Mercurial > repos > iuc > meme_fimo
changeset 19:01f5d04846c4 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 93fe7345e2b6a97000975d978bf06513b3a442d9
| author | iuc |
|---|---|
| date | Thu, 29 Aug 2024 10:19:40 +0000 (7 months ago) |
| parents | c5209f38700d |
| children | |
| files | fimo.xml macros.xml test-data/dreme_output_test1.html test-data/dreme_output_test1.txt test-data/dreme_output_test1.xml test-data/dreme_output_test2.html test-data/dreme_output_test2.txt test-data/dreme_output_test2.xml test-data/fimo_output_test1.gff test-data/fimo_output_test1.html test-data/fimo_output_test1.txt test-data/fimo_output_test1.xml test-data/fimo_output_test2.gff test-data/fimo_output_test2.html test-data/fimo_output_test2.txt test-data/fimo_output_test2.xml test-data/fimo_output_test3.html test-data/fimo_output_test3.txt test-data/fimo_output_test3.xml |
| diffstat | 19 files changed, 121 insertions(+), 679 deletions(-) [+] |
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--- a/fimo.xml Sat Apr 09 08:32:23 2022 +0000 +++ b/fimo.xml Thu Aug 29 10:19:40 2024 +0000 @@ -1,12 +1,12 @@ -<tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> +<tool id="meme_fimo" name="FIMO" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>- Scan a set of sequences for motifs</description> + <macros> + <import>macros.xml</import> + </macros> <xrefs> <xref type="bio.tools">meme_fimo</xref> </xrefs> - <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements" /> + <expand macro="requirements"/> <command detect_errors="exit_code"><![CDATA[ @CHECK_NON_COMMERCIAL_USE@ fimo @@ -56,8 +56,7 @@ && mv ./out/fimo.gff '${gff_outfile}' ]]></command> <inputs> - <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file" - help="DREME or MEME output XML file containing found motifs"/> + <param name="input_motifs" type="data" format="memexml" label="DREME or MEME output XML file" help="DREME or MEME output XML file containing found motifs"/> <conditional name="fasta_type"> <param name="fasta_type_selector" type="select" label="Source for sequence to search"> <option value="cached">Locally Cached sequences</option> @@ -65,16 +64,14 @@ </param> <when value="cached"> <param name="input_database" type="select" label="Genome to search"> - <options from_data_table="all_fasta" /> + <options from_data_table="all_fasta"/> </param> </when> <when value="history"> - <param format="fasta" name="input_database" type="data" label="Sequences"/> + <param name="input_database" type="data" format="fasta" label="Sequences"/> </when> </conditional> - <param name="scanrc" label="Check reverse complement strand" type="boolean" - truevalue="" falsevalue="--norc" checked="False" - help="Search for motifs also on reverse complement strand"/> + <param name="scanrc" type="boolean" truevalue="" falsevalue="--norc" checked="False" label="Check reverse complement strand" help="Search for motifs also on reverse complement strand"/> <conditional name="options_type"> <param name="options_type_selector" type="select" label="Options configuration"> <option value="basic" selected="true">Basic</option> @@ -82,12 +79,8 @@ </param> <when value="basic"/> <when value="advanced"> - <param name="thresh" type="float" value="1e-4" argument="--thresh" - label="Output threshold for displaying search results" - help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/> - <param name="qv_thresh" label="Apply output threshold to q-values?" argument="--qv-thresh" - type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" - help="Default: apply set threshold on p-values"/> + <param argument="--thresh" type="float" value="1e-4" label="Output threshold for displaying search results" help="Only output results with a p-value less than the given threshold. To apply set threshold to q-values rather than p-values, set --qv-thresh."/> + <param argument="--qv-thresh" type="boolean" truevalue="--qv_thresh" falsevalue="" checked="False" label="Apply output threshold to q-values?" help="Default: apply set threshold on p-values"/> <conditional name="bgfile_type"> <param name="bgfile_type_selector" type="select" label="Background model selection"> <option value="default" selected="true">Use embedded letter frequencies from non-redundant DNA/protein database</option> @@ -95,19 +88,15 @@ <option value="bgfile">Use 0-order letter frequencies from background file</option> <option value="uniform_distr">Use uniform letter frequencies</option> </param> - <when value="motif_file" /> - <when value="default" /> - <when value="uniform_distr" /> + <when value="motif_file"/> + <when value="default"/> + <when value="uniform_distr"/> <when value="bgfile"> <param name="bgfile" type="data" format="txt" optional="True" label="Background model file" help="File must be in Markov background model format (see MEME suite tool fasta-get-markov for details)"/> </when> </conditional> - <param name="max_strand" label="Report best match in case of overlapping matches on both strands?" argument="--max-strand" - type="boolean" truevalue="--max-strand" falsevalue="" checked="False" - 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. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/> - <param name="max_stored_scores" type="integer" value="100000" argument="--max-stored-scores" - label="Maximum number of scores that will be stored" - help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/> + <param argument="--max-strand" type="boolean" truevalue="--max-strand" falsevalue="" checked="False" label="Report best match in case of overlapping matches on both strands?" 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. If the scores are tied, the matching strand is chosen at random (default: report both matches)."/> + <param argument="--max-stored-scores" type="integer" value="100000" label="Maximum number of scores that will be stored" help="Keeping a complete list of scores may exceed available memory. Once the number of stored scores reaches the maximum allowed, the least significant 50% of scores will be dropped. In this case, the list of reported motifs may be incomplete and the q-value calculation will be approximate."/> <conditional name="motifs_cond"> <param name="motif_selector" type="select" label="Specify single input motifs for scanning?"> <option value="no" selected="true">No</option> @@ -117,21 +106,15 @@ <when value="yes"> <repeat name="motifs" title="Supply input motif ID"> <param name="motif" type="text" value="" label="Specify motif by id"> - <validator type="empty_field" /> + <validator type="empty_field"/> <validator type="regex" message="Value may include alphanumeric characters.">[A-Za-z]+</validator> </param> </repeat> </when> </conditional> - <param name="motif_pseudo" type="float" value="0.1" argument="--motif-pseudo" - 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="Disable q-value calculation?" - type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" argument="--no-qvalue" - help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/> - <param name="parse_genomic_coords" label="Check each sequence header for UCSC-style genomic coordinates?" - type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" argument="--parse-genomic-coord" - help=" If genomic coordinates are found they will be used as the coordinates in the output."/> + <param argument="--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 argument="--no-qvalue" type="boolean" truevalue="--no-qvalue" falsevalue="" checked="False" label="Disable q-value calculation?" help="The q-value calculation is that of Benjamini and Hochberg (1995) (default: calculate q-value for each p-value)"/> + <param name="parse_genomic_coords" argument="--parse-genomic-coord" type="boolean" truevalue="--parse-genomic-coord" falsevalue="" checked="False" label="Check each sequence header for UCSC-style genomic coordinates?" help=" If genomic coordinates are found they will be used as the coordinates in the output."/> <conditional name="psp_cond"> <param name="psp_selector" type="select" label="Use position-specific priors?"> <option value="no" selected="true">No</option> @@ -139,12 +122,8 @@ </param> <when value="no"/> <when value="yes"> - <param name="input_psp" type="data" format="txt" argument="--psp" - label="Select file containing position-specific priors" - help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/> - <param name="alpha" type="float" value="1.0" min="0" max="1.0" argument="--alpha" - 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)"/> + <param name="input_psp" argument="--psp" type="data" format="txt" label="Select file containing position-specific priors" help="File should be in MEME PSP format or wiggle format (can be generated by MEME suite tool create-priors)"/> + <param argument="--alpha" type="float" min="0" max="1.0" value="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)"/> </when> </conditional> <conditional name="prior_dist_cond"> @@ -154,14 +133,12 @@ </param> <when value="no"/> <when value="yes"> - <param name="input_prior_dist" type="data" format="txt" argument="--prior-dist" - label="Select dataset containing binned distribution of priors" - help="This file can be generated using the MEME suite tool create-priors"/> + <param name="input_prior_dist" argument="--prior-dist" type="data" format="txt" label="Select dataset containing binned distribution of priors" help="This file can be generated using the MEME suite tool create-priors"/> </when> </conditional> </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"> + <param name="non_commercial_use" type="boolean" truevalue="NON_COMMERCIAL_USE" falsevalue="COMMERCIAL_USE" checked="False" label="I certify that I am not using this tool for commercial purposes."> <validator type="expression" message="This tool is only available for non-commercial use.">value == True</validator> </param> <section name="output_options" title="Additional output options"> @@ -199,7 +176,7 @@ </conditional> </actions> </data> - <data format="txt" name="gff_outfile" label="${tool.name} on ${on_string} (gff)"> + <data format="gff" name="gff_outfile" label="${tool.name} on ${on_string} (gff)"> <filter>(output_options['gff_outfile'] is True)</filter> <actions> <conditional name="fasta_type.fasta_type_selector"> @@ -239,10 +216,39 @@ <param name="xml_outfile" value="True"/> <param name="gff_outfile" value="True"/> <param name="non_commercial_use" value="True"/> - <output name="html_outfile" file="fimo_output_test1.html" compare="contains"/> - <output name="txt_outfile" file="fimo_output_test1.txt" compare="contains"/> - <output name="xml_outfile" file="fimo_output_test1.xml" compare="contains"/> - <output name="gff_outfile" file="fimo_output_test1.gff" compare="contains"/> + <output name="html_outfile" ftype="html"> + <assert_contents> + <has_text text="TACTAAYM"/> + <has_text text="MEME file name"/> + </assert_contents> + </output> + <output name="txt_outfile"> + <assert_contents> + <has_text text="motif_id"/> + <has_text text="sequence_name"/> + <has_text text="matched_sequence"/> + <has_text text="TACTAATA"/> + </assert_contents> + </output> + <output name="xml_outfile" ftype="memexml"> + <assert_contents> + <has_text text="sequence-data num-sequences"/> + <has_text text="16569"/> + <has_text text="Cytosine"/> + <has_text text="TACTAACA"/> + </assert_contents> + </output> + <output name="gff_outfile" ftype="gff"> + <assert_contents> + <has_text text="gff-version 3"/> + <has_text text="TACTAAYM_chrM"/> + <has_text text="qvalue"/> + <has_text text="nucleotide_motif"/> + <has_text text="fimo"/> + <has_text text="chrM"/> + <has_n_lines n="12"/> + </assert_contents> + </output> </test> <test expect_num_outputs="4"> <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/> @@ -256,10 +262,41 @@ <param name="xml_outfile" value="True"/> <param name="gff_outfile" value="True"/> <param name="non_commercial_use" value="True"/> - <output name="html_outfile" file="fimo_output_test2.html" compare="contains"/> - <output name="txt_outfile" file="fimo_output_test2.txt" compare="contains"/> - <output name="xml_outfile" file="fimo_output_test2.xml" compare="contains"/> - <output name="gff_outfile" file="fimo_output_test2.gff" compare="contains"/> + <output name="html_outfile"> + <assert_contents> + <has_text text="MOTIF"/> + <has_text text="WIDTH"/> + <has_text text="TTAACA"/> + <has_text text="GAATGT"/> + </assert_contents> + </output> + <output name="txt_outfile"> + <assert_contents> + <has_text text="sequence_name"/> + <has_text text="motif_id"/> + <has_text text="matched_sequence"/> + <has_text text="ACTAAYH"/> + <has_text text="chrM"/> + </assert_contents> + </output> + <output name="xml_outfile" ftype="memexml"> + <assert_contents> + <has_text text="MEME file name"/> + <has_text text="pseudocount"/> + <has_text text="Not G"/> + <has_text text="Keto"/> + </assert_contents> + </output> + <output name="gff_outfile" ftype="gff"> + <assert_contents> + <has_text text="gff-version 3"/> + <has_text text="ID=ACTAAYH-DREME-1-4-chrM"/> + <has_text text="nucleotide_motif"/> + <has_text text="fimo"/> + <has_text text="chrM"/> + <has_n_lines n="12"/> + </assert_contents> + </output> </test> <test expect_num_outputs="3"> <param name="input_motifs" value="dreme_fimo_input_1.xml" ftype="memexml"/> @@ -277,9 +314,32 @@ <param name="xml_outfile" value="True"/> <param name="gff_outfile" value="False"/> <param name="non_commercial_use" value="True"/> - <output name="html_outfile" file="fimo_output_test3.html" compare="contains"/> - <output name="txt_outfile" file="fimo_output_test3.txt" compare="contains"/> - <output name="xml_outfile" file="fimo_output_test3.xml" compare="contains"/> + <output name="html_outfile"> + <assert_contents> + <has_text text="top_buttons"/> + <has_text text="database_and_motifs"/> + <has_text text="YTAACA"/> + <has_text text="ACTAAYH"/> + <has_text text="DREME"/> + </assert_contents> + </output> + <output name="txt_outfile"> + <assert_contents> + <has_text text="motif_alt_id"/> + <has_text text="matched_sequence"/> + <has_text text="ACTAAYH"/> + <has_text text="ACTAACA"/> + </assert_contents> + </output> + <output name="xml_outfile" ftype="memexml"> + <assert_contents> + <has_text text="complement"/> + <has_text text="letter"/> + <has_text text="16569"/> + <has_text text="dna"/> + <has_text text="ACTAAYH"/> + </assert_contents> + </output> </test> </tests> <help>
--- a/macros.xml Sat Apr 09 08:32:23 2022 +0000 +++ b/macros.xml Thu Aug 29 10:19:40 2024 +0000 @@ -1,7 +1,7 @@ -<?xml version='1.0' encoding='UTF-8'?> <macros> <token name="@VERSION_SUFFIX@">0</token> - <token name="@TOOL_VERSION@">5.4.1</token> + <token name="@TOOL_VERSION@">5.5.6</token> + <token name="@PROFILE@">23.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">meme</requirement>
--- a/test-data/dreme_output_test1.html Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ - </div> - <div class="box"> - <h4>Sequences</h4> - <table id="seq_info" class="inputs"> - <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th> - <th>Alphabet <div class="help" data-topic="pop_seq_alph"></div></th> - <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th> - </tr> - <tr> - <td id="ins_seq_source"></td> - <td id="ins_seq_alphabet"></td> - <td id="ins_seq_count"></td> - </tr> - </table> - <script> - { - var db = data.sequence_db; - $("ins_seq_source").innerHTML = db.file; - $("ins_seq_alphabet").innerHTML = current_alphabet.get_alphabet_name(); - $("ins_seq_count").innerHTML = db.count; - } - </script> - <h4>Control Sequences</h4> - <table id="seq_info" class="inputs"> - <tr><th>Source <div class="help" data-topic="pop_seq_source"></div></th> - <th>Sequence Count <div class="help" data-topic="pop_seq_count"></div></th> - </tr> - <tr> - <td id="ins_cseq_source"></td> - <td id="ins_cseq_count"></td> - </tr> - </table> - <script> - { - var db = data.control_db; - if (db.from == "shuffled") { - $("ins_cseq_source").innerHTML = "Shuffled Sequences"; - } else { - $("ins_cseq_source").innerHTML = db.file; - } - $("ins_cseq_count").innerHTML = db.count; - } - </script> - <h4>Background</h4> - <span id="alpha_bg"></span> - <script> - { - $("alpha_bg").appendChild(make_alpha_bg_table(current_alphabet, data.control_db.freqs)); - } - </script> - <h4>Other Settings</h4> - <table id="tbl_settings" class="inputs hide_advanced"> - <tr> - <th>Strand Handling</th> - <td id="opt_strand"> - <span class="strand_none">This alphabet only has one strand</span> - <span class="strand_given">Only the given strand is processed</span> - <span class="strand_both">Both the given and reverse complement strands are processed</span> - </td> - </tr> - <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr> - <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr> - <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr> - <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr> - <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr> - </table> - <script> - { - $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none"); - $("opt_ngen").innerHTML = data.options.ngen; - $("opt_seed").innerHTML = data.options.seed; - $("opt_stop_evalue").innerHTML = data.options.stop.evalue; - $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count."); - $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time."); - } - </script> - </div> - <!-- list information on this program --> - <div id="info_sec" class="bar" style="position:relative"> - <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div> - <div class="subsection"> - <h5 id="version">DREME version</h5> - <span id="ins_version"></span> - (Release date: <span id="ins_release"></span>)<br> - </div> - <script> - $("ins_version").innerHTML = data["version"]; - $("ins_release").innerHTML = data["release"]; - </script> - <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div> - <div class="subsection"> - <h5 id="command">Command line</h5> - <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly"> - </textarea> - <script>$("cmd").value = data["cmd"].join(" ");</script> - </div> - </div> - - </body> -</html>
--- a/test-data/dreme_output_test1.txt Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,64 +0,0 @@ -MOTIF UUYUCY DREME-1 - -# Word Pos Neg P-value E-value -# BEST UUYUCY 387 210 2.6e-018 1.2e-013 -# UUUUCC 147 75 1.8e-007 8.1e-003 -# UUUUCU 155 94 2.2e-005 1.0e+000 -# UUCUCU 94 51 1.3e-004 6.1e+000 -# UUCUCC 75 42 1.1e-003 5.0e+001 - -letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 1.2e-013 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.294118 0.000000 0.705882 -0.000000 0.000000 0.000000 1.000000 -0.000000 1.000000 0.000000 0.000000 -0.000000 0.474946 0.000000 0.525054 - - -MOTIF YAGG DREME-2 - -# Word Pos Neg P-value E-value -# BEST YAGG 600 416 1.1e-016 5.1e-012 -# CAGG 441 304 1.5e-010 6.6e-006 -# UAGG 232 165 1.1e-004 4.7e+000 - -letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 5.1e-012 -0.000000 0.692308 0.000000 0.307692 -1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 - - -MOTIF GAAGAW DREME-3 - -# Word Pos Neg P-value E-value -# BEST GAAGAW 81 22 8.2e-010 3.4e-005 -# GAAGAU 45 7 2.4e-008 9.9e-004 -# GAAGAA 40 16 7.9e-004 3.3e+001 - -letter-probability matrix: alength= 4 w= 6 nsites= 89 E= 3.4e-005 -0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000 -0.494382 0.000000 0.000000 0.505618 - - -MOTIF SMUGGA DREME-4 - -# Word Pos Neg P-value E-value -# BEST SMUGGA 110 47 9.1e-008 3.7e-003 -# GAUGGA 22 6 1.7e-003 7.1e+001 -# GCUGGA 33 14 3.6e-003 1.5e+002 -# CCUGGA 32 15 8.6e-003 3.5e+002 -# CAUGGA 29 13 9.1e-003 3.7e+002 - -letter-probability matrix: alength= 4 w= 6 nsites= 119 E= 3.7e-003 -0.000000 0.529412 0.470588 0.000000 -0.428571 0.571429 0.000000 0.000000 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -1.000000 0.000000 0.000000 0.000000
--- a/test-data/dreme_output_test1.xml Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,44 +0,0 @@ - <motifs> - <motif id="m01" alt="DREME-1" seq="UUYUCY" length="6" nsites="459" p="387" n="210" pvalue="2.6e-018" evalue="1.2e-013" unerased_evalue="1.2e-013"> - <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/> - <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/> - <pos A="0.000000" C="0.294118" G="0.000000" U="0.705882"/> - <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/> - <pos A="0.000000" C="1.000000" G="0.000000" U="0.000000"/> - <pos A="0.000000" C="0.474946" G="0.000000" U="0.525054"/> - <match seq="UUUUCC" p="147" n="75" pvalue="1.8e-007" evalue="8.1e-003"/> - <match seq="UUUUCU" p="155" n="94" pvalue="2.2e-005" evalue="1.0e+000"/> - <match seq="UUCUCU" p="94" n="51" pvalue="1.3e-004" evalue="6.1e+000"/> - <match seq="UUCUCC" p="75" n="42" pvalue="1.1e-003" evalue="5.0e+001"/> - </motif> - <motif id="m02" alt="DREME-2" seq="YAGG" length="4" nsites="793" p="600" n="416" pvalue="1.1e-016" evalue="5.1e-012" unerased_evalue="2.4e-012"> - <pos A="0.000000" C="0.692308" G="0.000000" U="0.307692"/> - <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/> - <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/> - <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/> - <match seq="CAGG" p="441" n="304" pvalue="1.5e-010" evalue="6.6e-006"/> - <match seq="UAGG" p="232" n="165" pvalue="1.1e-004" evalue="4.7e+000"/> - </motif> - <motif id="m03" alt="DREME-3" seq="GAAGAW" length="6" nsites="89" p="81" n="22" pvalue="8.2e-010" evalue="3.4e-005" unerased_evalue="3.5e-004"> - <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/> - <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/> - <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/> - <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/> - <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/> - <pos A="0.494382" C="0.000000" G="0.000000" U="0.505618"/> - <match seq="GAAGAU" p="45" n="7" pvalue="2.4e-008" evalue="9.9e-004"/> - <match seq="GAAGAA" p="40" n="16" pvalue="7.9e-004" evalue="3.3e+001"/> - </motif> - <motif id="m04" alt="DREME-4" seq="SMUGGA" length="6" nsites="119" p="110" n="47" pvalue="9.1e-008" evalue="3.7e-003" unerased_evalue="2.6e-005"> - <pos A="0.000000" C="0.529412" G="0.470588" U="0.000000"/> - <pos A="0.428571" C="0.571429" G="0.000000" U="0.000000"/> - <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/> - <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/> - <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/> - <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/> - <match seq="GAUGGA" p="22" n="6" pvalue="1.7e-003" evalue="7.1e+001"/> - <match seq="GCUGGA" p="33" n="14" pvalue="3.6e-003" evalue="1.5e+002"/> - <match seq="CCUGGA" p="32" n="15" pvalue="8.6e-003" evalue="3.5e+002"/> - <match seq="CAUGGA" p="29" n="13" pvalue="9.1e-003" evalue="3.7e+002"/> - </motif> - </motifs> \ No newline at end of file
--- a/test-data/dreme_output_test2.html Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,50 +0,0 @@ - <h4>Other Settings</h4> - <table id="tbl_settings" class="inputs hide_advanced"> - <tr> - <th>Strand Handling</th> - <td id="opt_strand"> - <span class="strand_none">This alphabet only has one strand</span> - <span class="strand_given">Only the given strand is processed</span> - <span class="strand_both">Both the given and reverse complement strands are processed</span> - </td> - </tr> - <tr><th># REs to Generalize</th><td id="opt_ngen"></td></tr> - <tr><th>Shuffle Seed</th><td id="opt_seed"></td></tr> - <tr><th>E-value Threshold</th><td id="opt_stop_evalue"></td></tr> - <tr><th>Max Motif Count</th><td id="opt_stop_count"></td></tr> - <tr><th>Max Run Time</th><td id="opt_stop_time"></td></tr> - </table> - <script> - { - $("opt_strand").className = (current_alphabet.has_complement() ? (data.options.revcomp ? "both" : "given") : "none"); - $("opt_ngen").innerHTML = data.options.ngen; - $("opt_seed").innerHTML = data.options.seed; - $("opt_stop_evalue").innerHTML = data.options.stop.evalue; - $("opt_stop_count").innerHTML = (typeof data.options.stop.count == "number" ? data.options.stop.count : "No maximum motif count."); - $("opt_stop_time").innerHTML = (typeof data.options.stop.time == "number" ? data.options.stop.time + " seconds." : "No maximum running time."); - } - </script> - </div> - <!-- list information on this program --> - <div id="info_sec" class="bar" style="position:relative"> - <div style="position: absolute; right: 0;"><a href="#inputs_sec">Previous</a> <a href="#">Top</a></div> - <div class="subsection"> - <h5 id="version">DREME version</h5> - <span id="ins_version"></span> - (Release date: <span id="ins_release"></span>)<br> - </div> - <script> - $("ins_version").innerHTML = data["version"]; - $("ins_release").innerHTML = data["release"]; - </script> - <div class="subsection" id="reference"> <script>print_citation("reference", "DREME");</script> </div> - <div class="subsection"> - <h5 id="command">Command line</h5> - <textarea id="cmd" rows="3" style="width:100%;" readonly="readonly"> - </textarea> - <script>$("cmd").value = data["cmd"].join(" ");</script> - </div> - </div> - - </body> -</html>
--- a/test-data/dreme_output_test2.txt Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,55 +0,0 @@ -ALPHABET "RNA" RNA-LIKE -A "Adenine" CC0000 -C "Cytosine" 0000CC -G "Guanine" FFB300 -U "Uracil" 008000 -N "Any base" = ACGU -X = ACGU -. = ACGU -V "Not U" = ACG -H "Not G" = ACU -D "Not C" = AGU -B "Not A" = CGU -M "Amino" = AC -R "Purine" = AG -W "Weak" = AU -S "Strong" = CG -Y "Pyrimidine" = CU -K "Keto" = GU -T = U -END ALPHABET - -Background letter frequencies (from dataset): -A 0.221 C 0.245 G 0.221 U 0.312 - - -MOTIF UUYUCY DREME-1 - -# Word Pos Neg P-value E-value -# BEST UUYUCY 387 210 2.6e-018 3.3e-013 -# UUUUCC 147 75 1.8e-007 2.2e-002 -# UUUUCU 155 94 2.2e-005 2.8e+000 -# UUCUCU 94 51 1.3e-004 1.7e+001 -# UUCUCC 75 42 1.1e-003 1.4e+002 - -letter-probability matrix: alength= 4 w= 6 nsites= 459 E= 3.3e-013 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.000000 0.000000 1.000000 -0.000000 0.294118 0.000000 0.705882 -0.000000 0.000000 0.000000 1.000000 -0.000000 1.000000 0.000000 0.000000 -0.000000 0.474946 0.000000 0.525054 - - -MOTIF YAGG DREME-2 - -# Word Pos Neg P-value E-value -# BEST YAGG 600 416 1.1e-016 1.4e-011 -# CAGG 441 304 1.5e-010 1.8e-005 -# UAGG 232 165 1.1e-004 1.3e+001 - -letter-probability matrix: alength= 4 w= 4 nsites= 793 E= 1.4e-011 -0.000000 0.692308 0.000000 0.307692 -1.000000 0.000000 0.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 -0.000000 0.000000 1.000000 0.000000 \ No newline at end of file
--- a/test-data/dreme_output_test2.xml Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ - <motifs> - <motif id="m01" alt="DREME-1" seq="UUYUCY" length="6" nsites="459" p="387" n="210" pvalue="2.6e-018" evalue="3.3e-013" unerased_evalue="3.3e-013"> - <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/> - <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/> - <pos A="0.000000" C="0.294118" G="0.000000" U="0.705882"/> - <pos A="0.000000" C="0.000000" G="0.000000" U="1.000000"/> - <pos A="0.000000" C="1.000000" G="0.000000" U="0.000000"/> - <pos A="0.000000" C="0.474946" G="0.000000" U="0.525054"/> - <match seq="UUUUCC" p="147" n="75" pvalue="1.8e-007" evalue="2.2e-002"/> - <match seq="UUUUCU" p="155" n="94" pvalue="2.2e-005" evalue="2.8e+000"/> - <match seq="UUCUCU" p="94" n="51" pvalue="1.3e-004" evalue="1.7e+001"/> - <match seq="UUCUCC" p="75" n="42" pvalue="1.1e-003" evalue="1.4e+002"/> - </motif> - <motif id="m02" alt="DREME-2" seq="YAGG" length="4" nsites="793" p="600" n="416" pvalue="1.1e-016" evalue="1.4e-011" unerased_evalue="6.3e-012"> - <pos A="0.000000" C="0.692308" G="0.000000" U="0.307692"/> - <pos A="1.000000" C="0.000000" G="0.000000" U="0.000000"/> - <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/> - <pos A="0.000000" C="0.000000" G="1.000000" U="0.000000"/> - <match seq="CAGG" p="441" n="304" pvalue="1.5e-010" evalue="1.8e-005"/> - <match seq="UAGG" p="232" n="165" pvalue="1.1e-004" evalue="1.3e+001"/> - </motif> - </motifs> \ No newline at end of file
--- a/test-data/fimo_output_test1.gff Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -##gff-version 3 -chrM fimo nucleotide_motif 6529 6536 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-1-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 7741 7748 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-2-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 13656 13663 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-3-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 13740 13747 46.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-4-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 2299 2306 46.6 - . Name=TACTAAYM_chrM-;Alias=MEME-1;ID=TACTAAYM-MEME-1-5-chrM;pvalue=2.18e-05;qvalue=0.142;sequence=TACTAACA; -chrM fimo nucleotide_motif 861 868 44 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-6-chrM;pvalue=3.96e-05;qvalue=0.185;sequence=TACTAACC; -chrM fimo nucleotide_motif 9346 9353 44 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-7-chrM;pvalue=3.96e-05;qvalue=0.185;sequence=TACTAACC; -chrM fimo nucleotide_motif 3767 3774 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-8-chrM;pvalue=6.62e-05;qvalue=0.216;sequence=TACTAATA; -chrM fimo nucleotide_motif 5497 5504 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-9-chrM;pvalue=6.62e-05;qvalue=0.216;sequence=TACTAATA; -chrM fimo nucleotide_motif 10105 10112 41.8 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-10-chrM;pvalue=6.62e-05;qvalue=0.216;sequence=TACTAATA; -chrM fimo nucleotide_motif 10959 10966 40.6 + . Name=TACTAAYM_chrM+;Alias=MEME-1;ID=TACTAAYM-MEME-1-11-chrM;pvalue=8.79e-05;qvalue=0.261;sequence=TACTAACT;
--- a/test-data/fimo_output_test1.html Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ - <td style="padding-right: 2em">background file name = --nrdb--</td> - <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td> - <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td> - </tr> <tr> - <td style="padding-right: 2em">allow clobber = false</td> - <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td> - <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td> - </tr> - <tr> - <td style="padding-right: 2em">text only = false</td> - <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td> - <td style="padding-left: 5em; padding-right: 2em">max strand = false</td> - </tr> - <tr> - <td style="padding-right: 2em">threshold type = p-value</td> - <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td> - <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td> - </tr> - <tr> - <td style="padding-right: 2em">alpha = 1</td> - <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td> - <td style="padding-left: 5em; padding-right: 2em"></td> - </tr> - -</table> -</pre> -<p> -This information can be useful in the event you wish to report a -problem with the FIMO software. -</p> -<hr> -<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span> -</body> -</html>
--- a/test-data/fimo_output_test1.txt Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence -TACTAAYM MEME-1 chrM 6529 6536 + 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 7741 7748 + 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 13656 13663 + 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 13740 13747 + 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 2299 2306 - 12.9701 2.18e-05 0.142 TACTAACA -TACTAAYM MEME-1 chrM 861 868 + 12.2836 3.96e-05 0.185 TACTAACC -TACTAAYM MEME-1 chrM 9346 9353 + 12.2836 3.96e-05 0.185 TACTAACC -TACTAAYM MEME-1 chrM 3767 3774 + 11.7164 6.62e-05 0.216 TACTAATA -TACTAAYM MEME-1 chrM 5497 5504 + 11.7164 6.62e-05 0.216 TACTAATA -TACTAAYM MEME-1 chrM 10105 10112 + 11.7164 6.62e-05 0.216 TACTAATA -TACTAAYM MEME-1 chrM 10959 10966 + 11.6567 8.79e-05 0.261 TACTAACT
--- a/test-data/fimo_output_test1.xml Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,39 +0,0 @@ -<setting name="background file name">--nrdb--</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">true</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">2</setting> -</settings> -<sequence-data num-sequences="1" num-residues="16569" /> -<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> -<motif name="TACTAAYM" alt="MEME-1" width="8" best-possible-match="TACTAACA"/> -<background source="--nrdb--"> -<value letter="A">0.275</value> -<value letter="C">0.225</value> -<value letter="G">0.225</value> -<value letter="T">0.275</value> -</background> -<cisml-file>cisml.xml</cisml-file> -</fimo>
--- a/test-data/fimo_output_test2.gff Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -##gff-version 3 -chrM fimo nucleotide_motif 440 446 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-1-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 2093 2099 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-2-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 2299 2305 40.9 - . Name=ACTAAYH_chrM-;Alias=DREME-1;ID=ACTAAYH-DREME-1-3-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 5186 5192 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-4-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 6530 6536 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-5-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 7742 7748 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-6-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 13657 13663 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-7-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 13741 13747 40.9 + . Name=ACTAAYH_chrM+;Alias=DREME-1;ID=ACTAAYH-DREME-1-8-chrM;pvalue=8.2e-05;qvalue=0.332;sequence=ACTAACA; -chrM fimo nucleotide_motif 510 516 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-1-chrM;pvalue=4.15e-05;qvalue=0.683;sequence=CCAGCAC; -chrM fimo nucleotide_motif 5137 5143 43.8 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-2-chrM;pvalue=4.15e-05;qvalue=0.683;sequence=CCAGCAC; -chrM fimo nucleotide_motif 4241 4247 40.3 + . Name=CCAGCAY_chrM+;Alias=DREME-5;ID=CCAGCAY-DREME-5-3-chrM;pvalue=9.37e-05;qvalue=1;sequence=CCAGCAT;
--- a/test-data/fimo_output_test2.html Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,33 +0,0 @@ - <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td> - <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td> - </tr> <tr> - <td style="padding-right: 2em">allow clobber = false</td> - <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td> - <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td> - </tr> - <tr> - <td style="padding-right: 2em">text only = false</td> - <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td> - <td style="padding-left: 5em; padding-right: 2em">max strand = false</td> - </tr> - <tr> - <td style="padding-right: 2em">threshold type = p-value</td> - <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.0001</td> - <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td> - </tr> - <tr> - <td style="padding-right: 2em">alpha = 1</td> - <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td> - <td style="padding-left: 5em; padding-right: 2em"></td> - </tr> - -</table> -</pre> -<p> -This information can be useful in the event you wish to report a -problem with the FIMO software. -</p> -<hr> -<span style="background-color: #DDDDFF"><a href="#top_buttons"><b>Go to top</b></a></span> -</body> -</html>
--- a/test-data/fimo_output_test2.txt Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence -CCAGCAY DREME-5 chrM 510 516 + 13.5843 4.15e-05 0.683 CCAGCAC -CCAGCAY DREME-5 chrM 5137 5143 + 13.5843 4.15e-05 0.683 CCAGCAC -ACTAAYH DREME-1 chrM 440 446 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 2093 2099 - 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 2299 2305 - 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 5186 5192 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 6530 6536 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 7742 7748 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 13657 13663 + 11.7286 8.2e-05 0.332 ACTAACA -ACTAAYH DREME-1 chrM 13741 13747 + 11.7286 8.2e-05 0.332 ACTAACA -CCAGCAY DREME-5 chrM 4241 4247 + 13.1461 9.37e-05 1 CCAGCAT \ No newline at end of file
--- a/test-data/fimo_output_test2.xml Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,34 +0,0 @@ -<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">true</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">2</setting> -</settings> -<sequence-data num-sequences="1" num-residues="16569" /> -<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> -<motif name="ACTAAYH" alt="DREME-1" width="7" best-possible-match="ACTAACA"/> -<motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/> -<motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/> -<motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/> -<motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/> -<motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/> \ No newline at end of file
--- a/test-data/fimo_output_test3.html Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ - <td style="padding-right: 2em">background file name = --uniform--</td> - <td style="padding-left: 5em; padding-right: 2em">alphabet = DNA</td> - <td style="padding-left: 5em; padding-right: 2em">max stored scores = 100000</td> - </tr> <tr> - <td style="padding-right: 2em">allow clobber = false</td> - <td style="padding-left: 5em; padding-right: 2em">compute q-values = true</td> - <td style="padding-left: 5em; padding-right: 2em">parse genomic coord. = false</td> - </tr> - <tr> - <td style="padding-right: 2em">text only = false</td> - <td style="padding-left: 5em; padding-right: 2em">scan both strands = true</td> - <td style="padding-left: 5em; padding-right: 2em">max strand = false</td> - </tr> - <tr> - <td style="padding-right: 2em">threshold type = p-value</td> - <td style="padding-left: 5em; padding-right: 2em">output theshold = 0.01</td> - <td style="padding-left: 5em; padding-right: 2em">pseudocount = 0.1</td> - </tr> - <tr> - <td style="padding-right: 2em">alpha = 1</td> - <td style="padding-left: 5em; padding-right: 2em">verbosity = 2</td> - <td style="padding-left: 5em; padding-right: 2em"></td> - </tr> \ No newline at end of file
--- a/test-data/fimo_output_test3.txt Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,40 +0,0 @@ -motif_id motif_alt_id sequence_name start stop strand score p-value q-value matched_sequence -ACTAAYH DREME-1 chrM 440 446 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 2093 2099 - 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 2299 2305 - 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 5186 5192 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 6530 6536 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 7742 7748 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 13657 13663 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 13741 13747 + 12.1831 6.1e-05 0.239 ACTAACA -ACTAAYH DREME-1 chrM 3768 3774 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 5498 5504 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 7736 7742 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 9872 9878 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 10106 10112 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 10313 10319 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 11818 11824 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 15903 15909 + 11.5915 0.000122 0.239 ACTAATA -ACTAAYH DREME-1 chrM 7732 7738 + 11.4507 0.000183 0.294 ACTAACT -ACTAAYH DREME-1 chrM 10960 10966 + 11.4507 0.000183 0.294 ACTAACT -ACTAAYH DREME-1 chrM 862 868 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 1832 1838 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 8679 8685 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 8770 8776 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 9347 9353 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 9359 9365 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 10302 10308 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 14765 14771 + 11.2394 0.000244 0.294 ACTAACC -ACTAAYH DREME-1 chrM 4466 4472 + 10.8592 0.000305 0.302 ACTAATT -ACTAAYH DREME-1 chrM 11248 11254 + 10.8592 0.000305 0.302 ACTAATT -ACTAAYH DREME-1 chrM 475 481 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 7930 7936 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 8649 8655 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 8670 8676 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 10768 10774 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 11053 11059 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 11101 11107 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 12720 12726 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 13149 13155 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 14216 14222 + 10.6479 0.000366 0.302 ACTAATC -ACTAAYH DREME-1 chrM 678 684 - -1.07042 0.000549 0.366 ACTAAGA \ No newline at end of file
--- a/test-data/fimo_output_test3.xml Sat Apr 09 08:32:23 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,32 +0,0 @@ -<sequence-data num-sequences="1" num-residues="16569" /> -<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> -<motif name="ACTAAYH" alt="DREME-1" width="7" best-possible-match="ACTAACA"/> -<motif name="YTAACA" alt="DREME-2" width="6" best-possible-match="TTAACA"/> -<motif name="TCTGT" alt="DREME-3" width="5" best-possible-match="TCTGT"/> -<motif name="SCCAGG" alt="DREME-4" width="6" best-possible-match="CCCAGG"/> -<motif name="CCAGCAY" alt="DREME-5" width="7" best-possible-match="CCAGCAC"/> -<motif name="GMATGT" alt="DREME-6" width="6" best-possible-match="GAATGT"/> -<background source="--uniform--"> -<value letter="A">0.250</value> -<value letter="C">0.250</value> -<value letter="G">0.250</value> -<value letter="T">0.250</value> -</background> -<cisml-file>cisml.xml</cisml-file> -</fimo>