<sequence id="sequence_24" name="chr21_46046964_46047014_+" length="50" weight="1.000000" /> +<sequence id="sequence_25" name="chr21_46057197_46057247_+" length="50" weight="1.000000" /> +<sequence id="sequence_26" name="chr21_46086869_46086919_-" length="50" weight="1.000000" /> +<sequence id="sequence_27" name="chr21_46102103_46102153_-" length="50" weight="1.000000" /> +<sequence id="sequence_28" name="chr21_47517957_47518007_+" length="50" weight="1.000000" /> +<sequence id="sequence_29" name="chr21_47575506_47575556_-" length="50" weight="1.000000" /> +<letter_frequencies> +<alphabet_array> +<value letter_id="A">0.294</value> +<value letter_id="C">0.231</value> +<value letter_id="G">0.257</value> +<value letter_id="T">0.217</value> +</alphabet_array> +</letter_frequencies> +</training_set> +<model> +<command_line>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_line> +<host>MacBook-Pro-2.local</host> +<type>zoops</type> +<nmotifs>1</nmotifs> +<evalue_threshold>inf</evalue_threshold> +<object_function>E-value of product of p-values</object_function> +<use_llr>0</use_llr> +<min_width>8</min_width> +<max_width>50</max_width> +<wg>11</wg> +<ws>1</ws> +<endgaps>yes</endgaps> +<substring>yes</substring> +<minsites>2</minsites> +<maxsites>30</maxsites> +<wnsites>0.8</wnsites> +<spmap>uni</spmap> +<spfuzz>0.5</spfuzz> +<prior>dirichlet</prior> +<beta>0.01</beta> +<maxiter>50</maxiter> +<distance>0.001</distance> +<num_sequences>30</num_sequences> +<num_positions>1500</num_positions> +<seed>0</seed> +<ctfrac>-1</ctfrac> +<maxwords>-1</maxwords> +<strands>forward</strands> +<priors_file>dataset_2577.dat</priors_file> +<reason_for_stopping>Stopped because requested number of motifs (1) found.</reason_for_stopping> +<background_frequencies source="dataset with add-one prior applied"> +<alphabet_array> +<value letter_id="A">0.294</value> +<value letter_id="C">0.231</value> +<value letter_id="G">0.257</value> +<value letter_id="T">0.217</value> +</alphabet_array> +</background_frequencies> +</model> +<motifs> +<motif id="motif_1" name="1" width="11" sites="30" ic="13.0" re="12.2" llr="254" e_value="5.1e-040" bayes_threshold="5.2854" elapsed_time="0.168106"> +<scores> +<alphabet_matrix> +<alphabet_array> +<value letter_id="A">-14</value> +<value letter_id="C">-179</value> +<value letter_id="G">114</value> +<value letter_id="T">-112</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">3</value> +<value letter_id="C">-1155</value> +<value letter_id="G">137</value> +<value letter_id="T">-270</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-114</value> +<value letter_id="C">20</value> +<value letter_id="G">86</value> +<value letter_id="T">-71</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">3</value> +<value letter_id="C">-279</value> +<value letter_id="G">122</value> +<value letter_id="T">-170</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-1155</value> +<value letter_id="C">-1155</value> +<value letter_id="G">-295</value> +<value letter_id="T">215</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">156</value> +<value letter_id="C">-179</value> +<value letter_id="G">-1155</value> +<value letter_id="T">-170</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">-1155</value> +<value letter_id="C">-1155</value> +<value letter_id="G">-1155</value> +<value letter_id="T">220</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">172</value> +<value letter_id="C">-279</value> +<value letter_id="G">-1155</value> +<value letter_id="T">-1155</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">125</value> +<value letter_id="C">-1155</value> +<value letter_id="G">-1155</value> +<value letter_id="T">46</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">167</value> +<value letter_id="C">-179</value> +<value letter_id="G">-1155</value> +<value letter_id="T">-1155</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">144</value> +<value letter_id="C">-1155</value> +<value letter_id="G">-63</value> +<value letter_id="T">-270</value> +</alphabet_array> +</alphabet_matrix> +</scores> +<probabilities> +<alphabet_matrix> +<alphabet_array> +<value letter_id="A">0.266667</value> +<value letter_id="C">0.066667</value> +<value letter_id="G">0.566667</value> +<value letter_id="T">0.100000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.300000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.666667</value> +<value letter_id="T">0.033333</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.133333</value> +<value letter_id="C">0.266667</value> +<value letter_id="G">0.466667</value> +<value letter_id="T">0.133333</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.300000</value> +<value letter_id="C">0.033333</value> +<value letter_id="G">0.600000</value> +<value letter_id="T">0.066667</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.000000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.033333</value> +<value letter_id="T">0.966667</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.866667</value> +<value letter_id="C">0.066667</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">0.066667</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.000000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">1.000000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.966667</value> +<value letter_id="C">0.033333</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">0.000000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.700000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">0.300000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.933333</value> +<value letter_id="C">0.066667</value> +<value letter_id="G">0.000000</value> +<value letter_id="T">0.000000</value> +</alphabet_array> +<alphabet_array> +<value letter_id="A">0.800000</value> +<value letter_id="C">0.000000</value> +<value letter_id="G">0.166667</value> +<value letter_id="T">0.033333</value> +</alphabet_array> +</alphabet_matrix> +</probabilities> +<regular_expression> +[GA][GA][GC][GA]TATA[AT]AA +</regular_expression> +<contributing_sites> +<contributing_site sequence_id="sequence_24" position="12" strand="plus" pvalue="4.51e-07" > +<left_flank>AAGGCCAGGA</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GCCTGAGAGC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_23" position="15" strand="plus" pvalue="2.22e-06" > +<left_flank>ATACCCAGGG</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>CCTCAGCAGC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_13" position="13" strand="plus" pvalue="2.74e-06" > +<left_flank>CCACCAGCTT</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>AGCCCTGTAC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_25" position="36" strand="plus" pvalue="4.86e-06" > +<left_flank>ACAGGCCCTG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GCC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_21" position="7" strand="plus" pvalue="4.86e-06" > +<left_flank>CCAAGGA</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GCCCCACAAA</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_19" position="9" strand="plus" pvalue="4.86e-06" > +<left_flank>CAGGCCCTG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GCCCCAGCAG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_9" position="13" strand="plus" pvalue="4.86e-06" > +<left_flank>GATTCACTGA</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GGCCCTCTGC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_28" position="32" strand="plus" pvalue="6.48e-06" > +<left_flank>CCGGCGGGGC</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +</site> +<right_flank>GGGGCGG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_20" position="4" strand="plus" pvalue="6.48e-06" > +<left_flank>CAGA</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +</site> +<right_flank>GTTCCGACCA</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_12" position="18" strand="plus" pvalue="6.48e-06" > +<left_flank>CACCAGAGCT</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>AGAAGGTTCT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_15" position="21" strand="plus" pvalue="1.38e-05" > +<left_flank>AATCACTGAG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GTCCCAGGGA</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_11" position="16" strand="plus" pvalue="1.38e-05" > +<left_flank>CACTATTGAA</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>TTTCATTTGC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_0" position="39" strand="plus" pvalue="1.41e-05" > +<left_flank>CCTCGGGACG</left_flank> +<site> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank></right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_6" position="15" strand="plus" pvalue="1.61e-05" > +<left_flank>CCCACTACTT</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>TCATTCTGAG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_22" position="2" strand="plus" pvalue="1.95e-05" > +<left_flank>GA</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GCCAACATCC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_14" position="17" strand="plus" pvalue="1.95e-05" > +<left_flank>CCCACCAGCA</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>AAGCTCAGGA</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_18" position="37" strand="plus" pvalue="2.16e-05" > +<left_flank>CGTGGTCGCG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_29" position="30" strand="plus" pvalue="3.04e-05" > +<left_flank>GCTGCCGGTG</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +</site> +<right_flank>GCCCTGGCG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_4" position="12" strand="plus" pvalue="3.04e-05" > +<left_flank>CAGGTCTAAG</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>CTTGGAGTCC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_5" position="0" strand="plus" pvalue="3.67e-05" > +<left_flank></left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>ATGGTCCTGT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_1" position="27" strand="plus" pvalue="3.93e-05" > +<left_flank>AGTCACAAGT</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>GGGTCGCACG</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_7" position="4" strand="plus" pvalue="5.65e-05" > +<left_flank>TCAG</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>ATGTTCCTGT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_3" position="14" strand="plus" pvalue="6.24e-05" > +<left_flank>CCCAGGTTTC</left_flank> +<site> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>TCGCCGCACC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_16" position="22" strand="plus" pvalue="7.15e-05" > +<left_flank>AGTTTCAGTT</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>attatataac</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_27" position="36" strand="plus" pvalue="1.39e-04" > +<left_flank>TGCCTGGGTC</left_flank> +<site> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +</site> +<right_flank>GCT</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_26" position="37" strand="plus" pvalue="1.39e-04" > +<left_flank>TGCCTGGGCC</left_flank> +<site> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="G"/> +</site> +<right_flank>GC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_17" position="2" strand="plus" pvalue="4.81e-04" > +<left_flank>ga</left_flank> +<site> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>ggggcctcac</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_8" position="13" strand="plus" pvalue="8.57e-04" > +<left_flank>TATAACTCAG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>TAATTTGTAC</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_10" position="7" strand="plus" pvalue="1.47e-03" > +<left_flank>aaactta</left_flank> +<site> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="A"/> +</site> +<right_flank>acttaaaact</right_flank> +</contributing_site> +<contributing_site sequence_id="sequence_2" position="26" strand="plus" pvalue="2.64e-03" > +<left_flank>GGTGGGGGTG</left_flank> +<site> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="G"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="T"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="A"/> +<letter_ref letter_id="C"/> +<letter_ref letter_id="T"/> +</site> +<right_flank>GGTCCACTAT</right_flank> +</contributing_site> +</contributing_sites> +</motif> +</motifs> +<scanned_sites_summary p_thresh="0.0001"> +<scanned_sites sequence_id="sequence_0" pvalue="5.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="39" pvalue="1.41e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_1" pvalue="1.57e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="27" pvalue="3.93e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_2" pvalue="1.00e-01" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_3" pvalue="2.49e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="14" pvalue="6.24e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_4" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="3.04e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_5" pvalue="1.47e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="0" pvalue="3.67e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_6" pvalue="6.45e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="1.61e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_7" pvalue="2.26e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="5.65e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_8" pvalue="3.37e-02" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_9" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="4.86e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_10" pvalue="5.73e-02" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_11" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="16" pvalue="1.38e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_12" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="18" pvalue="6.48e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_13" pvalue="1.10e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="13" pvalue="2.74e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_14" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="17" pvalue="1.95e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_15" pvalue="5.52e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="21" pvalue="1.38e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_16" pvalue="2.85e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="22" pvalue="7.15e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_17" pvalue="1.90e-02" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_18" pvalue="8.63e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="37" pvalue="2.16e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_19" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="9" pvalue="4.86e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_20" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="4" pvalue="6.48e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_21" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="7" pvalue="4.86e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_22" pvalue="7.78e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="2" pvalue="1.95e-05"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_23" pvalue="8.89e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="15" pvalue="2.22e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_24" pvalue="1.80e-05" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="12" pvalue="4.51e-07"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_25" pvalue="1.95e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="36" pvalue="4.86e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_26" pvalue="5.54e-03" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_27" pvalue="5.54e-03" num_sites="0"></scanned_sites> +<scanned_sites sequence_id="sequence_28" pvalue="2.59e-04" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="32" pvalue="6.48e-06"/> +</scanned_sites> +<scanned_sites sequence_id="sequence_29" pvalue="1.22e-03" num_sites="1"><scanned_site motif_id="motif_1" strand="plus" position="30" pvalue="3.04e-05"/> +</scanned_sites> +</scanned_sites_summary> +</MEME>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prior30.plib Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,275 @@ +Alphabet= ACDEFGHIKLMNPQRSTVWY +NumDistr= 30 +Number= 0 +Mixture= 0.055795 +B= 5.623820 +Alpha= 0.0855491 0.0221831 0.0111063 0.0209959 0.0505726 0.025437 0.0155389 0.132951 0.0247865 0.150287 0.0577239 0.0209317 0.0166629 0.0220905 0.0244295 0.0497608 0.070277 0.157532 0.0102219 0.0309633 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= HMM9.4 reestimated in henikoff29.2 + +Number= 1 +Mixture= 0.198333 +B= 0.097240 +Alpha= 0.0562629 0.0329597 0.0692513 0.0385232 0.0400041 0.143573 0.0428939 0.0226244 0.0442102 0.0665467 0.0117853 0.0447655 0.0833299 0.0395825 0.0611271 0.0588852 0.0513472 0.0317153 0.0237865 0.0368161 +FullUpdate= 1 +QUpdate= 1 +StructID= 24 +Comment= Outside + +Number= 2 +Mixture= 0.043566 +B= 1.648336 +Alpha= 0.0144564 0.00845337 0.00785519 0.00864933 0.255959 0.0110815 0.0509526 0.0234533 0.0120443 0.0561967 0.015111 0.0190974 0.00857653 0.0167812 0.0164918 0.0197108 0.0151013 0.0252782 0.050139 0.364613 +FullUpdate= 1 +QUpdate= 1 +StructID= 26 +Comment= Inside + +Number= 3 +Mixture= 0.060170 +B= 2.595432 +Alpha= 0.0452144 0.00587917 0.169731 0.0751478 0.00749471 0.0845832 0.0369819 0.00610072 0.0548186 0.011029 0.00382749 0.212785 0.0206532 0.0416705 0.0280716 0.117267 0.0533742 0.00943157 0.00216149 0.0137784 +FullUpdate= 1 +QUpdate= 1 +StructID= 19 +Comment= Outside Alpha + +Number= 4 +Mixture= 0.065466 +B= 3.112271 +Alpha= 0.0361167 0.0049157 0.0134924 0.0461325 0.00557631 0.0209043 0.0302551 0.016425 0.307554 0.0338255 0.0139435 0.0360733 0.0127659 0.0873761 0.222668 0.0369042 0.0354442 0.0228891 0.00434827 0.0123906 +FullUpdate= 1 +QUpdate= 1 +StructID= 21 +Comment= Outside Beta + +Number= 5 +Mixture= 0.067614 +B= 2.053644 +Alpha= 0.0194362 0.00765176 0.00188738 0.00372898 0.0849894 0.00421787 0.00400459 0.152735 0.00407958 0.4568 0.106051 0.00304386 0.00545956 0.00900935 0.00605071 0.00519029 0.016255 0.0861045 0.00787965 0.0154248 +FullUpdate= 1 +QUpdate= 1 +StructID= 22 +Comment= Inside alpha + +Number= 6 +Mixture= 0.080724 +B= 2.138987 +Alpha= 0.0423172 0.0153891 0.00409306 0.00565735 0.0197117 0.00590607 0.00139926 0.307863 0.00544884 0.115721 0.0285808 0.00522771 0.00474851 0.00328193 0.00351054 0.00892385 0.0348922 0.380003 0.00117673 0.00614917 +FullUpdate= 1 +QUpdate= 1 +StructID= 23 +Comment= Inside beta + +Number= 7 +Mixture= 0.051030 +B= 3.878926 +Alpha= 0.0548123 0.000759746 0.144127 0.46019 0.00249502 0.0192754 0.0106535 0.00938765 0.0562429 0.0163148 0.00717389 0.0245612 0.0177482 0.0744802 0.0199233 0.0323535 0.0257651 0.018574 0.00087086 0.00429088 +FullUpdate= 1 +QUpdate= 1 +StructID= 23 +Comment= Alpha helix + +Number= 8 +Mixture= 0.103529 +B= 1.486325 +Alpha= 0.315754 0.0384546 0.0116388 0.0133665 0.0111126 0.107921 0.00752325 0.0154885 0.0111281 0.0231087 0.011626 0.0228375 0.0304785 0.0166632 0.0156345 0.186379 0.0954421 0.0546691 0.00351538 0.00725682 +FullUpdate= 1 +QUpdate= 1 +StructID= 23 +Comment= Beta strand + +Number= 9 +Mixture= 0.062940 +B= 8.221215 +Alpha= 0.0869919 0.00672577 0.0600995 0.10763 0.0153489 0.0378086 0.0325335 0.023388 0.113765 0.041623 0.0196906 0.0625344 0.0262599 0.0788667 0.0707399 0.0886634 0.0666777 0.0361472 0.00484308 0.0196629 +FullUpdate= 1 +QUpdate= 1 +StructID= 23 +Comment= Other + +Number= 10 +Mixture= 0.012518 +B= 38.955631 +Alpha= 0.732922 0.0145131 0.00623235 0.00951423 0.00717778 0.0289521 0.00351664 0.0125081 0.00886593 0.0183651 0.00832812 0.00670968 0.00364556 0.00622169 0.00812899 0.0582399 0.0205067 0.0394327 0.00207485 0.00414489 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= A + +Number= 11 +Mixture= 0.004953 +B= 381.562195 +Alpha= 0.00563239 0.959814 0.00144129 0.00213042 0.00158645 0.00168393 0.000989765 0.00325263 0.00148501 0.00343924 0.00168673 0.00159054 0.00121534 0.00129942 0.00195209 0.00296106 0.0039912 0.00266944 0.000327808 0.000851203 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= C + +Number= 12 +Mixture= 0.013849 +B= 90.727570 +Alpha= 0.00897115 0.00169015 0.859473 0.0360829 0.00269485 0.00606504 0.00469816 0.00400134 0.0047981 0.00514968 0.00208395 0.029754 0.00241276 0.0045506 0.00433816 0.0088208 0.00511143 0.00527448 0.00104469 0.00298475 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= D + +Number= 13 +Mixture= 0.008388 +B= 404.591034 +Alpha= 0.00241514 0.000413991 0.0122981 0.96369 0.000665578 0.00187461 0.00106904 0.00149214 0.00121548 0.00129791 0.000554145 0.00253496 0.000624495 0.00316839 0.00115045 0.00171781 0.001468 0.0014564 0.000278652 0.000614791 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= E + +Number= 14 +Mixture= 0.008064 +B= 83.323669 +Alpha= 0.00839779 0.00428348 0.00298116 0.00358128 0.850936 0.00329382 0.00196832 0.0130534 0.00320345 0.0351883 0.00729724 0.00287304 0.00358482 0.00218728 0.00264753 0.00833798 0.00418729 0.0120684 0.00448366 0.025446 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= F + +Number= 15 +Mixture= 0.032205 +B= 32.644871 +Alpha= 0.0234448 0.00236512 0.0112957 0.00811395 0.00248143 0.868718 0.00345598 0.00342985 0.00859682 0.0040966 0.00239339 0.012342 0.00423123 0.00440054 0.00795347 0.0165095 0.0065024 0.00550512 0.00140604 0.00275817 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= G + +Number= 16 +Mixture= 0.005033 +B= 35.520824 +Alpha= 0.0100058 0.00386024 0.0131498 0.0108984 0.0122851 0.00738691 0.722249 0.00521193 0.00686054 0.0150103 0.00673014 0.0367074 0.00625526 0.0429912 0.0234127 0.0187246 0.0128445 0.00837399 0.00390723 0.0331349 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= H + +Number= 17 +Mixture= 0.007454 +B= 101.265472 +Alpha= 0.0106938 0.00267663 0.00404166 0.00466637 0.00838963 0.00372808 0.00182575 0.681615 0.0059102 0.0770333 0.0184335 0.004676 0.0027124 0.00372663 0.00418165 0.00773357 0.0109237 0.140679 0.00140417 0.00494911 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= I + +Number= 18 +Mixture= 0.009400 +B= 150.415985 +Alpha= 0.00688657 0.00169711 0.00222738 0.00346887 0.00115861 0.00302866 0.00209171 0.00400905 0.903944 0.0037747 0.00186061 0.00449531 0.00249618 0.00324487 0.041775 0.00392196 0.00461714 0.00296607 0.000893256 0.00144282 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= K + +Number= 19 +Mixture= 0.017057 +B= 31.896633 +Alpha= 0.0114646 0.00367926 0.00296188 0.00596126 0.0190009 0.00382486 0.00338381 0.0401936 0.00650072 0.790038 0.031659 0.00392791 0.0050046 0.00753591 0.00771818 0.00748621 0.0101555 0.0312597 0.00242405 0.00581952 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= L + +Number= 20 +Mixture= 0.002761 +B= 201.346268 +Alpha= 0.00353933 0.00165628 0.0014931 0.00161065 0.00279831 0.00194259 0.00101868 0.00969101 0.00211316 0.0217036 0.928022 0.00162899 0.0015681 0.0015629 0.00138977 0.00294601 0.00311476 0.00723178 0.00156295 0.00340569 +FullUpdate= 1 +QUpdate= 1 +StructID= 0 +Comment= M + +Number= 21 +Mixture= 0.005734 +B= 108.343185 +Alpha= 0.0067512 0.00239062 0.0140378 0.0043452 0.00365788 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Dec 22 17:01:51 2015 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="meme" version="4.11.0"> + <repository changeset_revision="6ee2e1225125" name="package_meme_4_11_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>