| Next changeset 1:465be78e9b05 (2023-04-06) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 186b72f369eb2a11d92f4d63cac2e8ebe386b9bd" |
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added:
homer_scanMotifGenomeWide.xml macros.xml test-data/CTCF_peaks.bed test-data/CTCF_peaks_first.txt test-data/CTCF_peaks_second.txt test-data/CTCF_peaks_shifted.bed test-data/CTCF_peaks_third.txt test-data/all_fasta.loc test-data/annotations_default.txt test-data/annotations_default_simplified.txt test-data/annotations_default_stats.txt test-data/annotations_exon_start.txt test-data/annotations_exon_start_stats.txt test-data/annotations_small_TSSTTS.txt test-data/annotations_small_TSSTTS_stats.txt test-data/chr2_subset.fa.gz test-data/fake_phix_peaks.bed test-data/fake_phix_peaks.subset.bed test-data/generate_tests.sh test-data/motif_test1/homerMotifs.all.motifs test-data/motif_test1/homerMotifs.motifs10 test-data/motif_test1/homerMotifs.motifs12 test-data/motif_test1/homerMotifs.motifs8 test-data/motif_test1/homerResults.html test-data/motif_test1/homerResults/motif1.info.html test-data/motif_test1/homerResults/motif1.logo.svg test-data/motif_test1/homerResults/motif1.motif test-data/motif_test1/homerResults/motif1.similar.html test-data/motif_test1/homerResults/motif1.similar1.motif test-data/motif_test1/homerResults/motif1.similar2.motif test-data/motif_test1/homerResults/motif1.similar3.motif test-data/motif_test1/homerResults/motif1RV.logo.svg test-data/motif_test1/homerResults/motif1RV.motif test-data/motif_test1/homerResults/motif2.info.html test-data/motif_test1/homerResults/motif2.logo.svg test-data/motif_test1/homerResults/motif2.motif test-data/motif_test1/homerResults/motif2.similar.html test-data/motif_test1/homerResults/motif2RV.logo.svg test-data/motif_test1/homerResults/motif2RV.motif test-data/motif_test1/homerResults/motif3.info.html test-data/motif_test1/homerResults/motif3.logo.svg test-data/motif_test1/homerResults/motif3.motif test-data/motif_test1/homerResults/motif3.similar.html test-data/motif_test1/homerResults/motif3.similar1.motif test-data/motif_test1/homerResults/motif3RV.logo.svg test-data/motif_test1/homerResults/motif3RV.motif test-data/motif_test1/homerResults/motif4.info.html test-data/motif_test1/homerResults/motif4.logo.svg test-data/motif_test1/homerResults/motif4.motif test-data/motif_test1/homerResults/motif4.similar.html test-data/motif_test1/homerResults/motif4.similar1.motif test-data/motif_test1/homerResults/motif4.similar2.motif test-data/motif_test1/homerResults/motif4RV.logo.svg test-data/motif_test1/homerResults/motif4RV.motif test-data/motif_test1/homerResults/motif5.info.html test-data/motif_test1/homerResults/motif5.logo.svg test-data/motif_test1/homerResults/motif5.motif test-data/motif_test1/homerResults/motif5.similar.html test-data/motif_test1/homerResults/motif5RV.logo.svg test-data/motif_test1/homerResults/motif5RV.motif test-data/motif_test1/homerResults/motif6.info.html test-data/motif_test1/homerResults/motif6.logo.svg test-data/motif_test1/homerResults/motif6.motif test-data/motif_test1/homerResults/motif6.similar.html test-data/motif_test1/homerResults/motif6.similar1.motif test-data/motif_test1/homerResults/motif6RV.logo.svg test-data/motif_test1/homerResults/motif6RV.motif test-data/motif_test1/homerResults/motif7.info.html test-data/motif_test1/homerResults/motif7.logo.svg test-data/motif_test1/homerResults/motif7.motif test-data/motif_test1/homerResults/motif7.similar.html test-data/motif_test1/homerResults/motif7RV.logo.svg test-data/motif_test1/homerResults/motif7RV.motif test-data/motif_test1/homerResults/motif8.info.html test-data/motif_test1/homerResults/motif8.logo.svg test-data/motif_test1/homerResults/motif8.motif test-data/motif_test1/homerResults/motif8.similar.html test-data/motif_test1/homerResults/motif8RV.logo.svg test-data/motif_test1/homerResults/motif8RV.motif test-data/motif_test1/knownResults.html test-data/motif_test1/knownResults.txt test-data/motif_test1/motifFindingParameters.txt test-data/motif_test1/seq.autonorm.tsv test-data/phiX174.fasta test-data/phiX_nothing.txt test-data/phiXcpg.txt test-data/scanMotif_res1.bed test-data/scanMotif_res1.txt test-data/small.gtf test-data/small_simplified.gtf tool-data/all_fasta.loc.sample tool-data/homer_preparse.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r db456c398880 homer_scanMotifGenomeWide.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/homer_scanMotifGenomeWide.xml Mon Dec 13 15:13:33 2021 +0000 |
| [ |
| @@ -0,0 +1,94 @@ +<tool id="homer_scanMotifGenomeWide" name="scanMotifGenomeWide" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT"> + <description/> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="xrefs"/> + <expand macro="requirements"/> + <command detect_errors="exit_code"><![CDATA[ +scanMotifGenomeWide.pl +'$motif' +#if str( $genome.source ) == "installed": + '$genome.all_fasta_source.fields.path' +#elif str( $genome.source ) == "history": + '$genome.fasta' +#end if +$bed +$keepAll +$mask +$Fivep +$homer1 +> +#if $bed: + '${output_bed}' +#else + '${output_text}' +#end if + ]]></command> + <inputs> + <param name="motif" type="data" format="txt" label="Motif file"/> + <conditional name="genome"> + <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?"> + <option value="installed">Installed</option> + <option value="history">From History</option> + </param> + <when value="installed"> + <param name="all_fasta_source" type="select" label="Source FASTA Sequence"> + <options from_data_table="all_fasta"> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No references are available"/> + </options> + </param> + </when> + <when value="history"> + <param name="fasta" type="data" format="fasta" label="Select reference genome"/> + </when> + </conditional> + <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false" label="Output bed format"/> + <param argument="-keepAll" type="boolean" truevalue="-keepAll" falsevalue="" checked="false" label="Report all motifs even if overlap" + help="By default, HOMER will remove a motif that overlaps itself, useful for palindromes. To report all, specify this option."/> + <param argument="-mask" type="boolean" truevalue="-mask" falsevalue="" checked="false" + label="Do not look for motifs in RepeatMasked sequence (lower case sequence in FASTA files)"/> + <param argument="-5p" name="Fivep" type="boolean" truevalue="-5p" falsevalue="" checked="false" + label="Report motif positions based on the 5' end of the motif sequence"/> + <param argument="-homer1" type="boolean" truevalue="-homer1" falsevalue="" checked="false" + label="Use homer1 instead of homer2"/> + </inputs> + <outputs> + <data format="tabular" name="output_text" label="${tool.name} on ${on_string}"> + <filter>bed is False</filter> + </data> + <data format="bed" name="output_bed" label="${tool.name} on ${on_string}"> + <filter>bed is True</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="motif" value="motif_test1/homerResults/motif1.motif"/> + <conditional name="genome"> + <param name="source" value="installed"/> + <param name="all_fasta_source" value="phiX174"/> + </conditional> + <output name="output_text" file="scanMotif_res1.txt" ftype="tabular"/> + </test> + <test expect_num_outputs="1"> + <param name="motif" value="motif_test1/homerResults/motif1.motif"/> + <conditional name="genome"> + <param name="source" value="history"/> + <param name="fasta" value="phiX174.fasta"/> + </conditional> + <param name="bed" value="-bed"/> + <output name="output_bed" file="scanMotif_res1.bed" ftype="bed"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + + This is a wrapper for scanMotifGenomeWide.pl from HOMER but not all options are included. + + The scanMotifGenomeWide.pl script will take a motif file (may contain multiple motifs) and look for instances across the genome. + + ]]></help> + <expand macro="citation"/> +</tool> |
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| diff -r 000000000000 -r db456c398880 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,49 @@ +<macros> + <token name="@TOOL_VERSION@">4.11</token> + <!-- HOMER index version compatible with this version of HOMER + This is the HOMER version that introduced the preparsed structure expected + by the current version. --> + <token name="@IDX_VERSION@">4.11</token> + <token name="@VERSION_SUFFIX@">2</token> + <xml name="xrefs"> + <xrefs> + <xref type="bio.tools">homer</xref> + </xrefs> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="4.11">homer</requirement> + </requirements> + </xml> + <xml name="choose_center"> + <conditional name="choose_center"> + <param name="center" type="select" label="Do you want to center your sequence on the peak center?"> + <option value="centered" selected="True">Yes</option> + <option value="manual">No, I want asymetric (raise an error if given was chosen above)</option> + </param> + <when value="centered"/> + <when value="manual"> + <param name="sizes" type="integer" value="-100" label="sequence start relative to center"/> + </when> + </conditional> + </xml> + <xml name="mask_size"> + <param argument="-mask" type="boolean" truevalue="True" falsevalue="False" label="mask repeats/lower case sequence"/> + <conditional name="fixed_size"> + <param name="size_fixed" type="select" label="Do you want a fixed fragment size?"> + <option value="fixed" selected="True">Yes</option> + <option value="given">No, I want to keep the size of my peaks (-size given)</option> + </param> + <when value="given"/> + <when value="fixed"> + <param argument="-size" type="integer" min="0" value="200" label="fragment size in bp"/> + <expand macro="choose_center"/> + </when> + </conditional> + </xml> + <xml name="citation"> + <citations> + <citation type="doi">10.1016/j.molcel.2010.05.004</citation> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks.bed Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,66 @@ +chr10 95489848 95489849 chr10:95489648-95490124 9.37574 + 95489848 95489848 236,28,36 +chr10 95550657 95550658 chr10:95550458-95550913 22.4312 + 95550657 95550657 236,28,36 +chr10 95551883 95551884 chr10:95551647-95552156 9.8358 + 95551883 95551883 236,28,36 +chr10 95557476 95557477 chr10:95557210-95557760 15.8474 + 95557476 95557476 236,28,36 +chr10 95858373 95858374 chr10:95858061-95858620 8.91987 - 95858373 95858373 46,49,145 +chr10 95894941 95894942 chr10:95894657-95895156 14.5144 - 95894941 95894941 46,49,145 +chr10 95898656 95898657 chr10:95898384-95898961 12.5406 + 95898656 95898656 236,28,36 +chr10 96033867 96033868 chr10:96033562-96034101 20.0255 - 96033867 96033867 46,49,145 +chr10 96080634 96080635 chr10:96080279-96080903 6.11901 - 96080634 96080634 46,49,145 +chr10 96105359 96105360 chr10:96104999-96105605 12.8558 - 96105359 96105359 46,49,145 +chr10 96132305 96132306 chr10:96131980-96132540 14.3011 + 96132305 96132305 236,28,36 +chr10 96182451 96182452 chr10:96182221-96182632 9.96549 + 96182451 96182451 236,28,36 +chr10 96214052 96214053 chr10:96213797-96214300 26.3993 + 96214052 96214052 236,28,36 +chr10 96616854 96616855 chr10:96616623-96617093 4.72295 - 96616854 96616854 46,49,145 +chr10 96618518 96618519 chr10:96618332-96618740 7.7811 + 96618518 96618518 236,28,36 +chr10 96934833 96934834 chr10:96934538-96935160 10.7794 - 96934833 96934833 46,49,145 +chr10 97160696 97160697 chr10:97160138-97160734 9.26797 - 97160696 97160696 46,49,145 +chr10 97313143 97313144 chr10:97312750-97313424 16.1617 - 97313143 97313143 46,49,145 +chr10 97340069 97340070 chr10:97339748-97340355 8.23779 - 97340069 97340069 46,49,145 +chr10 97345534 97345535 chr10:97345244-97345845 21.9543 + 97345534 97345534 236,28,36 +chr10 97375992 97375993 chr10:97375737-97376277 17.1427 + 97375992 97375992 236,28,36 +chr10 97670411 97670412 chr10:97670243-97670641 15.0213 - 97670411 97670411 46,49,145 +chr10 97689620 97689621 chr10:97689400-97689842 6.20282 - 97689620 97689620 46,49,145 +chr10 97704766 97704767 chr10:97704497-97705056 12.2858 - 97704766 97704766 46,49,145 +chr10 97712886 97712887 chr10:97712528-97713193 16.5834 + 97712886 97712886 236,28,36 +chr10 97768453 97768454 chr10:97768293-97768873 -1.29559 . 97768453 97768453 0,0,0 +chr2 73745858 73745859 chr2:73745562-73746116 15.583 - 73745858 73745858 46,49,145 +chr2 73792430 73792431 chr2:73792224-73792669 11.3969 + 73792430 73792430 236,28,36 +chr2 73868302 73868303 chr2:73868052-73868532 16.5297 - 73868302 73868302 46,49,145 +chr2 73925250 73925251 chr2:73924997-73925519 6.64944 + 73925250 73925250 236,28,36 +chr2 73947567 73947568 chr2:73947347-73947809 11.7 - 73947567 73947567 46,49,145 +chr2 73965796 73965797 chr2:73965501-73966069 18.8918 + 73965796 73965796 236,28,36 +chr2 73987358 73987359 chr2:73987054-73987519 5.75056 - 73987358 73987358 46,49,145 +chr2 73998748 73998749 chr2:73998449-73999023 4.45417 - 73998748 73998748 46,49,145 +chr2 74027927 74027928 chr2:74027638-74028176 17.1136 + 74027927 74027927 236,28,36 +chr2 74066830 74066831 chr2:74066544-74067106 4.26306 + 74066830 74066830 236,28,36 +chr2 74247701 74247702 chr2:74247519-74247926 19.6437 - 74247701 74247701 46,49,145 +chr2 74300454 74300455 chr2:74300183-74300724 21.3163 + 74300454 74300454 236,28,36 +chr2 74305972 74305973 chr2:74305723-74306142 15.4325 - 74305972 74305972 46,49,145 +chr2 74655531 74655532 chr2:74655214-74655823 11.0865 - 74655531 74655531 46,49,145 +chr2 74661783 74661784 chr2:74661581-74662231 6.32635 - 74661783 74661783 46,49,145 +chr2 74663751 74663752 chr2:74663455-74664030 5.5749 - 74663751 74663751 46,49,145 +chr2 74673182 74673183 chr2:74672881-74673432 11.6759 - 74673182 74673182 46,49,145 +chr2 74686486 74686487 chr2:74686220-74686785 8.18583 + 74686486 74686486 236,28,36 +chr2 74691769 74691770 chr2:74691505-74692018 10.8344 + 74691769 74691769 236,28,36 +chr2 74694233 74694234 chr2:74693923-74694529 6.49186 - 74694233 74694233 46,49,145 +chr2 74702401 74702402 chr2:74702109-74702707 16.3674 + 74702401 74702401 236,28,36 +chr2 74715927 74715928 chr2:74715602-74716472 18.4944 + 74715927 74715927 236,28,36 +chr2 74964543 74964544 chr2:74964211-74964829 19.6671 - 74964543 74964543 46,49,145 +chr2 74977548 74977549 chr2:74977360-74977813 6.64332 + 74977548 74977548 236,28,36 +chr2 75055369 75055370 chr2:75055077-75055687 25.0987 - 75055369 75055369 46,49,145 +chr2 75138095 75138096 chr2:75137844-75138351 14.9999 - 75138095 75138095 46,49,145 +chr2 75151177 75151178 chr2:75150910-75151415 21.6232 - 75151177 75151177 46,49,145 +chr2 75152696 75152697 chr2:75152384-75152964 19.3701 - 75152696 75152696 46,49,145 +chr2 75208425 75208426 chr2:75208163-75208613 20.9151 - 75208425 75208425 46,49,145 +chr2 75312439 75312440 chr2:75312148-75312690 12.976 - 75312439 75312439 46,49,145 +chr2 75318398 75318399 chr2:75318086-75318603 15.8984 - 75318398 75318398 46,49,145 +chr2 75515510 75515511 chr2:75515254-75515778 6.45021 - 75515510 75515510 46,49,145 +chr2 75563785 75563786 chr2:75563556-75564002 6.81984 - 75563785 75563785 46,49,145 +chr2 75588782 75588783 chr2:75588511-75588998 13.9441 - 75588782 75588782 46,49,145 +chr2 75590417 75590418 chr2:75590116-75590691 15.844 - 75590417 75590417 46,49,145 +chr2 75603329 75603330 chr2:75603091-75603554 11.5679 - 75603329 75603329 46,49,145 +chr2 75605891 75605892 chr2:75605600-75606199 11.5138 + 75605891 75605891 236,28,36 +chr2 75658764 75658765 chr2:75658517-75658909 0.26272 + 75658764 75658764 236,28,36 +chr2 75781339 75781340 chr2:75781071-75781581 10.7504 - 75781339 75781339 46,49,145 +chr2 75786285 75786286 chr2:75786025-75786608 17.3776 + 75786285 75786285 236,28,36 |
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| diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks_first.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks_first.txt Mon Dec 13 15:13:33 2021 +0000 |
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| b'@@ -0,0 +1,67 @@\n+PeakID (cmd=annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf -ann test-data/annotations_default_simplified.txt)\tChr\tStart\tEnd\tStrand\tPeak Score\tFocus Ratio/Region Size\tAnnotation\tDetailed Annotation\tDistance to TSS\tNearest PromoterID\tEntrez ID\tNearest Unigene\tNearest Refseq\tNearest Ensembl\tGene Name\tGene Alias\tGene Description\tGene Type\n+chr10:96213797-96214300\tchr10\t96214053\t96214053\t+\t26.3993\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75055077-75055687\tchr2\t75055370\t75055370\t-\t25.0987\tNA\tIntergenic\tNA\t-339374\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:95550458-95550913\tchr10\t95550658\t95550658\t+\t22.4312\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:97345244-97345845\tchr10\t97345535\t97345535\t+\t21.9543\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75150910-75151415\tchr2\t75151178\t75151178\t-\t21.6232\tNA\tIntergenic\tNA\t-435182\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:74300183-74300724\tchr2\t74300455\t74300455\t+\t21.3163\tNA\tIntergenic\tNA\t-367855\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:75208163-75208613\tchr2\t75208426\t75208426\t-\t20.9151\tNA\tIntergenic\tNA\t-492430\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:96033562-96034101\tchr10\t96033868\t96033868\t-\t20.0255\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:74964211-74964829\tchr2\t74964544\t74964544\t-\t19.6671\tNA\tIntergenic\tNA\t-248548\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:74247519-74247926\tchr2\t74247702\t74247702\t-\t19.6437\tNA\tIntergenic\tNA\t-420608\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:75152384-75152964\tchr2\t75152697\t75152697\t-\t19.3701\tNA\tIntergenic\tNA\t-436701\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:73965501-73966069\tchr2\t73965797\t73965797\t+\t18.8918\tNA\tIntergenic\tNA\t-702513\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74715602-74716472\tchr2\t74715928\t74715928\t+\t18.4944\tNA\tpromoter-TSS (ENSMUST00000145799)\tNA\t68\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:75786025-75786608\tchr2\t75786286\t75786286\t+\t17.3776\tNA\tIntergenic\tNA\t-1070290\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:97375737-97376277\tchr10\t97375993\t97375993\t+\t17.1427\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:74027638-74028176\tchr2\t74027928\t74027928\t+\t17.1136\tNA\tIntergenic\tNA\t-640382\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr10:97712528-97713193\tchr10\t97712887\t97712887\t+\t16.5834\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:73868052-73868532\tchr2\t73868303\t73868303\t-\t16.5297\tNA\tIntergenic\tNA\t-800007\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74702109-74702707\tchr2\t74702402\t74702402\t+\t16.3674\tNA\tIntergenic\tNA\t-1260\tENSMUST00000198895\tENSMUSG00000104570\tENSMUST00000198895\t\t\tGm44463\t\t\tmiRNA\n+chr10:97312750-97313424\tchr10\t97313144\t97313144\t-\t16.1617\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75318086-75318603\tchr2\t75318399\t75318399\t-\t15.8984\tNA\tIntergenic\tNA\t-602403\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:95557210-95557760\tchr10\t95557477\t95557477\t+\t15.8474\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75590116-75590691\tchr2\t75590418\t75590418\t-\t15.844\tNA\tIntergenic\tNA\t-874422\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:73745562-73746116\tchr2\t73745859\t73745859\t-\t15.583\tNA\tIntergenic\tNA\t-922451\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74305723-74306142\tchr2\t74305973\t74305973\t-\t15.4325\tNA\tIntergenic\tNA\t-362337\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr10:97670243-97670641\tchr10\t97670412\t97670412\t-\t15.0213\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75137844-75138351\tchr2\t75138096\t75138096\t-\t14.9999\tNA\tIntergenic\tNA\t-422100\tENS'..b'rotein_coding\n+chr2:75603091-75603554\tchr2\t75603330\t75603330\t-\t11.5679\tNA\tIntergenic\tNA\t-887334\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:75605600-75606199\tchr2\t75605892\t75605892\t+\t11.5138\tNA\tIntergenic\tNA\t-889896\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:73792224-73792669\tchr2\t73792431\t73792431\t+\t11.3969\tNA\tIntergenic\tNA\t-875879\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74655214-74655823\tchr2\t74655532\t74655532\t-\t11.0865\tNA\tIntergenic\tNA\t-12778\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74691505-74692018\tchr2\t74691770\t74691770\t+\t10.8344\tNA\tpromoter-TSS (ENSMUST00000061745)\tNA\t-154\tENSMUST00000061745\tENSMUSG00000050368\tENSMUST00000061745\t\t\tHoxd10\t\t\tprotein_coding\n+chr10:96934538-96935160\tchr10\t96934834\t96934834\t-\t10.7794\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75781071-75781581\tchr2\t75781340\t75781340\t-\t10.7504\tNA\tIntergenic\tNA\t-1065344\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:96182221-96182632\tchr10\t96182452\t96182452\t+\t9.96549\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:95551647-95552156\tchr10\t95551884\t95551884\t+\t9.8358\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:95489648-95490124\tchr10\t95489849\t95489849\t+\t9.37574\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:97160138-97160734\tchr10\t97160697\t97160697\t-\t9.26797\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:95858061-95858620\tchr10\t95858374\t95858374\t-\t8.91987\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:97339748-97340355\tchr10\t97340070\t97340070\t-\t8.23779\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:74686220-74686785\tchr2\t74686487\t74686487\t+\t8.18583\tNA\texon (ENSMUST00000048086, exon 2 of 2)\tNA\t3041\tENSMUST00000136302\tENSMUSG00000099521\tENSMUST00000136302\t\t\tGm28309\t\t\tprocessed_transcript\n+chr10:96618332-96618740\tchr10\t96618519\t96618519\t+\t7.7811\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75563556-75564002\tchr2\t75563786\t75563786\t-\t6.81984\tNA\tIntergenic\tNA\t-847790\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:73924997-73925519\tchr2\t73925251\t73925251\t+\t6.64944\tNA\tIntergenic\tNA\t-743059\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74977360-74977813\tchr2\t74977549\t74977549\t+\t6.64332\tNA\tIntergenic\tNA\t-261553\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:74693923-74694529\tchr2\t74694234\t74694234\t-\t6.49186\tNA\tTTS (ENSMUST00000136302)\tNA\t-1286\tENSMUST00000126966\tENSMUSG00000086077\tENSMUST00000126966\t\t\tGm14396\t\t\tlincRNA\n+chr2:75515254-75515778\tchr2\t75515511\t75515511\t-\t6.45021\tNA\tIntergenic\tNA\t-799515\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:74661581-74662231\tchr2\t74661784\t74661784\t-\t6.32635\tNA\tIntergenic\tNA\t-6526\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr10:97689400-97689842\tchr10\t97689621\t97689621\t-\t6.20282\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:96080279-96080903\tchr10\t96080635\t96080635\t-\t6.11901\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:73987054-73987519\tchr2\t73987359\t73987359\t-\t5.75056\tNA\tIntergenic\tNA\t-680951\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74663455-74664030\tchr2\t74663752\t74663752\t-\t5.5749\tNA\tIntergenic\tNA\t-4558\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr10:96616623-96617093\tchr10\t96616855\t96616855\t-\t4.72295\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:73998449-73999023\tchr2\t73998749\t73998749\t-\t4.45417\tNA\tIntergenic\tNA\t-669561\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74066544-74067106\tchr2\t74066831\t74066831\t+\t4.26306\tNA\tIntergenic\tNA\t-601479\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:75658517-75658909\tchr2\t75658765\t75658765\t+\t0.26272\tNA\tIntergenic\tNA\t-942769\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:97768293-97768873\tchr10\t97768454\t97768454\t+\t-1.29559\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n' |
| b |
| diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks_second.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks_second.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,67 @@ +PeakID (cmd=annotatePeaks.pl test-data/CTCF_peaks.bed none -ann test-data/annotations_default.txt) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type +chr10:96213797-96214300 chr10 96214053 96214053 + 26.3993 NA NA NA NA NA +chr2:75055077-75055687 chr2 75055370 75055370 - 25.0987 NA Intergenic NA NA NA +chr10:95550458-95550913 chr10 95550658 95550658 + 22.4312 NA NA NA NA NA +chr10:97345244-97345845 chr10 97345535 97345535 + 21.9543 NA NA NA NA NA +chr2:75150910-75151415 chr2 75151178 75151178 - 21.6232 NA Intergenic NA NA NA +chr2:74300183-74300724 chr2 74300455 74300455 + 21.3163 NA Intergenic NA NA NA +chr2:75208163-75208613 chr2 75208426 75208426 - 20.9151 NA Intergenic NA NA NA +chr10:96033562-96034101 chr10 96033868 96033868 - 20.0255 NA NA NA NA NA +chr2:74964211-74964829 chr2 74964544 74964544 - 19.6671 NA Intergenic NA NA NA +chr2:74247519-74247926 chr2 74247702 74247702 - 19.6437 NA Intergenic NA NA NA +chr2:75152384-75152964 chr2 75152697 75152697 - 19.3701 NA Intergenic NA NA NA +chr2:73965501-73966069 chr2 73965797 73965797 + 18.8918 NA Intergenic NA NA NA +chr2:74715602-74716472 chr2 74715928 74715928 + 18.4944 NA promoter-TSS (ENSMUST00000145799) NA NA NA +chr2:75786025-75786608 chr2 75786286 75786286 + 17.3776 NA Intergenic NA NA NA +chr10:97375737-97376277 chr10 97375993 97375993 + 17.1427 NA NA NA NA NA +chr2:74027638-74028176 chr2 74027928 74027928 + 17.1136 NA Intergenic NA NA NA +chr10:97712528-97713193 chr10 97712887 97712887 + 16.5834 NA NA NA NA NA +chr2:73868052-73868532 chr2 73868303 73868303 - 16.5297 NA Intergenic NA NA NA +chr2:74702109-74702707 chr2 74702402 74702402 + 16.3674 NA TTS (ENSMUST00000132326) NA NA NA +chr10:97312750-97313424 chr10 97313144 97313144 - 16.1617 NA NA NA NA NA +chr2:75318086-75318603 chr2 75318399 75318399 - 15.8984 NA Intergenic NA NA NA +chr10:95557210-95557760 chr10 95557477 95557477 + 15.8474 NA NA NA NA NA +chr2:75590116-75590691 chr2 75590418 75590418 - 15.844 NA Intergenic NA NA NA +chr2:73745562-73746116 chr2 73745859 73745859 - 15.583 NA Intergenic NA NA NA +chr2:74305723-74306142 chr2 74305973 74305973 - 15.4325 NA Intergenic NA NA NA +chr10:97670243-97670641 chr10 97670412 97670412 - 15.0213 NA NA NA NA NA +chr2:75137844-75138351 chr2 75138096 75138096 - 14.9999 NA Intergenic NA NA NA +chr10:95894657-95895156 chr10 95894942 95894942 - 14.5144 NA NA NA NA NA +chr10:96131980-96132540 chr10 96132306 96132306 + 14.3011 NA NA NA NA NA +chr2:75588511-75588998 chr2 75588783 75588783 - 13.9441 NA Intergenic NA NA NA +chr2:75312148-75312690 chr2 75312440 75312440 - 12.976 NA Intergenic NA NA NA +chr10:96104999-96105605 chr10 96105360 96105360 - 12.8558 NA NA NA NA NA +chr10:95898384-95898961 chr10 95898657 95898657 + 12.5406 NA NA NA NA NA +chr10:97704497-97705056 chr10 97704767 97704767 - 12.2858 NA NA NA NA NA +chr2:73947347-73947809 chr2 73947568 73947568 - 11.7 NA Intergenic NA NA NA +chr2:74672881-74673432 chr2 74673183 74673183 - 11.6759 NA Intergenic NA NA NA +chr2:75603091-75603554 chr2 75603330 75603330 - 11.5679 NA Intergenic NA NA NA +chr2:75605600-75606199 chr2 75605892 75605892 + 11.5138 NA Intergenic NA NA NA +chr2:73792224-73792669 chr2 73792431 73792431 + 11.3969 NA Intergenic NA NA NA +chr2:74655214-74655823 chr2 74655532 74655532 - 11.0865 NA Intergenic NA NA NA +chr2:74691505-74692018 chr2 74691770 74691770 + 10.8344 NA promoter-TSS (ENSMUST00000061745) NA NA NA +chr10:96934538-96935160 chr10 96934834 96934834 - 10.7794 NA NA NA NA NA +chr2:75781071-75781581 chr2 75781340 75781340 - 10.7504 NA Intergenic NA NA NA +chr10:96182221-96182632 chr10 96182452 96182452 + 9.96549 NA NA NA NA NA +chr10:95551647-95552156 chr10 95551884 95551884 + 9.8358 NA NA NA NA NA +chr10:95489648-95490124 chr10 95489849 95489849 + 9.37574 NA NA NA NA NA +chr10:97160138-97160734 chr10 97160697 97160697 - 9.26797 NA NA NA NA NA +chr10:95858061-95858620 chr10 95858374 95858374 - 8.91987 NA NA NA NA NA +chr10:97339748-97340355 chr10 97340070 97340070 - 8.23779 NA NA NA NA NA +chr2:74686220-74686785 chr2 74686487 74686487 + 8.18583 NA exon (ENSMUST00000048086, exon 2 of 2) NA NA NA +chr10:96618332-96618740 chr10 96618519 96618519 + 7.7811 NA NA NA NA NA +chr2:75563556-75564002 chr2 75563786 75563786 - 6.81984 NA Intergenic NA NA NA +chr2:73924997-73925519 chr2 73925251 73925251 + 6.64944 NA Intergenic NA NA NA +chr2:74977360-74977813 chr2 74977549 74977549 + 6.64332 NA Intergenic NA NA NA +chr2:74693923-74694529 chr2 74694234 74694234 - 6.49186 NA TTS (ENSMUST00000136302) NA NA NA +chr2:75515254-75515778 chr2 75515511 75515511 - 6.45021 NA Intergenic NA NA NA +chr2:74661581-74662231 chr2 74661784 74661784 - 6.32635 NA Intergenic NA NA NA +chr10:97689400-97689842 chr10 97689621 97689621 - 6.20282 NA NA NA NA NA +chr10:96080279-96080903 chr10 96080635 96080635 - 6.11901 NA NA NA NA NA +chr2:73987054-73987519 chr2 73987359 73987359 - 5.75056 NA Intergenic NA NA NA +chr2:74663455-74664030 chr2 74663752 74663752 - 5.5749 NA Intergenic NA NA NA +chr10:96616623-96617093 chr10 96616855 96616855 - 4.72295 NA NA NA NA NA +chr2:73998449-73999023 chr2 73998749 73998749 - 4.45417 NA Intergenic NA NA NA +chr2:74066544-74067106 chr2 74066831 74066831 + 4.26306 NA Intergenic NA NA NA +chr2:75658517-75658909 chr2 75658765 75658765 + 0.26272 NA Intergenic NA NA NA +chr10:97768293-97768873 chr10 97768454 97768454 + -1.29559 NA NA NA NA NA |
| b |
| diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks_shifted.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks_shifted.bed Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,24 @@ +mm10_dna 5858 5859 chr2:73745562-73746116 15.583 - 73745858 73745858 46,49,145 +mm10_dna 52430 52431 chr2:73792224-73792669 11.3969 + 73792430 73792430 236,28,36 +mm10_dna 128302 128303 chr2:73868052-73868532 16.5297 - 73868302 73868302 46,49,145 +mm10_dna 185250 185251 chr2:73924997-73925519 6.64944 + 73925250 73925250 236,28,36 +mm10_dna 207567 207568 chr2:73947347-73947809 11.7 - 73947567 73947567 46,49,145 +mm10_dna 225796 225797 chr2:73965501-73966069 18.8918 + 73965796 73965796 236,28,36 +mm10_dna 247358 247359 chr2:73987054-73987519 5.75056 - 73987358 73987358 46,49,145 +mm10_dna 258748 258749 chr2:73998449-73999023 4.45417 - 73998748 73998748 46,49,145 +mm10_dna 287927 287928 chr2:74027638-74028176 17.1136 + 74027927 74027927 236,28,36 +mm10_dna 326830 326831 chr2:74066544-74067106 4.26306 + 74066830 74066830 236,28,36 +mm10_dna 507701 507702 chr2:74247519-74247926 19.6437 - 74247701 74247701 46,49,145 +mm10_dna 560454 560455 chr2:74300183-74300724 21.3163 + 74300454 74300454 236,28,36 +mm10_dna 565972 565973 chr2:74305723-74306142 15.4325 - 74305972 74305972 46,49,145 +mm10_dna 915531 915532 chr2:74655214-74655823 11.0865 - 74655531 74655531 46,49,145 +mm10_dna 921783 921784 chr2:74661581-74662231 6.32635 - 74661783 74661783 46,49,145 +mm10_dna 923751 923752 chr2:74663455-74664030 5.5749 - 74663751 74663751 46,49,145 +mm10_dna 933182 933183 chr2:74672881-74673432 11.6759 - 74673182 74673182 46,49,145 +mm10_dna 946486 946487 chr2:74686220-74686785 8.18583 + 74686486 74686486 236,28,36 +mm10_dna 951769 951770 chr2:74691505-74692018 10.8344 + 74691769 74691769 236,28,36 +mm10_dna 954233 954234 chr2:74693923-74694529 6.49186 - 74694233 74694233 46,49,145 +mm10_dna 962401 962402 chr2:74702109-74702707 16.3674 + 74702401 74702401 236,28,36 +mm10_dna 975927 975928 chr2:74715602-74716472 18.4944 + 74715927 74715927 236,28,36 +mm10_dna 1224543 1224544 chr2:74964211-74964829 19.6671 - 74964543 74964543 46,49,145 +mm10_dna 1237548 1237549 chr2:74977360-74977813 6.64332 + 74977548 74977548 236,28,36 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/CTCF_peaks_third.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CTCF_peaks_third.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| b'@@ -0,0 +1,67 @@\n+PeakID (cmd=annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf)\tChr\tStart\tEnd\tStrand\tPeak Score\tFocus Ratio/Region Size\tAnnotation\tDetailed Annotation\tDistance to TSS\tNearest PromoterID\tEntrez ID\tNearest Unigene\tNearest Refseq\tNearest Ensembl\tGene Name\tGene Alias\tGene Description\tGene Type\n+chr10:96213797-96214300\tchr10\t96214053\t96214053\t+\t26.3993\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75055077-75055687\tchr2\t75055370\t75055370\t-\t25.0987\tNA\tIntergenic\tIntergenic\t-339374\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:95550458-95550913\tchr10\t95550658\t95550658\t+\t22.4312\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:97345244-97345845\tchr10\t97345535\t97345535\t+\t21.9543\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75150910-75151415\tchr2\t75151178\t75151178\t-\t21.6232\tNA\tIntergenic\tIntergenic\t-435182\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:74300183-74300724\tchr2\t74300455\t74300455\t+\t21.3163\tNA\tIntergenic\tIntergenic\t-367855\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:75208163-75208613\tchr2\t75208426\t75208426\t-\t20.9151\tNA\tIntergenic\tIntergenic\t-492430\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:96033562-96034101\tchr10\t96033868\t96033868\t-\t20.0255\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:74964211-74964829\tchr2\t74964544\t74964544\t-\t19.6671\tNA\tIntergenic\tIntergenic\t-248548\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:74247519-74247926\tchr2\t74247702\t74247702\t-\t19.6437\tNA\tIntergenic\tIntergenic\t-420608\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:75152384-75152964\tchr2\t75152697\t75152697\t-\t19.3701\tNA\tIntergenic\tIntergenic\t-436701\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:73965501-73966069\tchr2\t73965797\t73965797\t+\t18.8918\tNA\tIntergenic\tIntergenic\t-702513\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74715602-74716472\tchr2\t74715928\t74715928\t+\t18.4944\tNA\tpromoter-TSS (ENSMUST00000145799)\tantisense-promoter-TSS (ENSMUST00000145799)\t68\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:75786025-75786608\tchr2\t75786286\t75786286\t+\t17.3776\tNA\tIntergenic\tIntergenic\t-1070290\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:97375737-97376277\tchr10\t97375993\t97375993\t+\t17.1427\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:74027638-74028176\tchr2\t74027928\t74027928\t+\t17.1136\tNA\tIntergenic\tIntergenic\t-640382\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr10:97712528-97713193\tchr10\t97712887\t97712887\t+\t16.5834\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:73868052-73868532\tchr2\t73868303\t73868303\t-\t16.5297\tNA\tIntergenic\tIntergenic\t-800007\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74702109-74702707\tchr2\t74702402\t74702402\t+\t16.3674\tNA\tIntergenic\tIntergenic\t-1260\tENSMUST00000198895\tENSMUSG00000104570\tENSMUST00000198895\t\t\tGm44463\t\t\tmiRNA\n+chr10:97312750-97313424\tchr10\t97313144\t97313144\t-\t16.1617\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75318086-75318603\tchr2\t75318399\t75318399\t-\t15.8984\tNA\tIntergenic\tIntergenic\t-602403\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:95557210-95557760\tchr10\t95557477\t95557477\t+\t15.8474\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75590116-75590691\tchr2\t75590418\t75590418\t-\t15.844\tNA\tIntergenic\tIntergenic\t-874422\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:73745562-73746116\tchr2\t73745859\t73745859\t-\t15.583\tNA\tIntergenic\tIntergenic\t-922451\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74305723-74306142\tchr2\t74305973\t74305973\t-\t15.4325\tNA\tIntergenic\tIntergenic\t-362337\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr10:97670243-97670641\tchr10\t97670412\t97670412'..b'genic\t-889896\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:73792224-73792669\tchr2\t73792431\t73792431\t+\t11.3969\tNA\tIntergenic\tIntergenic\t-875879\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74655214-74655823\tchr2\t74655532\t74655532\t-\t11.0865\tNA\tIntergenic\tIntergenic\t-12778\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74691505-74692018\tchr2\t74691770\t74691770\t+\t10.8344\tNA\tpromoter-TSS (ENSMUST00000061745)\tprotein_coding-promoter-TSS (ENSMUST00000061745)\t-154\tENSMUST00000061745\tENSMUSG00000050368\tENSMUST00000061745\t\t\tHoxd10\t\t\tprotein_coding\n+chr10:96934538-96935160\tchr10\t96934834\t96934834\t-\t10.7794\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75781071-75781581\tchr2\t75781340\t75781340\t-\t10.7504\tNA\tIntergenic\tIntergenic\t-1065344\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:96182221-96182632\tchr10\t96182452\t96182452\t+\t9.96549\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:95551647-95552156\tchr10\t95551884\t95551884\t+\t9.8358\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:95489648-95490124\tchr10\t95489849\t95489849\t+\t9.37574\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:97160138-97160734\tchr10\t97160697\t97160697\t-\t9.26797\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:95858061-95858620\tchr10\t95858374\t95858374\t-\t8.91987\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:97339748-97340355\tchr10\t97340070\t97340070\t-\t8.23779\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:74686220-74686785\tchr2\t74686487\t74686487\t+\t8.18583\tNA\texon (ENSMUST00000048086, exon 2 of 2)\tprotein_coding-exon (ENSMUST00000048086, exon 2 of 2)\t3041\tENSMUST00000136302\tENSMUSG00000099521\tENSMUST00000136302\t\t\tGm28309\t\t\tprocessed_transcript\n+chr10:96618332-96618740\tchr10\t96618519\t96618519\t+\t7.7811\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:75563556-75564002\tchr2\t75563786\t75563786\t-\t6.81984\tNA\tIntergenic\tIntergenic\t-847790\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:73924997-73925519\tchr2\t73925251\t73925251\t+\t6.64944\tNA\tIntergenic\tIntergenic\t-743059\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74977360-74977813\tchr2\t74977549\t74977549\t+\t6.64332\tNA\tIntergenic\tIntergenic\t-261553\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:74693923-74694529\tchr2\t74694234\t74694234\t-\t6.49186\tNA\tTTS (ENSMUST00000136302)\tprocessed_transcript-TTS (ENSMUST00000136302)\t-1286\tENSMUST00000126966\tENSMUSG00000086077\tENSMUST00000126966\t\t\tGm14396\t\t\tlincRNA\n+chr2:75515254-75515778\tchr2\t75515511\t75515511\t-\t6.45021\tNA\tIntergenic\tIntergenic\t-799515\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr2:74661581-74662231\tchr2\t74661784\t74661784\t-\t6.32635\tNA\tIntergenic\tIntergenic\t-6526\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr10:97689400-97689842\tchr10\t97689621\t97689621\t-\t6.20282\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr10:96080279-96080903\tchr10\t96080635\t96080635\t-\t6.11901\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:73987054-73987519\tchr2\t73987359\t73987359\t-\t5.75056\tNA\tIntergenic\tIntergenic\t-680951\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74663455-74664030\tchr2\t74663752\t74663752\t-\t5.5749\tNA\tIntergenic\tIntergenic\t-4558\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr10:96616623-96617093\tchr10\t96616855\t96616855\t-\t4.72295\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n+chr2:73998449-73999023\tchr2\t73998749\t73998749\t-\t4.45417\tNA\tIntergenic\tIntergenic\t-669561\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:74066544-74067106\tchr2\t74066831\t74066831\t+\t4.26306\tNA\tIntergenic\tIntergenic\t-601479\tENSMUST00000001872\tENSMUSG00000001819\tENSMUST00000001872\t\t\tHoxd13\t\t\tprotein_coding\n+chr2:75658517-75658909\tchr2\t75658765\t75658765\t+\t0.26272\tNA\tIntergenic\tIntergenic\t-942769\tENSMUST00000145799\tENSMUSG00000052371\tENSMUST00000145799\t\t\tHoxd3os1\t\t\tantisense\n+chr10:97768293-97768873\tchr10\t97768454\t97768454\t+\t-1.29559\tNA\tNA\tNA\tNA\tNA\t\t\t\t\t\t\t\t\n' |
| b |
| diff -r 000000000000 -r db456c398880 test-data/all_fasta.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/all_fasta.loc Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - dbkey (Database key) +# - name (Galaxy shows this in the UI) +# - path (the reference file) +# +phiX174 phiX174 phiX174 ${__HERE__}/phiX174.fasta |
| b |
| diff -r 000000000000 -r db456c398880 test-data/annotations_default.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_default.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,115 @@ +Intergenic chr2 1 74667309 + N 1900000000 +promoter-TSS (ENSMUST00000001872) chr2 74667310 74668410 + P 1 +exon (ENSMUST00000001872, exon 1 of 2) chr2 74668411 74669078 + E 59 +intron (ENSMUST00000001872, intron 1 of 1) chr2 74669079 74669885 + I 158 +exon (ENSMUST00000001872, exon 2 of 2) chr2 74669886 74670136 + E 61 +3' UTR (ENSMUST00000001872, exon 2 of 2) chr2 74670137 74671498 + 3UTR 60 +TTS (ENSMUST00000001872) chr2 74671499 74672599 + TTS 30 +Intergenic--2 chr2 74672600 74674012 + N 1900000000 +promoter-TSS (ENSMUST00000001878) chr2 74674013 74675113 + P 2 +exon (ENSMUST00000001878, exon 1 of 2) chr2 74675114 74675654 + E 63 +intron (ENSMUST00000001878, intron 1 of 1) chr2 74675655 74675813 + I 158 +exon (ENSMUST00000001878, exon 2 of 2) chr2 74675814 74676052 + E 65 +3' UTR (ENSMUST00000001878, exon 2 of 2) chr2 74676053 74677604 + 3UTR 64 +TTS (ENSMUST00000001878) chr2 74677605 74678556 + TTS 31 +promoter-TSS (ENSMUST00000048086) chr2 74678557 74679657 + P 6 +exon (ENSMUST00000048086, exon 1 of 2) chr2 74679658 74679809 + E 83 +intron (ENSMUST00000048086, intron 1 of 1) chr2 74679810 74681322 + I 158 +promoter-TSS (ENSMUST00000142312) chr2 74681323 74682423 + P 20 +exon (ENSMUST00000142312, exon 1 of 2) chr2 74682424 74682445 + E 131 +promoter-TSS (ENSMUST00000136302) chr2 74682446 74683546 + P 17 +intron (ENSMUST00000136302, intron 1 of 2) chr2 74683547 74683902 + I 158 +exon (ENSMUST00000048086, exon 2 of 2) chr2 74683903 74684067 + E 84 +TTS (ENSMUST00000142312) chr2 74684068 74685168 + TTS 49 +intron (ENSMUST00000136302, intron 2 of 2) chr2 74684357 74685168 + I 158 +exon (ENSMUST00000048086, exon 2 of 2)--2 chr2 74685169 74686915 + E 84 +TTS (ENSMUST00000048086) chr2 74686916 74688016 + TTS 35 +intron (ENSMUST00000136302, intron 2 of 2)--2 chr2 74688017 74690923 + I 158 +promoter-TSS (ENSMUST00000061745) chr2 74690924 74692024 + P 9 +exon (ENSMUST00000061745, exon 1 of 2) chr2 74692025 74692724 + E 96 +intron (ENSMUST00000061745, intron 1 of 1) chr2 74692725 74694090 + I 158 +exon (ENSMUST00000061745, exon 2 of 2) chr2 74694091 74694093 + E 98 +TTS (ENSMUST00000136302) chr2 74694094 74694519 + TTS 46 +promoter-TSS (ENSMUST00000126966) chr2 74694520 74695620 + P 15 +promoter-TSS (ENSMUST00000152027) chr2 74695621 74695701 + P 25 +TTS (ENSMUST00000061745) chr2 74695702 74696105 + TTS 38 +TTS (ENSMUST00000190845) chr2 74696106 74696726 - TTS 57 +promoter-TSS (ENSMUST00000059272) chr2 74696727 74697827 + P 8 +promoter-TSS (ENSMUST00000190845) chr2 74697828 74698586 - P 28 +exon (ENSMUST00000059272, exon 1 of 2) chr2 74698587 74698833 + E 92 +intron (ENSMUST00000059272, intron 1 of 1) chr2 74698834 74699179 + I 158 +exon (ENSMUST00000059272, exon 2 of 2) chr2 74699180 74699421 + E 94 +3' UTR (ENSMUST00000059272, exon 2 of 2) chr2 74699422 74700005 + 3UTR 93 +TTS (ENSMUST00000198895) chr2 74700006 74700107 - TTS 58 +TTS (ENSMUST00000059272) chr2 74700108 74701041 + TTS 37 +promoter-TSS (ENSMUST00000198895) chr2 74701042 74702142 - P 29 +Intergenic--3 chr2 74702143 74702247 + N 1900000000 +TTS (ENSMUST00000132326) chr2 74702248 74703348 - TTS 45 +exon (ENSMUST00000132326, exon 2 of 2) chr2 74703349 74703614 - E 120 +promoter-TSS (ENSMUST00000151380) chr2 74703615 74703904 + P 24 +promoter-TSS (ENSMUST00000019749) chr2 74703905 74705005 + P 3 +promoter-TSS (ENSMUST00000074721) chr2 74705006 74705252 + P 10 +5' UTR (ENSMUST00000019749, exon 1 of 2) chr2 74705253 74705547 + 5UTR 66 +exon (ENSMUST00000019749, exon 1 of 2) chr2 74705548 74706118 + E 67 +intron (ENSMUST00000074721, intron 1 of 1) chr2 74706119 74706513 + I 158 +exon (ENSMUST00000019749, exon 2 of 2) chr2 74706514 74706711 + E 69 +TTS (ENSMUST00000151380) chr2 74706712 74707206 + TTS 53 +TTS (ENSMUST00000074721) chr2 74707207 74707832 + TTS 39 +TTS (ENSMUST00000019749) chr2 74707833 74708933 + TTS 32 +intron (ENSMUST00000132326, intron 1 of 1) chr2 74708934 74709042 - I 158 +TTS (ENSMUST00000156342) chr2 74709043 74709192 - TTS 55 +TTS (ENSMUST00000145799) chr2 74709193 74710293 - TTS 52 +intron (ENSMUST00000145799, intron 2 of 2) chr2 74710294 74710926 - I 158 +promoter-TSS (ENSMUST00000111983) chr2 74710927 74712027 + P 14 +promoter-TSS (ENSMUST00000132326) chr2 74712028 74713054 - P 16 +promoter-TSS (ENSMUST00000156342) chr2 74713055 74713526 - P 26 +exon (ENSMUST00000139005, exon 2 of 2) chr2 74713527 74714401 - E 125 +intron (ENSMUST00000145799, intron 1 of 2) chr2 74714402 74715705 - I 158 +exon (ENSMUST00000139005, exon 1 of 2) chr2 74715706 74715895 - E 126 +promoter-TSS (ENSMUST00000145799) chr2 74715896 74716029 - P 23 +promoter-TSS (ENSMUST00000139005) chr2 74716030 74717130 - P 18 +intron (ENSMUST00000111983, intron 1 of 2) chr2 74717131 74720977 + I 158 +promoter-TSS (ENSMUST00000047904) chr2 74720978 74722078 + P 5 +5' UTR (ENSMUST00000047904, exon 1 of 6) chr2 74722079 74722177 + 5UTR 75 +intron (ENSMUST00000047904, intron 1 of 5) chr2 74722178 74722552 + I 158 +5' UTR (ENSMUST00000047904, exon 2 of 6) chr2 74722553 74722631 + 5UTR 76 +intron (ENSMUST00000144040, intron 2 of 6) chr2 74722632 74723331 + I 158 +5' UTR (ENSMUST00000047904, exon 3 of 6) chr2 74723332 74723367 + 5UTR 77 +intron (ENSMUST00000144040, intron 3 of 6) chr2 74723368 74725069 + I 158 +promoter-TSS (ENSMUST00000083566) chr2 74725070 74725727 + P 11 +promoter-TSS (ENSMUST00000053932) chr2 74725728 74726828 + P 7 +promoter-TSS (ENSMUST00000111980) chr2 74726829 74727174 + P 12 +5' UTR (ENSMUST00000047904, exon 5 of 6) chr2 74727175 74727278 + 5UTR 79 +exon (ENSMUST00000047904, exon 5 of 6) chr2 74727279 74727705 + E 80 +intron (ENSMUST00000053932, intron 1 of 3) chr2 74727706 74728261 + I 158 +exon (ENSMUST00000047904, exon 6 of 6) chr2 74728262 74728587 + E 82 +3' UTR (ENSMUST00000047904, exon 6 of 6) chr2 74728588 74728767 + 3UTR 81 +TTS (ENSMUST00000144040) chr2 74728768 74729022 + TTS 50 +TTS (ENSMUST00000111980) chr2 74729023 74729059 + TTS 41 +TTS (ENSMUST00000047904) chr2 74729060 74730160 + TTS 34 +intron (ENSMUST00000053932, intron 2 of 3) chr2 74730161 74731912 + I 158 +promoter-TSS (ENSMUST00000144544) chr2 74731913 74733013 + P 22 +5' UTR (ENSMUST00000144544, exon 1 of 2) chr2 74733014 74733040 + 5UTR 141 +intron (ENSMUST00000144544, intron 1 of 1) chr2 74733041 74735514 + I 158 +promoter-TSS (ENSMUST00000111982) chr2 74735515 74736615 + P 13 +5' UTR (ENSMUST00000111982, exon 1 of 3) chr2 74736616 74736705 + 5UTR 108 +intron (ENSMUST00000111982, intron 1 of 2) chr2 74736706 74738618 + I 158 +promoter-TSS (ENSMUST00000047830) chr2 74738619 74739719 + P 4 +intron (ENSMUST00000047830, intron 1 of 2) chr2 74739720 74743927 + I 158 +5' UTR (ENSMUST00000047830, exon 2 of 3) chr2 74743928 74744011 + 5UTR 71 +exon (ENSMUST00000047830, exon 2 of 3) chr2 74744012 74744113 + E 72 +TTS (ENSMUST00000144544) chr2 74744114 74744673 + TTS 51 +promoter-TSS (ENSMUST00000140666) chr2 74744674 74745774 + P 19 +promoter-TSS (ENSMUST00000190553) chr2 74745775 74745822 + P 27 +5' UTR (ENSMUST00000140666, exon 1 of 2) chr2 74745823 74746156 + 5UTR 127 +exon (ENSMUST00000140666, exon 1 of 2) chr2 74746157 74746220 + E 128 +exon (ENSMUST00000190553, exon 1 of 1) chr2 74746221 74746321 + E 155 +exon (ENSMUST00000047830, exon 3 of 3) chr2 74746322 74746495 + E 74 +TTS (ENSMUST00000140666) chr2 74746496 74747596 + TTS 48 +3' UTR (ENSMUST00000111983, exon 3 of 3) chr2 74747080 74747799 + 3UTR 116 +3' UTR (ENSMUST00000047830, exon 3 of 3) chr2 74747597 74747799 + 3UTR 73 +TTS (ENSMUST00000047830) chr2 74747800 74748900 + TTS 33 +TTS (ENSMUST00000053932) chr2 74748901 74748918 + TTS 36 +TTS (ENSMUST00000111983) chr2 74748919 74749271 + TTS 43 +TTS (ENSMUST00000190553) chr2 74749272 74749442 + TTS 56 +Intergenic--4 chr2 74749443 1500000000 + N 1900000000 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/annotations_default_simplified.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_default_simplified.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,87 @@ +Intergenic chr2 1 74667309 + N 1900000000 +promoter-TSS (ENSMUST00000001872) chr2 74667310 74668410 + P 1 +exon (ENSMUST00000001872, exon 1 of 2) chr2 74668411 74669078 + E 33 +intron (ENSMUST00000001872, intron 1 of 1) chr2 74669079 74669885 + I 88 +exon (ENSMUST00000001872, exon 2 of 2) chr2 74669886 74670136 + E 35 +3' UTR (ENSMUST00000001872, exon 2 of 2) chr2 74670137 74671498 + 3UTR 34 +TTS (ENSMUST00000001872) chr2 74671499 74672599 + TTS 17 +Intergenic--2 chr2 74672600 74674012 + N 1900000000 +promoter-TSS (ENSMUST00000001878) chr2 74674013 74675113 + P 2 +exon (ENSMUST00000001878, exon 1 of 2) chr2 74675114 74675654 + E 37 +intron (ENSMUST00000001878, intron 1 of 1) chr2 74675655 74675813 + I 88 +exon (ENSMUST00000001878, exon 2 of 2) chr2 74675814 74676052 + E 39 +3' UTR (ENSMUST00000001878, exon 2 of 2) chr2 74676053 74677604 + 3UTR 38 +TTS (ENSMUST00000001878) chr2 74677605 74678556 + TTS 18 +promoter-TSS (ENSMUST00000048086) chr2 74678557 74679657 + P 4 +exon (ENSMUST00000048086, exon 1 of 2) chr2 74679658 74679809 + E 44 +intron (ENSMUST00000048086, intron 1 of 1) chr2 74679810 74681322 + I 88 +promoter-TSS (ENSMUST00000142312) chr2 74681323 74682423 + P 11 +exon (ENSMUST00000142312, exon 1 of 2) chr2 74682424 74682445 + E 69 +promoter-TSS (ENSMUST00000136302) chr2 74682446 74683546 + P 10 +intron (ENSMUST00000136302, intron 1 of 2) chr2 74683547 74683902 + I 88 +exon (ENSMUST00000048086, exon 2 of 2) chr2 74683903 74684067 + E 45 +TTS (ENSMUST00000142312) chr2 74684068 74685168 + TTS 27 +intron (ENSMUST00000136302, intron 2 of 2) chr2 74684357 74685168 + I 88 +exon (ENSMUST00000048086, exon 2 of 2)--2 chr2 74685169 74686915 + E 45 +TTS (ENSMUST00000048086) chr2 74686916 74688016 + TTS 20 +intron (ENSMUST00000136302, intron 2 of 2)--2 chr2 74688017 74690923 + I 88 +promoter-TSS (ENSMUST00000061745) chr2 74690924 74692024 + P 6 +exon (ENSMUST00000061745, exon 1 of 2) chr2 74692025 74692724 + E 51 +intron (ENSMUST00000061745, intron 1 of 1) chr2 74692725 74694090 + I 88 +exon (ENSMUST00000061745, exon 2 of 2) chr2 74694091 74694093 + E 53 +TTS (ENSMUST00000136302) chr2 74694094 74694519 + TTS 26 +promoter-TSS (ENSMUST00000126966) chr2 74694520 74695620 + P 9 +TTS (ENSMUST00000061745) chr2 74695621 74696105 + TTS 22 +TTS (ENSMUST00000190845) chr2 74696106 74696726 - TTS 31 +promoter-TSS (ENSMUST00000059272) chr2 74696727 74697827 + P 5 +promoter-TSS (ENSMUST00000190845) chr2 74697828 74698586 - P 15 +exon (ENSMUST00000059272, exon 1 of 2) chr2 74698587 74698833 + E 47 +intron (ENSMUST00000059272, intron 1 of 1) chr2 74698834 74699179 + I 88 +exon (ENSMUST00000059272, exon 2 of 2) chr2 74699180 74699421 + E 49 +3' UTR (ENSMUST00000059272, exon 2 of 2) chr2 74699422 74700005 + 3UTR 48 +TTS (ENSMUST00000198895) chr2 74700006 74700107 - TTS 32 +TTS (ENSMUST00000059272) chr2 74700108 74701041 + TTS 21 +promoter-TSS (ENSMUST00000198895) chr2 74701042 74702142 - P 16 +Intergenic--3 chr2 74702143 74703614 + N 1900000000 +promoter-TSS (ENSMUST00000151380) chr2 74703615 74703904 + P 14 +promoter-TSS (ENSMUST00000019749) chr2 74703905 74705005 + P 3 +promoter-TSS (ENSMUST00000074721) chr2 74705006 74705252 + P 7 +5' UTR (ENSMUST00000019749, exon 1 of 2) chr2 74705253 74705547 + 5UTR 40 +exon (ENSMUST00000019749, exon 1 of 2) chr2 74705548 74706118 + E 41 +intron (ENSMUST00000074721, intron 1 of 1) chr2 74706119 74706513 + I 88 +exon (ENSMUST00000019749, exon 2 of 2) chr2 74706514 74706711 + E 43 +TTS (ENSMUST00000151380) chr2 74706712 74707206 + TTS 30 +TTS (ENSMUST00000074721) chr2 74707207 74707832 + TTS 23 +TTS (ENSMUST00000019749) chr2 74707833 74708933 + TTS 19 +Intergenic--4 chr2 74708934 74709192 + N 1900000000 +TTS (ENSMUST00000145799) chr2 74709193 74710293 - TTS 29 +intron (ENSMUST00000145799, intron 2 of 2) chr2 74710294 74710926 - I 88 +promoter-TSS (ENSMUST00000111983) chr2 74710927 74712027 + P 8 +promoter-TSS (ENSMUST00000144040) chr2 74712028 74712029 + P 12 +5' UTR (ENSMUST00000111983, exon 1 of 3) chr2 74712030 74712316 + 5UTR 58 +intron (ENSMUST00000111983, intron 1 of 2) chr2 74712317 74714270 + I 88 +exon (ENSMUST00000145799, exon 2 of 3) chr2 74714271 74714401 - E 80 +intron (ENSMUST00000145799, intron 1 of 2) chr2 74714402 74715705 - I 88 +exon (ENSMUST00000145799, exon 1 of 3) chr2 74715706 74715895 - E 81 +promoter-TSS (ENSMUST00000145799) chr2 74715896 74716996 - P 13 +intron (ENSMUST00000111983, intron 1 of 2)--2 chr2 74716997 74722552 + I 88 +exon (ENSMUST00000144040, exon 2 of 7) chr2 74722553 74722631 + E 73 +intron (ENSMUST00000144040, intron 2 of 6) chr2 74722632 74723331 + I 88 +exon (ENSMUST00000144040, exon 3 of 7) chr2 74723332 74723367 + E 74 +intron (ENSMUST00000144040, intron 3 of 6) chr2 74723368 74725462 + I 88 +exon (ENSMUST00000144040, exon 4 of 7) chr2 74725463 74725597 + E 75 +intron (ENSMUST00000144040, intron 4 of 6) chr2 74725598 74725844 + I 88 +exon (ENSMUST00000144040, exon 5 of 7) chr2 74725845 74725978 + E 76 +intron (ENSMUST00000144040, intron 5 of 6) chr2 74725979 74726875 + I 88 +exon (ENSMUST00000144040, exon 6 of 7) chr2 74726876 74726932 + E 77 +intron (ENSMUST00000144040, intron 6 of 6) chr2 74726933 74728358 + I 88 +exon (ENSMUST00000144040, exon 7 of 7) chr2 74728359 74728767 + E 78 +TTS (ENSMUST00000144040) chr2 74728768 74729868 + TTS 28 +intron (ENSMUST00000111983, intron 1 of 2)--3 chr2 74729869 74743927 + I 88 +5' UTR (ENSMUST00000111983, exon 2 of 3) chr2 74743928 74744011 + 5UTR 59 +exon (ENSMUST00000111983, exon 2 of 3) chr2 74744012 74744555 + E 60 +intron (ENSMUST00000111983, intron 2 of 2) chr2 74744556 74746321 + I 88 +exon (ENSMUST00000111983, exon 3 of 3) chr2 74746322 74747079 + E 62 +3' UTR (ENSMUST00000111983, exon 3 of 3) chr2 74747080 74748170 + 3UTR 61 +TTS (ENSMUST00000111983) chr2 74748171 74749271 + TTS 24 +Intergenic--5 chr2 74749272 1500000000 + N 1900000000 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/annotations_default_stats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_default_stats.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +Annotation Number of peaks Total size (bp) Log2 Ratio (obs/exp) LogP enrichment (+values depleted) +3UTR 5.0 4601 8.659 -26.809 +TTS 47.0 16013 10.092 -290.509 +Exon 32.0 8271 10.491 -205.971 +Intron 24.0 28234 8.304 -118.153 +Intergenic 0.0 74668827 -17.479 1369.495 +Promoter 81.0 23880 10.301 -519.342 +5UTR 12.0 1148 11.925 -89.692 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/annotations_exon_start.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_exon_start.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,110 @@ +Intergenic chr2 1 74667309 + N 1900000000 +promoter-TSS (ENSMUST00000001872) chr2 74667310 74668410 + P 1 +exon (ENSMUST00000001872, exon 1 of 2) chr2 74668411 74669078 + E 59 +intron (ENSMUST00000001872, intron 1 of 1) chr2 74669079 74669885 + I 145 +exon (ENSMUST00000001872, exon 2 of 2) chr2 74669886 74671498 + E 60 +TTS (ENSMUST00000001872) chr2 74671499 74672599 + TTS 30 +Intergenic--2 chr2 74672600 74674012 + N 1900000000 +promoter-TSS (ENSMUST00000001878) chr2 74674013 74675113 + P 2 +exon (ENSMUST00000001878, exon 1 of 2) chr2 74675114 74675654 + E 62 +intron (ENSMUST00000001878, intron 1 of 1) chr2 74675655 74675813 + I 145 +exon (ENSMUST00000001878, exon 2 of 2) chr2 74675814 74677604 + E 63 +TTS (ENSMUST00000001878) chr2 74677605 74678556 + TTS 31 +promoter-TSS (ENSMUST00000048086) chr2 74678557 74679657 + P 6 +exon (ENSMUST00000048086, exon 1 of 2) chr2 74679658 74679809 + E 78 +intron (ENSMUST00000048086, intron 1 of 1) chr2 74679810 74681322 + I 145 +promoter-TSS (ENSMUST00000142312) chr2 74681323 74682423 + P 20 +exon (ENSMUST00000142312, exon 1 of 2) chr2 74682424 74682445 + E 119 +promoter-TSS (ENSMUST00000136302) chr2 74682446 74683546 + P 17 +intron (ENSMUST00000136302, intron 1 of 2) chr2 74683547 74683902 + I 145 +exon (ENSMUST00000048086, exon 2 of 2) chr2 74683903 74684067 + E 79 +TTS (ENSMUST00000142312) chr2 74684068 74685168 + TTS 49 +intron (ENSMUST00000136302, intron 2 of 2) chr2 74684357 74685168 + I 145 +exon (ENSMUST00000048086, exon 2 of 2)--2 chr2 74685169 74686915 + E 79 +TTS (ENSMUST00000048086) chr2 74686916 74688016 + TTS 35 +intron (ENSMUST00000136302, intron 2 of 2)--2 chr2 74688017 74690923 + I 145 +promoter-TSS (ENSMUST00000061745) chr2 74690924 74692024 + P 9 +exon (ENSMUST00000061745, exon 1 of 2) chr2 74692025 74692724 + E 89 +intron (ENSMUST00000061745, intron 1 of 1) chr2 74692725 74694090 + I 145 +exon (ENSMUST00000061745, exon 2 of 2) chr2 74694091 74694093 + E 90 +TTS (ENSMUST00000136302) chr2 74694094 74694519 + TTS 46 +promoter-TSS (ENSMUST00000126966) chr2 74694520 74695620 + P 15 +promoter-TSS (ENSMUST00000152027) chr2 74695621 74695701 + P 25 +TTS (ENSMUST00000061745) chr2 74695702 74696105 + TTS 38 +TTS (ENSMUST00000190845) chr2 74696106 74696726 - TTS 57 +promoter-TSS (ENSMUST00000059272) chr2 74696727 74697827 + P 8 +promoter-TSS (ENSMUST00000190845) chr2 74697828 74698586 - P 28 +exon (ENSMUST00000059272, exon 1 of 2) chr2 74698587 74698833 + E 86 +intron (ENSMUST00000059272, intron 1 of 1) chr2 74698834 74699179 + I 145 +exon (ENSMUST00000059272, exon 2 of 2) chr2 74699180 74700005 + E 87 +TTS (ENSMUST00000198895) chr2 74700006 74700107 - TTS 58 +TTS (ENSMUST00000059272) chr2 74700108 74701041 + TTS 37 +promoter-TSS (ENSMUST00000198895) chr2 74701042 74702142 - P 29 +Intergenic--3 chr2 74702143 74702247 + N 1900000000 +TTS (ENSMUST00000132326) chr2 74702248 74703348 - TTS 45 +exon (ENSMUST00000132326, exon 2 of 2) chr2 74703349 74703614 - E 108 +promoter-TSS (ENSMUST00000151380) chr2 74703615 74703904 + P 24 +promoter-TSS (ENSMUST00000019749) chr2 74703905 74705005 + P 3 +promoter-TSS (ENSMUST00000074721) chr2 74705006 74705252 + P 10 +5' UTR (ENSMUST00000019749, exon 1 of 2) chr2 74705253 74705547 + 5UTR 64 +exon (ENSMUST00000019749, exon 1 of 2) chr2 74705548 74706118 + E 65 +intron (ENSMUST00000074721, intron 1 of 1) chr2 74706119 74706513 + I 145 +exon (ENSMUST00000019749, exon 2 of 2) chr2 74706514 74706711 + E 66 +TTS (ENSMUST00000151380) chr2 74706712 74707206 + TTS 53 +TTS (ENSMUST00000074721) chr2 74707207 74707832 + TTS 39 +TTS (ENSMUST00000019749) chr2 74707833 74708933 + TTS 32 +intron (ENSMUST00000132326, intron 1 of 1) chr2 74708934 74709042 - I 145 +TTS (ENSMUST00000156342) chr2 74709043 74709192 - TTS 55 +TTS (ENSMUST00000145799) chr2 74709193 74710293 - TTS 52 +intron (ENSMUST00000145799, intron 2 of 2) chr2 74710294 74710926 - I 145 +promoter-TSS (ENSMUST00000111983) chr2 74710927 74712027 + P 14 +promoter-TSS (ENSMUST00000132326) chr2 74712028 74713054 - P 16 +promoter-TSS (ENSMUST00000156342) chr2 74713055 74713526 - P 26 +exon (ENSMUST00000139005, exon 2 of 2) chr2 74713527 74714401 - E 113 +intron (ENSMUST00000145799, intron 1 of 2) chr2 74714402 74715705 - I 145 +exon (ENSMUST00000139005, exon 1 of 2) chr2 74715706 74715895 - E 114 +promoter-TSS (ENSMUST00000145799) chr2 74715896 74716029 - P 23 +promoter-TSS (ENSMUST00000139005) chr2 74716030 74717130 - P 18 +intron (ENSMUST00000111983, intron 1 of 2) chr2 74717131 74720977 + I 145 +promoter-TSS (ENSMUST00000047904) chr2 74720978 74722078 + P 5 +5' UTR (ENSMUST00000047904, exon 1 of 6) chr2 74722079 74722177 + 5UTR 71 +intron (ENSMUST00000047904, intron 1 of 5) chr2 74722178 74722552 + I 145 +5' UTR (ENSMUST00000047904, exon 2 of 6) chr2 74722553 74722631 + 5UTR 72 +intron (ENSMUST00000144040, intron 2 of 6) chr2 74722632 74723331 + I 145 +5' UTR (ENSMUST00000047904, exon 3 of 6) chr2 74723332 74723367 + 5UTR 73 +intron (ENSMUST00000144040, intron 3 of 6) chr2 74723368 74725069 + I 145 +promoter-TSS (ENSMUST00000083566) chr2 74725070 74725727 + P 11 +promoter-TSS (ENSMUST00000053932) chr2 74725728 74726828 + P 7 +promoter-TSS (ENSMUST00000111980) chr2 74726829 74727174 + P 12 +5' UTR (ENSMUST00000047904, exon 5 of 6) chr2 74727175 74727278 + 5UTR 75 +exon (ENSMUST00000047904, exon 5 of 6) chr2 74727279 74727705 + E 76 +intron (ENSMUST00000053932, intron 1 of 3) chr2 74727706 74728261 + I 145 +exon (ENSMUST00000047904, exon 6 of 6) chr2 74728262 74728767 + E 77 +TTS (ENSMUST00000144040) chr2 74728768 74729022 + TTS 50 +TTS (ENSMUST00000111980) chr2 74729023 74729059 + TTS 41 +TTS (ENSMUST00000047904) chr2 74729060 74730160 + TTS 34 +intron (ENSMUST00000053932, intron 2 of 3) chr2 74730161 74731912 + I 145 +promoter-TSS (ENSMUST00000144544) chr2 74731913 74733013 + P 22 +5' UTR (ENSMUST00000144544, exon 1 of 2) chr2 74733014 74733040 + 5UTR 128 +intron (ENSMUST00000144544, intron 1 of 1) chr2 74733041 74735514 + I 145 +promoter-TSS (ENSMUST00000111982) chr2 74735515 74736615 + P 13 +5' UTR (ENSMUST00000111982, exon 1 of 3) chr2 74736616 74736705 + 5UTR 98 +intron (ENSMUST00000111982, intron 1 of 2) chr2 74736706 74738618 + I 145 +promoter-TSS (ENSMUST00000047830) chr2 74738619 74739719 + P 4 +intron (ENSMUST00000047830, intron 1 of 2) chr2 74739720 74743927 + I 145 +5' UTR (ENSMUST00000047830, exon 2 of 3) chr2 74743928 74744011 + 5UTR 68 +exon (ENSMUST00000047830, exon 2 of 3) chr2 74744012 74744113 + E 69 +TTS (ENSMUST00000144544) chr2 74744114 74744673 + TTS 51 +promoter-TSS (ENSMUST00000140666) chr2 74744674 74745774 + P 19 +promoter-TSS (ENSMUST00000190553) chr2 74745775 74745822 + P 27 +5' UTR (ENSMUST00000140666, exon 1 of 2) chr2 74745823 74746156 + 5UTR 115 +exon (ENSMUST00000140666, exon 1 of 2) chr2 74746157 74746220 + E 116 +exon (ENSMUST00000190553, exon 1 of 1) chr2 74746221 74746321 + E 142 +exon (ENSMUST00000047830, exon 3 of 3) chr2 74746322 74746495 + E 70 +TTS (ENSMUST00000140666) chr2 74746496 74747596 + TTS 48 +exon (ENSMUST00000047830, exon 3 of 3)--2 chr2 74747597 74747799 + E 70 +TTS (ENSMUST00000047830) chr2 74747800 74748900 + TTS 33 +TTS (ENSMUST00000053932) chr2 74748901 74748918 + TTS 36 +TTS (ENSMUST00000111983) chr2 74748919 74749271 + TTS 43 +TTS (ENSMUST00000190553) chr2 74749272 74749442 + TTS 56 +Intergenic--4 chr2 74749443 1500000000 + N 1900000000 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/annotations_exon_start_stats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_exon_start_stats.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,7 @@ +Annotation Number of peaks Total size (bp) Log2 Ratio (obs/exp) LogP enrichment (+values depleted) +TTS 41.0 16013 9.992 -250.473 +Exon 30.0 12152 9.939 -181.768 +Intron 24.0 28234 8.401 -119.856 +Intergenic 0.0 74668827 -17.395 1282.574 +Promoter 81.0 23880 10.397 -526.320 +5UTR 12.0 1148 12.021 -90.517 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/annotations_small_TSSTTS.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_small_TSSTTS.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| b"@@ -0,0 +1,164 @@\n+Intergenic\tchr2\t1\t74668259\t+\tN\t1900000000\n+promoter-TSS (ENSMUST00000001872)\tchr2\t74668260\t74668360\t+\tP\t1\n+exon (ENSMUST00000001872, exon 1 of 2)\tchr2\t74668361\t74669078\t+\tE\t59\n+intron (ENSMUST00000001872, intron 1 of 1)\tchr2\t74669079\t74669885\t+\tI\t158\n+exon (ENSMUST00000001872, exon 2 of 2)\tchr2\t74669886\t74670136\t+\tE\t61\n+3' UTR (ENSMUST00000001872, exon 2 of 2)\tchr2\t74670137\t74671548\t+\t3UTR\t60\n+TTS (ENSMUST00000001872)\tchr2\t74671549\t74671649\t+\tTTS\t30\n+Intergenic--2\tchr2\t74671650\t74674962\t+\tN\t1900000000\n+promoter-TSS (ENSMUST00000001878)\tchr2\t74674963\t74675063\t+\tP\t2\n+5' UTR (ENSMUST00000001878, exon 1 of 2)\tchr2\t74675064\t74675086\t+\t5UTR\t62\n+exon (ENSMUST00000001878, exon 1 of 2)\tchr2\t74675087\t74675654\t+\tE\t63\n+intron (ENSMUST00000001878, intron 1 of 1)\tchr2\t74675655\t74675813\t+\tI\t158\n+exon (ENSMUST00000001878, exon 2 of 2)\tchr2\t74675814\t74676052\t+\tE\t65\n+3' UTR (ENSMUST00000001878, exon 2 of 2)\tchr2\t74676053\t74677654\t+\t3UTR\t64\n+TTS (ENSMUST00000001878)\tchr2\t74677655\t74677755\t+\tTTS\t31\n+Intergenic--3\tchr2\t74677756\t74679506\t+\tN\t1900000000\n+promoter-TSS (ENSMUST00000048086)\tchr2\t74679507\t74679607\t+\tP\t6\n+exon (ENSMUST00000048086, exon 1 of 2)\tchr2\t74679608\t74679809\t+\tE\t83\n+intron (ENSMUST00000048086, intron 1 of 1)\tchr2\t74679810\t74682272\t+\tI\t158\n+promoter-TSS (ENSMUST00000142312)\tchr2\t74682273\t74682373\t+\tP\t20\n+5' UTR (ENSMUST00000142312, exon 1 of 2)\tchr2\t74682374\t74682392\t+\t5UTR\t130\n+exon (ENSMUST00000142312, exon 1 of 2)\tchr2\t74682393\t74683167\t+\tE\t131\n+intron (ENSMUST00000142312, intron 1 of 1)\tchr2\t74683168\t74683395\t+\tI\t158\n+promoter-TSS (ENSMUST00000136302)\tchr2\t74683396\t74683496\t+\tP\t17\n+exon (ENSMUST00000136302, exon 1 of 3)\tchr2\t74683497\t74683509\t+\tE\t122\n+intron (ENSMUST00000136302, intron 1 of 2)\tchr2\t74683510\t74683902\t+\tI\t158\n+exon (ENSMUST00000048086, exon 2 of 2)\tchr2\t74683903\t74684117\t+\tE\t84\n+TTS (ENSMUST00000142312)\tchr2\t74684118\t74684218\t+\tTTS\t49\n+exon (ENSMUST00000048086, exon 2 of 2)--2\tchr2\t74684219\t74686965\t+\tE\t84\n+TTS (ENSMUST00000048086)\tchr2\t74686966\t74687066\t+\tTTS\t35\n+intron (ENSMUST00000136302, intron 2 of 2)\tchr2\t74687067\t74691873\t+\tI\t158\n+promoter-TSS (ENSMUST00000061745)\tchr2\t74691874\t74691974\t+\tP\t9\n+5' UTR (ENSMUST00000061745, exon 1 of 2)\tchr2\t74691975\t74691979\t+\t5UTR\t95\n+exon (ENSMUST00000061745, exon 1 of 2)\tchr2\t74691980\t74692724\t+\tE\t96\n+intron (ENSMUST00000061745, intron 1 of 1)\tchr2\t74692725\t74694090\t+\tI\t158\n+exon (ENSMUST00000061745, exon 2 of 2)\tchr2\t74694091\t74694143\t+\tE\t98\n+TTS (ENSMUST00000136302)\tchr2\t74694144\t74694244\t+\tTTS\t46\n+exon (ENSMUST00000061745, exon 2 of 2)--2\tchr2\t74694245\t74694368\t+\tE\t98\n+3' UTR (ENSMUST00000061745, exon 2 of 2)\tchr2\t74694369\t74695054\t+\t3UTR\t97\n+TTS (ENSMUST00000061745)\tchr2\t74695055\t74695155\t+\tTTS\t38\n+Intergenic--4\tchr2\t74695156\t74695469\t+\tN\t1900000000\n+promoter-TSS (ENSMUST00000126966)\tchr2\t74695470\t74695570\t+\tP\t15\n+promoter-TSS (ENSMUST00000152027)\tchr2\t74695571\t74695651\t+\tP\t25\n+exon (ENSMUST00000126966, exon 1 of 2)\tchr2\t74695652\t74695732\t+\tE\t118\n+intron (ENSMUST00000126966, intron 1 of 1)\tchr2\t74695733\t74696717\t+\tI\t158\n+TTS (ENSMUST00000190845)\tchr2\t74696718\t74696818\t-\tTTS\t57\n+exon (ENSMUST00000190845, exon 2 of 2)\tchr2\t74696819\t74696841\t-\tE\t156\n+intron (ENSMUST00000190845, intron 1 of 1)\tchr2\t74696842\t74697030\t-\tI\t158\n+exon (ENSMUST00000126966, exon 2 of 2)\tchr2\t74697031\t74697314\t+\tE\t119\n+TTS (ENSMUST00000126966)\tchr2\t74697315\t74697415\t+\tTTS\t44\n+exon (ENSMUST00000190845, exon 1 of 2)\tchr2\t74697416\t74697535\t-\tE\t157\n+promoter-TSS (ENSMUST00000190845)\tchr2\t74697536\t74697636\t-\tP\t28\n+Intergenic--5\tchr2\t74697637\t74697676\t+\tN\t1900000000\n+promoter-TSS (ENSMUST00000059272)\tchr2\t74697677\t74697777\t+\tP\t8\n+5' UTR (ENSMUST00000059272, exon 1 of 2)\tchr2\t74697778\t74698055\t+\t5UTR\t91\n+exon (ENSMUST00000059272, exon 1 of 2)\tchr2\t74698056\t74698833\t+\tE\t92\n+intron (ENSMUST00000059272, intron 1 of 1)\tchr2\t74698834\t74699179\t+\tI\t158\n+exon (ENSMUST00000059272, exon 2 of 2)\tchr2\t74699180\t74699421\t+\tE\t94\n+3' UTR (ENSMUST00000059272, exon 2 of 2)\tchr2\t74699422\t74700157\t+\t3U"..b"2028\t+\tP\t5\n+5' UTR (ENSMUST00000047904, exon 1 of 6)\tchr2\t74722029\t74722177\t+\t5UTR\t75\n+intron (ENSMUST00000047904, intron 1 of 5)\tchr2\t74722178\t74722552\t+\tI\t158\n+5' UTR (ENSMUST00000047904, exon 2 of 6)\tchr2\t74722553\t74722631\t+\t5UTR\t76\n+intron (ENSMUST00000144040, intron 2 of 6)\tchr2\t74722632\t74723331\t+\tI\t158\n+5' UTR (ENSMUST00000047904, exon 3 of 6)\tchr2\t74723332\t74723367\t+\t5UTR\t77\n+intron (ENSMUST00000144040, intron 3 of 6)\tchr2\t74723368\t74725462\t+\tI\t158\n+5' UTR (ENSMUST00000047904, exon 4 of 6)\tchr2\t74725463\t74725978\t+\t5UTR\t78\n+intron (ENSMUST00000144040, intron 5 of 6)\tchr2\t74725979\t74726019\t+\tI\t158\n+promoter-TSS (ENSMUST00000083566)\tchr2\t74726020\t74726120\t+\tP\t11\n+TTS (ENSMUST00000083566)\tchr2\t74726121\t74726187\t+\tTTS\t40\n+intron (ENSMUST00000144040, intron 5 of 6)--2\tchr2\t74726188\t74726677\t+\tI\t158\n+promoter-TSS (ENSMUST00000053932)\tchr2\t74726678\t74726778\t+\tP\t7\n+5' UTR (ENSMUST00000053932, exon 1 of 4)\tchr2\t74726779\t74726875\t+\t5UTR\t85\n+5' UTR (ENSMUST00000047904, exon 5 of 6)\tchr2\t74726876\t74727023\t+\t5UTR\t79\n+promoter-TSS (ENSMUST00000111980)\tchr2\t74727024\t74727124\t+\tP\t12\n+5' UTR (ENSMUST00000111980, exon 1 of 2)\tchr2\t74727074\t74727124\t+\t5UTR\t104\n+5' UTR (ENSMUST00000047904, exon 5 of 6)--2\tchr2\t74727125\t74727278\t+\t5UTR\t79\n+exon (ENSMUST00000047904, exon 5 of 6)\tchr2\t74727279\t74727705\t+\tE\t80\n+intron (ENSMUST00000053932, intron 1 of 3)\tchr2\t74727706\t74728261\t+\tI\t158\n+exon (ENSMUST00000047904, exon 6 of 6)\tchr2\t74728262\t74728587\t+\tE\t82\n+3' UTR (ENSMUST00000047904, exon 6 of 6)\tchr2\t74728588\t74728817\t+\t3UTR\t81\n+TTS (ENSMUST00000144040)\tchr2\t74728818\t74728918\t+\tTTS\t50\n+3' UTR (ENSMUST00000047904, exon 6 of 6)--2\tchr2\t74728919\t74729072\t+\t3UTR\t81\n+TTS (ENSMUST00000111980)\tchr2\t74729073\t74729109\t+\tTTS\t41\n+TTS (ENSMUST00000047904)\tchr2\t74729110\t74729210\t+\tTTS\t34\n+intron (ENSMUST00000053932, intron 2 of 3)\tchr2\t74729211\t74732862\t+\tI\t158\n+promoter-TSS (ENSMUST00000144544)\tchr2\t74732863\t74732963\t+\tP\t22\n+5' UTR (ENSMUST00000144544, exon 1 of 2)\tchr2\t74732964\t74733040\t+\t5UTR\t141\n+intron (ENSMUST00000144544, intron 1 of 1)\tchr2\t74733041\t74736464\t+\tI\t158\n+promoter-TSS (ENSMUST00000111982)\tchr2\t74736465\t74736565\t+\tP\t13\n+5' UTR (ENSMUST00000111982, exon 1 of 3)\tchr2\t74736566\t74736705\t+\t5UTR\t108\n+intron (ENSMUST00000111982, intron 1 of 2)\tchr2\t74736706\t74739568\t+\tI\t158\n+promoter-TSS (ENSMUST00000047830)\tchr2\t74739569\t74739669\t+\tP\t4\n+5' UTR (ENSMUST00000047830, exon 1 of 3)\tchr2\t74739670\t74739703\t+\t5UTR\t70\n+intron (ENSMUST00000047830, intron 1 of 2)\tchr2\t74739704\t74743927\t+\tI\t158\n+5' UTR (ENSMUST00000047830, exon 2 of 3)\tchr2\t74743928\t74744011\t+\t5UTR\t71\n+exon (ENSMUST00000047830, exon 2 of 3)\tchr2\t74744012\t74744163\t+\tE\t72\n+TTS (ENSMUST00000144544)\tchr2\t74744164\t74744264\t+\tTTS\t51\n+exon (ENSMUST00000047830, exon 2 of 3)--2\tchr2\t74744265\t74744555\t+\tE\t72\n+intron (ENSMUST00000111983, intron 2 of 2)\tchr2\t74744556\t74745623\t+\tI\t158\n+promoter-TSS (ENSMUST00000140666)\tchr2\t74745624\t74745724\t+\tP\t19\n+promoter-TSS (ENSMUST00000190553)\tchr2\t74745725\t74745772\t+\tP\t27\n+5' UTR (ENSMUST00000140666, exon 1 of 2)\tchr2\t74745773\t74746156\t+\t5UTR\t127\n+exon (ENSMUST00000140666, exon 1 of 2)\tchr2\t74746157\t74746220\t+\tE\t128\n+exon (ENSMUST00000190553, exon 1 of 1)\tchr2\t74746221\t74746321\t+\tE\t155\n+exon (ENSMUST00000047830, exon 3 of 3)\tchr2\t74746322\t74746545\t+\tE\t74\n+TTS (ENSMUST00000140666)\tchr2\t74746546\t74746646\t+\tTTS\t48\n+exon (ENSMUST00000047830, exon 3 of 3)--2\tchr2\t74746647\t74747079\t+\tE\t74\n+3' UTR (ENSMUST00000047830, exon 3 of 3)\tchr2\t74747080\t74747849\t+\t3UTR\t73\n+3' UTR (ENSMUST00000111983, exon 3 of 3)\tchr2\t74747080\t74747849\t+\t3UTR\t116\n+TTS (ENSMUST00000047830)\tchr2\t74747850\t74747950\t+\tTTS\t33\n+TTS (ENSMUST00000053932)\tchr2\t74747951\t74747968\t+\tTTS\t36\n+3' UTR (ENSMUST00000111983, exon 3 of 3)--2\tchr2\t74747969\t74748220\t+\t3UTR\t116\n+TTS (ENSMUST00000111983)\tchr2\t74748221\t74748321\t+\tTTS\t43\n+exon (ENSMUST00000190553, exon 1 of 1)--2\tchr2\t74748322\t74748391\t+\tE\t155\n+TTS (ENSMUST00000190553)\tchr2\t74748392\t74748492\t+\tTTS\t56\n+Intergenic--8\tchr2\t74748493\t1500000000\t+\tN\t1900000000\n" |
| b |
| diff -r 000000000000 -r db456c398880 test-data/annotations_small_TSSTTS_stats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/annotations_small_TSSTTS_stats.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +Annotation Number of peaks Total size (bp) Log2 Ratio (obs/exp) LogP enrichment (+values depleted) +3UTR 13.0 7531 9.326 -73.660 +TTS 38.0 2546 12.438 -296.106 +Exon 48.0 13188 10.403 -307.101 +Intron 36.0 43852 8.254 -176.111 +Intergenic 0.0 74676379 -17.650 1393.260 +Promoter 38.0 2757 12.324 -293.081 +5UTR 28.0 3111 11.709 -203.812 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/chr2_subset.fa.gz |
| b |
| Binary file test-data/chr2_subset.fa.gz has changed |
| b |
| diff -r 000000000000 -r db456c398880 test-data/fake_phix_peaks.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake_phix_peaks.bed Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +phiX174 1400 1500 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/fake_phix_peaks.subset.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fake_phix_peaks.subset.bed Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +phiX174 1200 1300 +phiX174 1550 1800 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/generate_tests.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/generate_tests.sh Mon Dec 13 15:13:33 2021 +0000 |
| [ |
| @@ -0,0 +1,60 @@ +#! /usr/bin/bash +## Generate input data: +if [ ! -e test-data/small_simplified.gtf ]; then + wget http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz -O /tmp/Mus_musculus.GRCm38.102.gtf.gz + zcat /tmp/Mus_musculus.GRCm38.102.gtf.gz | head -n 5 > test-data/small.gtf + zcat /tmp/Mus_musculus.GRCm38.102.gtf.gz | awk -v OFS="\t" -v start=74667792 -v end=74748393 '$1 == "2" && $5 > start && $4 < end{print "chr"$0}' >> test-data/small.gtf + # annotatePeaks.pl gives different results all time. I need to simplify the gtf. + cat test-data/small.gtf | grep -v -P "ENSMUST00000152027|ENSMUST00000156342|ENSMUST00000139005|ENSMUST00000144544|ENSMUST00000111982|ENSMUST00000140666|ENSMUST00000190553|ENSMUST00000132326|ENSMUST00000047830|ENSMUST00000047904|ENSMUST00000111980|ENSMUSG00000065500|ENSMUSG00000100642" > test-data/small_simplified.gtf +fi +if [ ! -e test-data/CTCF_peaks.bed ]; then + wget https://raw.githubusercontent.com/lldelisle/scriptsForWilleminEtAl2021/main/CTCF/E12_Limbs_Wt_CTCF_colored.bed -O test-data/CTCF_peaks.bed +fi +if [ ! -e test-data/CTCF_peaks_shifted.bed ]; then + cat test-data/CTCF_peaks.bed | grep "chr2" | awk -v OFS="\t" '$3<75000000 && $2>73740000{$1="mm10_dna"; $2-=73740000; $3-=73740000; print}' > test-data/CTCF_peaks_shifted.bed +fi +# chr2_subset.fa was downloaded from UCSC +# https://genome.ucsc.edu/cgi-bin/hgc?hgsid=1234982067_JnS4z30UVCNarTg26Ztd1Oh6nfu6&g=htcGetDna2&table=&i=mixed&o=56694975&l=56694975&r=56714605&getDnaPos=chr2%3A73740000-75000000&db=mm10&hgSeq.cdsExon=1&hgSeq.padding5=0&hgSeq.padding3=0&hgSeq.casing=upper&hgSeq.maskRepeats=on&boolshad.hgSeq.maskRepeats=0&hgSeq.repMasking=lower&boolshad.hgSeq.revComp=0&submit=get+DNA + +. <(planemo conda_env homer_gtf_to_annotation.xml) +echo "$(which homer)" +## homer_gtf_to_annotation +## First test +parseGTF.pl test-data/small.gtf ann -features exon start_codon stop_codon > /tmp/annotations.txt +assignGenomeAnnotation /tmp/annotations.txt /tmp/annotations.txt -prioritize test-data/annotations_default.txt > test-data/annotations_default_stats.txt +## Second test +parseGTF.pl test-data/small.gtf ann -features exon start_codon > /tmp/annotations2.txt +assignGenomeAnnotation /tmp/annotations2.txt /tmp/annotations2.txt -prioritize test-data/annotations_exon_start.txt > test-data/annotations_exon_start_stats.txt +## Third test +parseGTF.pl test-data/small.gtf ann -features exon start_codon stop_codon -annTSSstartOffset -50 -annTSSendOffset 50 -annTTSstartOffset -50 -annTTSendOffset 50 > /tmp/annotations3.txt +assignGenomeAnnotation /tmp/annotations3.txt /tmp/annotations3.txt -prioritize test-data/annotations_small_TSSTTS.txt > test-data/annotations_small_TSSTTS_stats.txt + +## For annotatePeaks.pl +parseGTF.pl test-data/small_simplified.gtf ann -features exon start_codon stop_codon > /tmp/annotations.txt +assignGenomeAnnotation /tmp/annotations.txt /tmp/annotations.txt -prioritize test-data/annotations_default_simplified.txt + +## homer_annotatePeaks +## First test +annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf -ann test-data/annotations_default_simplified.txt > test-data/CTCF_peaks_first.txt +## Second test +annotatePeaks.pl test-data/CTCF_peaks.bed none -ann test-data/annotations_default.txt > test-data/CTCF_peaks_second.txt +## Third test +annotatePeaks.pl test-data/CTCF_peaks.bed none -gtf test-data/small_simplified.gtf > test-data/CTCF_peaks_third.txt +## Fourth test +annotatePeaks.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta -CpG > test-data/phiXcpg.txt +## Fifth test +annotatePeaks.pl test-data/fake_phix_peaks.bed none > test-data/phiX_nothing.txt + +## findMotifsGenome +# ! Genome preparsing is giving different results... +findMotifsGenome.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta fake_phix_peaks_bed_motif +mv fake_phix_peaks_bed_motif test-data/motif_test1 +# Thus I needed to use has_text for the other outputs +# gunzip -c test-data/chr2_subset.fa.gz > test-data/chr2_subset.fa +# findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif +# mv CTCF_peaks_shifted_bed_motif test-data/motif_test2 +# findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mask +# mv CTCF_peaks_shifted_bed_motif test-data/motif_test3 +# findMotifsGenome.pl test-data/CTCF_peaks_shifted.bed test-data/chr2_subset.fa CTCF_peaks_shifted_bed_motif -mset plants -nomotif +# mv CTCF_peaks_shifted_bed_motif test-data/motif_test4 + |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerMotifs.all.motifs --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerMotifs.all.motifs Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,165 @@ +>CTAATGAGCT 1-CTAATGAGCT 10.296193 -2.906976 0 T:1.0(100.00%),B:219.7(5.48%),P:1e-1 Tpos:101.0,Tstd:0.0,Bpos:96.2,Bstd:70.8,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +>ATCAAGATGA 2-ATCAAGATGA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 Tpos:113.0,Tstd:0.0,Bpos:94.6,Bstd:75.6,StrandBias:10.0,Multiplicity:1.00 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +>GTTGCTGCCA 3-GTTGCTGCCA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.9(5.49%),P:1e-1 Tpos:140.0,Tstd:0.0,Bpos:103.4,Bstd:83.3,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>CCTGAGACTG 4-CCTGAGACTG 10.296193 -2.902420 0 T:1.0(100.00%),B:220.0(5.49%),P:1e-1 Tpos:181.0,Tstd:0.0,Bpos:96.7,Bstd:84.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>CGAGGCTAAC 5-CGAGGCTAAC 10.296193 -2.897885 0 T:1.0(100.00%),B:221.5(5.53%),P:1e-1 Tpos:90.0,Tstd:0.0,Bpos:103.4,Bstd:66.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +>ATGAGCTTAATC 1-ATGAGCTTAATC 12.355432 -2.920769 0 T:1.0(100.00%),B:216.0(5.39%),P:1e-1 Tpos:105.0,Tstd:0.0,Bpos:97.7,Bstd:71.4,StrandBias:10.0,Multiplicity:1.00 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +>TGCCATCTCAAA 2-TGCCATCTCAAA 12.355432 -2.920769 0 T:1.0(100.00%),B:216.2(5.39%),P:1e-1 Tpos:146.0,Tstd:0.0,Bpos:105.7,Bstd:83.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +>CGAGGCTAACCC 3-CGAGGCTAACCC 12.355432 -2.916150 0 T:1.0(100.00%),B:217.8(5.43%),P:1e-1 Tpos:91.0,Tstd:0.0,Bpos:101.8,Bstd:65.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +>CTCCTGAGACTG 4-CTCCTGAGACTG 12.355432 -2.911553 0 T:1.0(100.00%),B:218.1(5.44%),P:1e-1 Tpos:180.0,Tstd:0.0,Bpos:95.7,Bstd:83.7,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>GATGATGCTCGT 5-GATGATGCTCGT 12.355432 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 Tpos:119.0,Tstd:0.0,Bpos:93.3,Bstd:77.5,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 +>CCCTAATG 1-CCCTAATG 8.236954 -2.897885 0 T:1.0(100.00%),B:221.6(5.53%),P:1e-1 Tpos:98.0,Tstd:0.0,Bpos:97.0,Bstd:70.2,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>TGCTGCCA 2-TGCTGCCA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.8(5.53%),P:1e-1 Tpos:141.0,Tstd:0.0,Bpos:102.6,Bstd:84.0,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>GAGACTGA 3-GAGACTGA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.9(5.54%),P:1e-1 Tpos:183.0,Tstd:0.0,Bpos:97.7,Bstd:84.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +>CTTAATCA 4-CTTAATCA 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 Tpos:108.0,Tstd:0.0,Bpos:94.6,Bstd:75.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>GATGATGC 5-GATGATGC 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 Tpos:117.0,Tstd:0.0,Bpos:93.3,Bstd:78.0,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerMotifs.motifs10 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerMotifs.motifs10 Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,55 @@ +>CTAATGAGCT 1-CTAATGAGCT 10.296193 -2.906976 0 T:1.0(100.00%),B:219.7(5.48%),P:1e-1 Tpos:101.0,Tstd:0.0,Bpos:96.2,Bstd:70.8,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +>ATCAAGATGA 2-ATCAAGATGA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 Tpos:113.0,Tstd:0.0,Bpos:94.6,Bstd:75.6,StrandBias:10.0,Multiplicity:1.00 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +>GTTGCTGCCA 3-GTTGCTGCCA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.9(5.49%),P:1e-1 Tpos:140.0,Tstd:0.0,Bpos:103.4,Bstd:83.3,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>CCTGAGACTG 4-CCTGAGACTG 10.296193 -2.902420 0 T:1.0(100.00%),B:220.0(5.49%),P:1e-1 Tpos:181.0,Tstd:0.0,Bpos:96.7,Bstd:84.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>CGAGGCTAAC 5-CGAGGCTAAC 10.296193 -2.897885 0 T:1.0(100.00%),B:221.5(5.53%),P:1e-1 Tpos:90.0,Tstd:0.0,Bpos:103.4,Bstd:66.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerMotifs.motifs12 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerMotifs.motifs12 Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,65 @@ +>ATGAGCTTAATC 1-ATGAGCTTAATC 12.355432 -2.920769 0 T:1.0(100.00%),B:216.0(5.39%),P:1e-1 Tpos:105.0,Tstd:0.0,Bpos:97.7,Bstd:71.4,StrandBias:10.0,Multiplicity:1.00 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +>TGCCATCTCAAA 2-TGCCATCTCAAA 12.355432 -2.920769 0 T:1.0(100.00%),B:216.2(5.39%),P:1e-1 Tpos:146.0,Tstd:0.0,Bpos:105.7,Bstd:83.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +>CGAGGCTAACCC 3-CGAGGCTAACCC 12.355432 -2.916150 0 T:1.0(100.00%),B:217.8(5.43%),P:1e-1 Tpos:91.0,Tstd:0.0,Bpos:101.8,Bstd:65.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +>CTCCTGAGACTG 4-CTCCTGAGACTG 12.355432 -2.911553 0 T:1.0(100.00%),B:218.1(5.44%),P:1e-1 Tpos:180.0,Tstd:0.0,Bpos:95.7,Bstd:83.7,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>GATGATGCTCGT 5-GATGATGCTCGT 12.355432 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 Tpos:119.0,Tstd:0.0,Bpos:93.3,Bstd:77.5,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerMotifs.motifs8 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerMotifs.motifs8 Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,45 @@ +>CCCTAATG 1-CCCTAATG 8.236954 -2.897885 0 T:1.0(100.00%),B:221.6(5.53%),P:1e-1 Tpos:98.0,Tstd:0.0,Bpos:97.0,Bstd:70.2,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +>TGCTGCCA 2-TGCTGCCA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.8(5.53%),P:1e-1 Tpos:141.0,Tstd:0.0,Bpos:102.6,Bstd:84.0,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>GAGACTGA 3-GAGACTGA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.9(5.54%),P:1e-1 Tpos:183.0,Tstd:0.0,Bpos:97.7,Bstd:84.4,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +>CTTAATCA 4-CTTAATCA 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 Tpos:108.0,Tstd:0.0,Bpos:94.6,Bstd:75.1,StrandBias:10.0,Multiplicity:1.00 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +>GATGATGC 5-GATGATGC 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 Tpos:117.0,Tstd:0.0,Bpos:93.3,Bstd:78.0,StrandBias:10.0,Multiplicity:1.00 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults.html Mon Dec 13 15:13:33 2021 +0000 |
| b |
| b'@@ -0,0 +1,489 @@\n+<HTML><HEAD><TITLE>fake_phix_peaks_bed_motif/ - Homer de novo Motif Results</TITLE></HEAD>\n+<BODY>\n+<H1>Homer <i>de novo</i> Motif Results (fake_phix_peaks_bed_motif/)</H1>\n+<A HREF="knownResults.html">Known Motif Enrichment Results</A><BR/>\n+<A HREF="geneOntology.html">Gene Ontology Enrichment Results</A><BR/>\n+If Homer is having trouble matching a motif to a known motif, try copy/pasting the matrix file into \n+<A HREF="http://www.benoslab.pitt.edu/stamp/">STAMP</A><BR/>\n+More information on motif finding results: <A HREF="http://biowhat.ucsd.edu/homer/">HOMER</A>\n+ | <A HREF="http://biowhat.ucsd.edu/homer/motif/index.html">Description of Results</A>\n+ | <A HREF="http://biowhat.ucsd.edu/homer/motif/practicalTips.html">Tips</A>\n+<BR/>\n+Total target sequences = 1<BR/>\n+Total background sequences = 4009<BR/>\n+<FONT color="red">* - possible false positive</FONT><BR/>\n+<TABLE border="1" cellpading="0" cellspacing="0">\n+<TR><TD>Rank</TD><TD>Motif</TD><TD>P-value</TD><TD>log P-pvalue</TD><TD>% of Targets</TD><TD>% of Background</TD>\n+<TD>STD(Bg STD)</TD>\n+<TD>Best Match/Details</TD><TD>Motif File</TD></TR>\n+<TR><TD>1\n+<FONT color="red">*</FONT></TD><TD><svg width="305" height="50">\n+ <g font-family="Arial" font-weight="bold" font-size="66.5">\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,2,34)">A</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,26,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,51,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,50,34)">G</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,75,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,76,39)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,77,34)">A</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,102,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,100,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,100,34)">G</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,127,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,125,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,126,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,125,34)">C</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,150,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,150,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,151,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,177,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,175,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,175,3'..b'="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,175,34)">G</text>\n+ \n+ </g>\n+</svg>\n+</TD><TD>1e-1</TD><TD>-2.898e+00</TD><TD>100.00%</TD><TD>5.53%</TD><TD>0.0bp (70.2bp)</TD><TD>HNRNPA1L2(RRM)/Homo_sapiens-RNCMPT00023-PBM/HughesRNA(0.812)<BR/><A target="_blank" HREF="homerResults/motif7.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif7.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif7.motif">motif file (matrix)</A></TD></TR>\n+<TR><TD>8\n+<FONT color="red">*</FONT></TD><TD><svg width="205" height="50">\n+ <g font-family="Arial" font-weight="bold" font-size="66.5">\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,0,34)">G</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,27,34)">A</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,50,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,51,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,77,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,76,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,75,34)">G</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,100,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,100,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,102,34)">A</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,127,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,125,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,125,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,126,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,150,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,151,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,150,34)">G</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,177,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,175,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,175,34)">C</text>\n+ \n+ </g>\n+</svg>\n+</TD><TD>1e-1</TD><TD>-2.889e+00</TD><TD>100.00%</TD><TD>5.58%</TD><TD>0.0bp (78.0bp)</TD><TD>AGL42/MA1201.1/Jaspar(0.903)<BR/><A target="_blank" HREF="homerResults/motif8.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif8.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif8.motif">motif file (matrix)</A></TD></TR>\n+</TABLE>\n+<P></P>\n+</BODY></HTML>\n' |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif1.info.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif1.info.html Mon Dec 13 15:13:33 2021 +0000 |
| b |
| b'@@ -0,0 +1,1753 @@\n+<HTML><HEAD><TITLE>Motif 1</TITLE></HEAD>\n+<H2>Information for 1-ATGAGCTTAATC (Motif 1)</H2>\n+<svg width="305" height="50">\n+ <g font-family="Arial" font-weight="bold" font-size="66.5">\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,2,34)">A</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,26,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text>\n+ <text 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| @@ -0,0 +1,13 @@ +>GATGATGCTCGT 5-GATGATGCTCGT 12.355432 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 |
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bp:</TD><TD>1.530</TD></TR>\n+<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR>\n+<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR>\n+<TR><TD>Number of Background Sequences with motif</TD><TD>216.2</TD></TR>\n+<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.39%</TD></TR>\n+<TR><TD>Average Position of motif in Targets</TD><TD>146.0 +/- 0.0bp</TD></TR>\n+<TR><TD>Average Position of motif in Background</TD><TD>105.7 +/- 83.1bp</TD></TR>\n+<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR>\n+<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR>\n+<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif2.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif2RV.motif">reverse opposite</A></TD></TR>\n+</TABLE>\n+<H3>Similar de novo motifs found</H3>\n+<TABLE border="1" cellpading="0" cellspacing="0">\n+<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant 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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif2RV.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif2RV.motif Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,13 @@ +>CGAGGCTAACCC 3-CGAGGCTAACCC,BestGuess:PH0015.1_Crx/Jaspar(0.629) 12.355432 -2.916150 0 T:1.0(100.00%),B:217.8(5.43%),P:1e-1 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 |
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</g>\n+</svg>\n+\n+</TD><TD>1e-1</TD><TD>-2.897885</TD><TD>100.00%</TD><TD>5.53%</TD><TD><A target="_blank" HREF="motif3.similar1.motif">motif file (matrix)</A></TD></TR>\n+</TABLE>\n+<P></P>\n+</BODY></HTML>\n' |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif3.similar1.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif3.similar1.motif Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,11 @@ +>CGAGGCTAAC 5-CGAGGCTAAC 10.296193 -2.897885 0 T:1.0(100.00%),B:221.5(5.53%),P:1e-1 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif3RV.logo.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif3RV.logo.svg Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,64 @@ +<svg width="305" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,0,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,25,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,51,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,50,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,77,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,75,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,76,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,102,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,100,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,100,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,101,34)">T</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,125,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,125,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,126,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,127,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,150,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,151,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,150,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,177,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,175,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,175,34)">C</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,202,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,200,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,201,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,200,34)">C</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,227,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,225,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,225,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,226,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,252,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,250,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,251,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,250,34)">C</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,277,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,275,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,276,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,275,34)">G</text> + + </g> +</svg> |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif3RV.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif3RV.motif Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,13 @@ +>GGGTTAGCCTCG 3-CGAGGCTAACCC 12.355432 -2.916150 0 T:1.0(100.00%),B:217.8(5.43%),P:1e-1 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.700 0.100 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif4.info.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif4.info.html Mon Dec 13 15:13:33 2021 +0000 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif4RV.logo.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif4RV.logo.svg Mon Dec 13 15:13:33 2021 +0000 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif5.motif Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,11 @@ +>ATCAAGATGA 2-ATCAAGATGA,BestGuess:SNRNP70K(RRM)/Drosophila_melanogaster-RNCMPT00143-PBM/HughesRNA(0.785) 10.296193 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5.similar.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif5.similar.html Mon Dec 13 15:13:33 2021 +0000 |
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| b'@@ -0,0 +1,132 @@\n+<HTML><HEAD><TITLE>motif5</TITLE></HEAD>\n+<H2>Information for motif5</H2>\n+<svg width="255" height="50">\n+ <g font-family="Arial" font-weight="bold" font-size="66.5">\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,2,34)">A</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,26,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text>\n+ <text fill="#F9A500" 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transform="matrix(0.55,0,0,0.700,175,34)">G</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,200,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,200,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,201,39)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,202,34)">A</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,227,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,225,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,225,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,226,34)">T</text>\n+ \n+ </g>\n+</svg>\n+<BR/>\n+<TABLE border="1" cellpading="0" cellspacing="0">\n+<TR><TD>p-value:</TD><TD>1e-1</TD></TR>\n+<TR><TD>log p-value:</TD><TD>-2.907e+00</TD></TR>\n+<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR>\n+<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR>\n+<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR>\n+<TR><TD>Number of Background Sequences with motif</TD><TD>219.8</TD></TR>\n+<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.48%</TD></TR>\n+<TR><TD>Average Position of motif in Targets</TD><TD>113.0 +/- 0.0bp</TD></TR>\n+<TR><TD>Average Position of motif in Background</TD><TD>94.6 +/- 75.6bp</TD></TR>\n+<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR>\n+<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR>\n+<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif5.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif5RV.motif">reverse opposite</A></TD></TR>\n+</TABLE>\n+<H3>Similar de novo motifs found</H3>\n+<TABLE border="1" cellpading="0" cellspacing="0">\n+<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR>\n+</TABLE>\n+<P></P>\n+</BODY></HTML>\n' |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5RV.logo.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif5RV.logo.svg Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,54 @@ +<svg width="255" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,1,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,25,34)">C</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,50,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,51,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,52,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,77,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,75,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,76,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,102,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,100,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,100,34)">C</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,127,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,125,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,125,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,126,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,150,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,150,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,151,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,177,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,175,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,175,34)">G</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,200,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,200,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,201,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,202,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,227,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,225,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,225,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,226,34)">T</text> + + </g> +</svg> |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif5RV.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif5RV.motif Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,11 @@ +>TCATCTTGAT 2-ATCAAGATGA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.8(5.48%),P:1e-1 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.info.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif6.info.html Mon Dec 13 15:13:33 2021 +0000 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.logo.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif6.logo.svg Mon Dec 13 15:13:33 2021 +0000 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif6.motif Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,11 @@ +>GTTGCTGCCA 3-GTTGCTGCCA,BestGuess:DEL1(E2FDP)/colamp-DEL1-DAP-Seq(GSE60143)/Homer(0.657) 10.296193 -2.906976 0 T:1.0(100.00%),B:219.9(5.49%),P:1e-1 +0.100 0.100 0.700 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.similar.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif6.similar.html Mon Dec 13 15:13:33 2021 +0000 |
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| b'@@ -0,0 +1,178 @@\n+<HTML><HEAD><TITLE>motif6</TITLE></HEAD>\n+<H2>Information for motif6</H2>\n+<svg width="255" height="50">\n+ <g font-family="Arial" font-weight="bold" font-size="66.5">\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,0,34)">G</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,26,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,50,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,51,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,77,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,76,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,75,34)">G</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,102,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,100,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,100,34)">C</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,127,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,125,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,125,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,126,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,150,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,151,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,150,34)">G</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,177,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,175,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,175,34)">C</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,202,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,200,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,201,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,200,34)">C</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,225,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,225,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,226,39)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,227,34)">A</text>\n+ \n+ </g>\n+</svg>\n+<BR/>\n+Reverse Opposite:<BR/><svg width="255" height="50">\n+ <g font-family="Arial" font-weight="bold" font-size="66.5">\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="ma'..b'TR>\n+<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.49%</TD></TR>\n+<TR><TD>Average Position of motif in Targets</TD><TD>140.0 +/- 0.0bp</TD></TR>\n+<TR><TD>Average Position of motif in Background</TD><TD>103.4 +/- 83.3bp</TD></TR>\n+<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR>\n+<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR>\n+<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif6.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif6RV.motif">reverse opposite</A></TD></TR>\n+</TABLE>\n+<H3>Similar de novo motifs found</H3>\n+<TABLE border="1" cellpading="0" cellspacing="0">\n+<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR>\n+<TR><TD>1</TD><TD>0.894</TD><TD><svg width="205" height="50">\n+ <g font-family="Arial" font-weight="bold" font-size="66.5">\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,1,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,25,34)">G</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,50,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,51,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,50,34)">C</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,77,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,75,44)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,75,39)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,76,34)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,102,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,100,44)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,100,34)">G</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,127,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,125,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,126,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,125,34)">C</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,150,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,151,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,150,34)">C</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,175,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,175,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,177,34)">A</text>\n+ \n+ </g>\n+</svg>\n+\n+</TD><TD>1e-1</TD><TD>-2.897885</TD><TD>100.00%</TD><TD>5.53%</TD><TD><A target="_blank" HREF="motif6.similar1.motif">motif file (matrix)</A></TD></TR>\n+</TABLE>\n+<P></P>\n+</BODY></HTML>\n' |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6.similar1.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif6.similar1.motif Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,9 @@ +>TGCTGCCA 2-TGCTGCCA 8.236954 -2.897885 0 T:1.0(100.00%),B:221.8(5.53%),P:1e-1 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6RV.logo.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif6RV.logo.svg Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,54 @@ +<svg width="255" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,39)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.700,1,34)">T</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,25,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,25,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,51,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,50,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,77,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,75,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,76,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,75,34)">C</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,100,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,100,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,101,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,102,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,127,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,125,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,126,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,125,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,152,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,150,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,151,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,150,34)">C</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,175,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,175,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,176,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,177,34)">A</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,200,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,200,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,201,39)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.700,202,34)">A</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,227,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,225,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,226,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,225,34)">C</text> + + </g> +</svg> |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif6RV.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif6RV.motif Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,11 @@ +>TGGCAGCAAC 3-GTTGCTGCCA 10.296193 -2.906976 0 T:1.0(100.00%),B:219.9(5.49%),P:1e-1 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.700 0.100 0.100 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif7.info.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif7.info.html Mon Dec 13 15:13:33 2021 +0000 |
| b |
| b'@@ -0,0 +1,1363 @@\n+<HTML><HEAD><TITLE>Motif 7</TITLE></HEAD>\n+<H2>Information for 1-CCCTAATG (Motif 7)</H2>\n+<svg width="205" height="50">\n+ <g font-family="Arial" font-weight="bold" font-size="66.5">\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,0,34)">C</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,25,34)">C</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text>\n+ <text 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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif7.logo.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif7.logo.svg Mon Dec 13 15:13:33 2021 +0000 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif7.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif7.motif Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,9 @@ +>CCCTAATG 1-CCCTAATG,BestGuess:HNRNPA1L2(RRM)/Homo_sapiens-RNCMPT00023-PBM/HughesRNA(0.812) 8.236954 -2.897885 0 T:1.0(100.00%),B:221.6(5.53%),P:1e-1 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.700 0.100 0.100 +0.100 0.100 0.100 0.700 +0.700 0.100 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.100 0.700 0.100 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif7.similar.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif7.similar.html Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,112 @@ +<HTML><HEAD><TITLE>motif7</TITLE></HEAD> +<H2>Information for motif7</H2> +<svg width="205" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,0,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,0,34)">C</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,25,34)">C</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,52,49)">A</text> + <text fill="#F9A500" x="0" y="0" 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p-value:</TD><TD>-2.898e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>221.6</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.53%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>98.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>97.0 +/- 70.2bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif7.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif7RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR> +</TABLE> +<P></P> +</BODY></HTML> |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif8.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif8.motif Mon Dec 13 15:13:33 2021 +0000 |
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width="205" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,2,49)">A</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,0,44)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,1,39)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.700,0,34)">G</text> + + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.100,27,49)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,25,44)">G</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.100,26,39)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.700,25,34)">C</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.100,50,49)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.100,50,44)">G</text> + <text fill="#DD0000" x="0" y="0" 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p-value:</TD><TD>-2.889e+00</TD></TR> +<TR><TD>Information Content per bp:</TD><TD>1.530</TD></TR> +<TR><TD>Number of Target Sequences with motif</TD><TD>1.0</TD></TR> +<TR><TD>Percentage of Target Sequences with motif</TD><TD>100.00%</TD></TR> +<TR><TD>Number of Background Sequences with motif</TD><TD>223.5</TD></TR> +<TR><TD>Percentage of Background Sequences with motif</TD><TD>5.58%</TD></TR> +<TR><TD>Average Position of motif in Targets</TD><TD>117.0 +/- 0.0bp</TD></TR> +<TR><TD>Average Position of motif in Background</TD><TD>93.3 +/- 78.0bp</TD></TR> +<TR><TD>Strand Bias (log2 ratio + to - strand density)</TD><TD>10.0</TD></TR> +<TR><TD>Multiplicity (# of sites on avg that occur together)</TD><TD>1.00</TD></TR> +<TR><TD>Motif File:</TD><TD><A target="_blank" HREF="motif8.motif">file (matrix)</A><BR/><A target="_blank" HREF="motif8RV.motif">reverse opposite</A></TD></TR> +</TABLE> +<H3>Similar de novo motifs found</H3> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Match Score</TD><TD>Redundant Motif</TD><TD>P-value</TD><TD>log P-value</TD><TD>% of Targets</TD><TD>% of Background</TD><TD>Motif file</TD></TR> +</TABLE> +<P></P> +</BODY></HTML> |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif8RV.logo.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif8RV.logo.svg Mon Dec 13 15:13:33 2021 +0000 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/homerResults/motif8RV.motif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/homerResults/motif8RV.motif Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,9 @@ +>GCATCATC 5-GATGATGC 8.236954 -2.888876 0 T:1.0(100.00%),B:223.5(5.58%),P:1e-1 +0.100 0.100 0.700 0.100 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 +0.700 0.100 0.100 0.100 +0.100 0.100 0.100 0.700 +0.100 0.700 0.100 0.100 |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/knownResults.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/knownResults.html Mon Dec 13 15:13:33 2021 +0000 |
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| @@ -0,0 +1,11 @@ +<HTML><HEAD><TITLE>fake_phix_peaks_bed_motif - Homer Known Motif Enrichment Results</TITLE></HEAD> +<BODY> +<H1>Homer Known Motif Enrichment Results (fake_phix_peaks_bed_motif)</H1> +<A HREF="homerResults.html">Homer <i>de novo</i> Motif Results</A><BR/> +<A HREF="geneOntology.html">Gene Ontology Enrichment Results</A><BR/> +<A HREF="knownResults.txt">Known Motif Enrichment Results (txt file)</A><BR/> +Total Target Sequences = 1, Total Background Sequences = 4006</BR> +<TABLE border="1" cellpading="0" cellspacing="0"> +<TR><TD>Rank</TD><TD>Motif</TD><TD>Name</TD><TD>P-value</TD><TD>log P-pvalue</TD><TD>q-value (Benjamini)</TD><TD># Target Sequences with Motif</TD><TD>% of Targets Sequences with Motif</TD><TD># Background Sequences with Motif</TD><TD>% of Background Sequences with Motif</TD><TD>Motif File</TD> +<TD>SVG</TD></TR> +</TABLE></BODY></HTML> |
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| diff -r 000000000000 -r db456c398880 test-data/motif_test1/knownResults.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/knownResults.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| b'@@ -0,0 +1,977 @@\n+Motif Name\tConsensus\tP-value\tLog P-value\tq-value (Benjamini)\t# of Target Sequences with Motif(of 1)\t% of Target Sequences with Motif\t# of Background Sequences with Motif(of 4006)\t% of Background Sequences with Motif\n+EBF2(EBF)/BrownAdipose-EBF2-ChIP-Seq(GSE97114)/Homer\tNABTCCCWDGGGAVH\t1e-1\t-2.921e+00\t1.0000\t1.0\t100.00%\t216.3\t5.40%\n+Phox2a(Homeobox)/Neuron-Phox2a-ChIP-Seq(GSE31456)/Homer\tYTAATYNRATTA\t1e-1\t-2.916e+00\t1.0000\t1.0\t100.00%\t217.9\t5.44%\n+TBP3(MYBrelated)/col-TBP3-DAP-Seq(GSE60143)/Homer\tVYTAGGGCAN\t1e-1\t-2.898e+00\t1.0000\t1.0\t100.00%\t221.6\t5.53%\n+Elk4(ETS)/Hela-Elk4-ChIP-Seq(GSE31477)/Homer\tNRYTTCCGGY\t1e-1\t-2.889e+00\t1.0000\t1.0\t100.00%\t223.6\t5.58%\n+EHF(ETS)/LoVo-EHF-ChIP-Seq(GSE49402)/Homer\tAVCAGGAAGT\t1e-1\t-2.871e+00\t1.0000\t1.0\t100.00%\t227.4\t5.67%\n+ELF3(ETS)/PDAC-ELF3-ChIP-Seq(GSE64557)/Homer\tANCAGGAAGT\t1e-1\t-2.871e+00\t1.0000\t1.0\t100.00%\t227.4\t5.67%\n+Elf4(ETS)/BMDM-Elf4-ChIP-Seq(GSE88699)/Homer\tACTTCCKGKT\t1e-1\t-2.871e+00\t1.0000\t1.0\t100.00%\t227.4\t5.67%\n+ELF5(ETS)/T47D-ELF5-ChIP-Seq(GSE30407)/Homer\tACVAGGAAGT\t1e-1\t-2.871e+00\t1.0000\t1.0\t100.00%\t227.4\t5.67%\n+OCT4-SOX2-TCF-NANOG(POU,Homeobox,HMG)/mES-Oct4-ChIP-Seq(GSE11431)/Homer\tATTTGCATAACAATG\t1e-1\t-2.779e+00\t1.0000\t1.0\t100.00%\t249.4\t6.22%\n+CHR(?)/Hela-CellCycle-Expression/Homer\tSRGTTTCAAA\t1e-1\t-2.771e+00\t1.0000\t1.0\t100.00%\t251.3\t6.27%\n+bZIP52(bZIP)/colamp-bZIP52-DAP-Seq(GSE60143)/Homer\tNDNHCAGCTGTCANN\t1e-1\t-2.755e+00\t1.0000\t1.0\t100.00%\t255.0\t6.36%\n+Etv2(ETS)/ES-ER71-ChIP-Seq(GSE59402)/Homer(0.967)\tNNAYTTCCTGHN\t1e-1\t-2.732e+00\t1.0000\t1.0\t100.00%\t261.1\t6.51%\n+ETS1(ETS)/Jurkat-ETS1-ChIP-Seq(GSE17954)/Homer\tACAGGAAGTG\t1e-1\t-2.651e+00\t1.0000\t1.0\t100.00%\t283.5\t7.07%\n+ERG(ETS)/VCaP-ERG-ChIP-Seq(GSE14097)/Homer\tACAGGAAGTG\t1e-1\t-2.644e+00\t1.0000\t1.0\t100.00%\t285.4\t7.12%\n+Mef2a(MADS)/HL1-Mef2a.biotin-ChIP-Seq(GSE21529)/Homer\tCYAAAAATAG\t1e-1\t-2.609e+00\t1.0000\t1.0\t100.00%\t296.0\t7.38%\n+Fli1(ETS)/CD8-FLI-ChIP-Seq(GSE20898)/Homer\tNRYTTCCGGH\t1e-1\t-2.450e+00\t1.0000\t1.0\t100.00%\t346.9\t8.65%\n+AT2G20110(CPP)/colamp-AT2G20110-DAP-Seq(GSE60143)/Homer\tATTYAAATHY\t1e-1\t-2.356e+00\t1.0000\t1.0\t100.00%\t380.2\t9.49%\n+Prop1(Homeobox)/GHFT1-PROP1.biotin-ChIP-Seq(GSE77302)/Homer\tNTAATBNAATTA\t1e-1\t-2.343e+00\t1.0000\t1.0\t100.00%\t385.2\t9.61%\n+IRF4(IRF)/GM12878-IRF4-ChIP-Seq(GSE32465)/Homer\tACTGAAACCA\t1e-1\t-2.320e+00\t1.0000\t1.0\t100.00%\t394.7\t9.85%\n+SPL14(SBP)/col-SPL14-DAP-Seq(GSE60143)/Homer\tNNWHTGTACGGAHNH\t1e0\t-2.285e+00\t1.0000\t1.0\t100.00%\t408.0\t10.18%\n+bHLH28(bHLH)/col-bHLH28-DAP-Seq(GSE60143)/Homer\tNHHTGTACGGAH\t1e0\t-2.277e+00\t1.0000\t1.0\t100.00%\t411.7\t10.27%\n+SPL13(SBP)/col-SPL13-DAP-Seq(GSE60143)/Homer\tWAHTGTACGGAH\t1e0\t-2.277e+00\t1.0000\t1.0\t100.00%\t411.7\t10.27%\n+AT1G69570(C2C2dof)/col-AT1G69570-DAP-Seq(GSE60143)/Homer\tWAAAAGTGHH\t1e0\t-2.265e+00\t1.0000\t1.0\t100.00%\t416.9\t10.40%\n+HIC1(Zf)/Treg-ZBTB29-ChIP-Seq(GSE99889)/Homer\tTGCCAGCB\t1e0\t-2.253e+00\t1.0000\t1.0\t100.00%\t421.8\t10.52%\n+Lhx2(Homeobox)/HFSC-Lhx2-ChIP-Seq(GSE48068)/Homer\tTAATTAGN\t1e0\t-2.246e+00\t1.0000\t1.0\t100.00%\t424.3\t10.59%\n+DPL-1(E2F)/cElegans-Adult-ChIP-Seq(modEncode)/Homer\tTAGCGCGC\t1e0\t-2.169e+00\t1.0000\t1.0\t100.00%\t458.1\t11.43%\n+Oct2(POU,Homeobox)/Bcell-Oct2-ChIP-Seq(GSE21512)/Homer\tATATGCAAAT\t1e0\t-2.054e+00\t1.0000\t1.0\t100.00%\t514.3\t12.83%\n+AT1G72740(MYBrelated)/colamp-AT1G72740-DAP-Seq(GSE60143)/Homer\tNNWWAMCCTAAHWNN\t1e0\t-2.029e+00\t1.0000\t1.0\t100.00%\t527.4\t13.16%\n+Cdx2(Homeobox)/mES-Cdx2-ChIP-Seq(GSE14586)/Homer\tGYMATAAAAH\t1e0\t-2.019e+00\t1.0000\t1.0\t100.00%\t532.9\t13.30%\n+SPL5(SBP)/colamp-SPL5-DAP-Seq(GSE60143)/Homer\tNNHGTACGGHNN\t1e0\t-2.003e+00\t1.0000\t1.0\t100.00%\t541.8\t13.52%\n+AT3G25990(Trihelix)/colamp-AT3G25990-DAP-Seq(GSE60143)/Homer\tTTAACCATAG\t1e0\t-1.992e+00\t1.0000\t1.0\t100.00%\t547.8\t13.67%\n+PABPC1(?)/MEL-PABC1-CLIP-Seq(GSE69755)/Homer\tHAATAAAGNN\t1e0\t-1.945e+00\t1.0000\t1.0\t100.00%\t573.6\t14.31%\n+RKD2(RWPRK)/colamp-RKD2-DAP-Seq(GSE60143)/Homer\tGACKTTTCRDCTTCC\t1e0\t-1.935e+00\t1.0000\t1.0\t100.00%\t579.4\t14.46%\n+TCX2(CPP)/colamp-TCX2-DAP-Seq(GSE60143)/Homer\tNNWWTTYRAAHN\t1e0\t-1.913e+00\t1.0000\t1.0\t100.00%\t593.0\t14.79%\n+SOL1(CPP)/colamp-S'..b'TCAAC\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t994.3\t24.81%\n+WRKY42(WRKY)/colamp-WRKY42-DAP-Seq(GSE60143)/Homer\tNAAAGTCAACGN\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t547.1\t13.65%\n+WRKY43(WRKY)/colamp-WRKY43-DAP-Seq(GSE60143)/Homer\tNCGTTGACTTTT\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t733.1\t18.29%\n+WRKY45(WRKY)/col-WRKY45-DAP-Seq(GSE60143)/Homer\tHNNNKTTGACTWWNH\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t723.8\t18.06%\n+WRKY46(WRKY)/colamp-WRKY46-DAP-Seq(GSE60143)/Homer\tAAAGTCAACGSN\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+WRKY47(WRKY)/colamp-WRKY47-DAP-Seq(GSE60143)/Homer\tWAAGTCAACGBT\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t712.6\t17.78%\n+WRKY50(WRKY)/col-WRKY50-DAP-Seq(GSE60143)/Homer\tNNTTGACTWNNGNNN\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t1178.4\t29.40%\n+WRKY55(WRKY)/col-WRKY55-DAP-Seq(GSE60143)/Homer\tNCGTTGACTT\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t1057.5\t26.38%\n+WRKY65(WRKY)/colamp-WRKY65-DAP-Seq(GSE60143)/Homer\tAWWWAGTCAACG\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t927.3\t23.14%\n+WRKY6(WRKY)/colamp-WRKY6-DAP-Seq(GSE60143)/Homer\tNCGTTGACTWWD\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t1113.8\t27.79%\n+WRKY71(WRKY)/col-WRKY71-DAP-Seq(GSE60143)/Homer\tCKTTGACYWW\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t994.3\t24.81%\n+WRKY75(WRKY)/col-WRKY75-DAP-Seq(GSE60143)/Homer\tCGTTGACTWW\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t1331.5\t33.22%\n+WRKY7(WRKY)/colamp-WRKY7-DAP-Seq(GSE60143)/Homer\tAAAAGTCAACGSHWD\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+WRKY8(WRKY)/colamp-WRKY8-DAP-Seq(GSE60143)/Homer\tCGTTGACTTT\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t276.1\t6.89%\n+WUS1(Homeobox)/colamp-WUS1-DAP-Seq(GSE60143)/Homer\tCAWTCATTCA\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t372.7\t9.30%\n+ZIM(C2C2gata)/col-ZIM-DAP-Seq(GSE60143)/Homer\tATCSRACGGTYRAGA\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+ZML1(C2C2gata)/colamp-ZML1-DAP-Seq(GSE60143)/Homer\tATCWYRACCGTTSRW\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+ZML2(C2C2gata)/col-ZML2-DAP-Seq(GSE60143)/Homer\tCATCATCATC\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t167.7\t4.18%\n+CELF2(RRM)/JSL1-CELF2-CLIP-Seq(GSE71264)/Homer\tRGTGTCAG\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+RBFox2(?)/Heart-RBFox2-CLIP-Seq(GSE57926)/Homer\tTGCATGCA\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t496.1\t12.38%\n+CES-1(Homeobox)/cElegans-L1-CES1-ChIP-Seq(modEncode)/Homer\tAAATTSAATTTN\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t258.9\t6.46%\n+EFL-1(E2F)/cElegans-L1-EFL1-ChIP-Seq(modEncode)/Homer\tTGCAARYGCGCTCYA\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+ELT-3(Gata)/cElegans-L1-ELT3-ChIP-Seq(modEncode)/Homer\tAWTGATAAGA\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t476.4\t11.89%\n+GEI-11(Myb?)/cElegans-L4-GEI11-ChIP-Seq(modEncode)/Homer\tCCGACAYYTYACGGG\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+HLH-1(bHLH)/cElegans-Embryo-HLH1-ChIP-Seq(modEncode)/Homer\tRACAGCTGTTBH\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t168.1\t4.19%\n+LIN-15B(Zf)/cElegans-L3-LIN15B-ChIP-Seq(modEncode)/Homer\tCARTGGAGCGCRYTTGCATT\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+LIN-39(Homeobox)/cElegans.L3-LIN39-ChIP-Seq(modEncode)/Homer\tATGATTRATG\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t1057.3\t26.38%\n+PHA-4(Forkhead)/cElegans-Embryos-PHA4-ChIP-Seq(modEncode)/Homer\tKTGTTTGC\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t613.0\t15.29%\n+PQM-1(?)/cElegans-L3-ChIP-Seq(modEncode)/Homer\tACTGATAAGA\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t601.6\t15.01%\n+ABF1/SacCer-Promoters/Homer\tCGTRNAAARTGA\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t83.7\t2.09%\n+Cbf1(bHLH)/Yeast-Cbf1-ChIP-Seq(GSE29506)/Homer\tTCACGTGAYH\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+GAGA-repeat/SacCer-Promoters/Homer\tCTYTCTYTCTCTCTC\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t974.9\t24.32%\n+Pho2(bHLH)/Yeast-Pho2-ChIP-Seq(GSE29506)/Homer\tCCCACGTGCT\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t41.0\t1.02%\n+Pho4(bHLH)/Yeast-Pho4-ChIP-Seq(GSE29506)/Homer\tAAGCACGTGBGD\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+REB1/SacCer-Promoters/Homer\tKCCGGGTAAYRR\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t223.9\t5.59%\n+RLR1?/SacCer-Promoters/Homer\tWTTTTCYYTTTT\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t347.0\t8.66%\n+SFP1/SacCer-Promoters/Homer\tDDAAAAATTTTY\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+TATA-box/SacCer-Promoters/Homer\tBBHWTATATA\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n+TOD6?/SacCer-Promoters/Homer\tGCGATGAGMT\t1e0\t0.000e+00\t1.0000\t0.0\t0.00%\t0.0\t0.00%\n' |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/motifFindingParameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/motifFindingParameters.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +cmd = test-data/fake_phix_peaks.bed test-data/phiX174.fasta fake_phix_peaks_bed_motif |
| b |
| diff -r 000000000000 -r db456c398880 test-data/motif_test1/seq.autonorm.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/motif_test1/seq.autonorm.tsv Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,85 @@ +Oligo TargetCounts BackgroundCounts NormalizationFactor +A 50.00% 28.55% 1.752 +C 50.00% 21.45% 2.331 +G 50.00% 21.45% 2.331 +T 50.00% 28.55% 1.752 +AA 50.00% 9.36% 5.343 +CA 50.00% 6.88% 7.271 +GA 50.00% 6.29% 7.951 +TA 50.00% 6.02% 8.305 +AC 50.00% 5.29% 9.450 +CC 50.00% 4.09% 12.224 +GC 50.00% 5.78% 8.644 +TC 50.00% 6.29% 7.951 +AG 50.00% 6.21% 8.053 +CG 50.00% 4.27% 11.696 +GG 50.00% 4.09% 12.224 +TG 50.00% 6.88% 7.271 +AT 50.00% 7.69% 6.499 +CT 50.00% 6.21% 8.053 +GT 50.00% 5.29% 9.450 +TT 50.00% 9.36% 5.343 +AAA 50.00% 3.00% 16.681 +CAA 50.00% 2.20% 22.680 +GAA 50.00% 1.98% 25.245 +TAA 50.00% 2.18% 22.960 +ACA 50.00% 1.18% 42.245 +CCA 50.00% 1.70% 29.393 +GCA 50.00% 1.65% 30.319 +TCA 50.00% 2.34% 21.350 +AGA 50.00% 1.81% 27.551 +CGA 50.00% 1.08% 46.235 +GGA 50.00% 1.05% 47.776 +TGA 50.00% 2.34% 21.350 +ATA 50.00% 1.81% 27.573 +CTA 50.00% 0.98% 50.945 +GTA 50.00% 1.05% 47.770 +TTA 50.00% 2.18% 22.960 +AAC 50.00% 2.00% 25.034 +CAC 50.00% 0.94% 52.984 +GAC 50.00% 1.30% 38.363 +TAC 50.00% 1.05% 47.770 +ACC 50.00% 1.52% 32.917 +CCC 50.00% 0.47% 105.420 +GCC 50.00% 1.05% 47.646 +TCC 50.00% 1.05% 47.776 +AGC 50.00% 1.87% 26.722 +CGC 50.00% 1.21% 41.155 +GGC 50.00% 1.05% 47.646 +TGC 50.00% 1.65% 30.319 +ATC 50.00% 1.61% 30.994 +CTC 50.00% 1.39% 35.864 +GTC 50.00% 1.30% 38.363 +TTC 50.00% 1.98% 25.245 +AAG 50.00% 2.09% 23.947 +CAG 50.00% 1.74% 28.691 +GAG 50.00% 1.39% 35.864 +TAG 50.00% 0.98% 50.945 +ACG 50.00% 1.19% 42.093 +CCG 50.00% 0.79% 63.182 +GCG 50.00% 1.21% 41.155 +TCG 50.00% 1.08% 46.235 +AGG 50.00% 1.12% 44.508 +CGG 50.00% 0.79% 63.182 +GGG 50.00% 0.47% 105.420 +TGG 50.00% 1.70% 29.393 +ATG 50.00% 1.99% 25.159 +CTG 50.00% 1.74% 28.691 +GTG 50.00% 0.94% 52.984 +TTG 50.00% 2.20% 22.680 +AAT 50.00% 2.28% 21.947 +CAT 50.00% 1.99% 25.159 +GAT 50.00% 1.61% 30.994 +TAT 50.00% 1.81% 27.573 +ACT 50.00% 1.40% 35.701 +CCT 50.00% 1.12% 44.508 +GCT 50.00% 1.87% 26.722 +TCT 50.00% 1.81% 27.551 +AGT 50.00% 1.40% 35.701 +CGT 50.00% 1.19% 42.093 +GGT 50.00% 1.52% 32.917 +TGT 50.00% 1.18% 42.245 +ATT 50.00% 2.28% 21.947 +CTT 50.00% 2.09% 23.947 +GTT 50.00% 2.00% 25.034 +TTT 50.00% 3.00% 16.681 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/phiX174.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX174.fasta Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -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 + |
| b |
| diff -r 000000000000 -r db456c398880 test-data/phiX_nothing.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX_nothing.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +PeakID (cmd=annotatePeaks.pl test-data/fake_phix_peaks.bed none) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type +1 phiX174 1401 1500 + 0 NA NA NA NA NA |
| b |
| diff -r 000000000000 -r db456c398880 test-data/phiXcpg.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiXcpg.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,2 @@ +PeakID (cmd=annotatePeaks.pl test-data/fake_phix_peaks.bed test-data/phiX174.fasta -CpG) Chr Start End Strand Peak Score Focus Ratio/Region Size Annotation Detailed Annotation Distance to TSS Nearest PromoterID Entrez ID Nearest Unigene Nearest Refseq Nearest Ensembl Gene Name Gene Alias Gene Description Gene Type CpG% GC% +1 phiX174 1401 1500 + 0 NA NA NA NA NA 0.060606 0.470000 |
| b |
| diff -r 000000000000 -r db456c398880 test-data/scanMotif_res1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scanMotif_res1.bed Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +phiX174 1449 1460 1-ATGAGCTTAATC,BestGuess:Oc 12.355433 + |
| b |
| diff -r 000000000000 -r db456c398880 test-data/scanMotif_res1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scanMotif_res1.txt Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,1 @@ +1-ATGAGCTTAATC,BestGuess:Oc/dmmpmm(Noyes_hd)/fly(0.654)-1 phiX174 1449 1460 + 12.355433 ATGAGCTTAATC |
| b |
| diff -r 000000000000 -r db456c398880 test-data/small.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.gtf Mon Dec 13 15:13:33 2021 +0000 |
| b |
| b'@@ -0,0 +1,221 @@\n+#!genome-build GRCm38.p6\n+#!genome-version GRCm38\n+#!genome-date 2012-01\n+#!genome-build-accession NCBI:GCA_000001635.8\n+#!genebuild-last-updated 2020-02\n+chr2\tensembl_havana\tgene\t74668310\t74671599\t.\t+\t.\tgene_id "ENSMUSG00000001819"; gene_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2";\n+chr2\tensembl_havana\ttranscript\t74668310\t74671599\t.\t+\t.\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\texon\t74668310\t74669078\t.\t+\t.\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; exon_id "ENSMUSE00000336629"; exon_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\tCDS\t74668310\t74669078\t.\t+\t0\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; protein_id "ENSMUSP00000001872"; protein_version "4"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\tstart_codon\t74668310\t74668312\t.\t+\t0\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\texon\t74669886\t74671599\t.\t+\t.\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; exon_id "ENSMUSE00000601614"; exon_version "3"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\tCDS\t74669886\t74670133\t.\t+\t2\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; protein_id "ENSMUSP00000001872"; protein_version "4"; tag "basic"; transcript_support_level "1";\n'..b'ne_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; protein_id "ENSMUSP00000051355"; protein_version "6"; tag "basic"; transcript_support_level "1";\n+chr2\thavana\tstop_codon\t74728364\t74728366\t.\t+\t0\tgene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "2"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\thavana\texon\t74743928\t74744555\t.\t+\t.\tgene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "3"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; exon_id "ENSMUSE00001323912"; exon_version "1"; tag "basic"; transcript_support_level "1";\n+chr2\thavana\texon\t74746322\t74747918\t.\t+\t.\tgene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; exon_number "4"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; exon_id "ENSMUSE00000601603"; exon_version "3"; tag "basic"; transcript_support_level "1";\n+chr2\thavana\tfive_prime_utr\t74726728\t74727278\t.\t+\t.\tgene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\thavana\tthree_prime_utr\t74728367\t74728682\t.\t+\t.\tgene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\thavana\tthree_prime_utr\t74743928\t74744555\t.\t+\t.\tgene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\thavana\tthree_prime_utr\t74746322\t74747918\t.\t+\t.\tgene_id "ENSMUSG00000100642"; gene_version "1"; transcript_id "ENSMUST00000053932"; transcript_version "6"; gene_name "Gm28230"; gene_source "havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000045590"; havana_gene_version "1"; transcript_name "Gm28230-201"; transcript_source "havana"; transcript_biotype "nonsense_mediated_decay"; havana_transcript "OTTMUST00000040122"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";\n' |
| b |
| diff -r 000000000000 -r db456c398880 test-data/small_simplified.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small_simplified.gtf Mon Dec 13 15:13:33 2021 +0000 |
| b |
| b'@@ -0,0 +1,128 @@\n+#!genome-build GRCm38.p6\n+#!genome-version GRCm38\n+#!genome-date 2012-01\n+#!genome-build-accession NCBI:GCA_000001635.8\n+#!genebuild-last-updated 2020-02\n+chr2\tensembl_havana\tgene\t74668310\t74671599\t.\t+\t.\tgene_id "ENSMUSG00000001819"; gene_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2";\n+chr2\tensembl_havana\ttranscript\t74668310\t74671599\t.\t+\t.\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\texon\t74668310\t74669078\t.\t+\t.\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; exon_id "ENSMUSE00000336629"; exon_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\tCDS\t74668310\t74669078\t.\t+\t0\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; protein_id "ENSMUSP00000001872"; protein_version "4"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\tstart_codon\t74668310\t74668312\t.\t+\t0\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "1"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\texon\t74669886\t74671599\t.\t+\t.\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; exon_id "ENSMUSE00000601614"; exon_version "3"; tag "basic"; transcript_support_level "1";\n+chr2\tensembl_havana\tCDS\t74669886\t74670133\t.\t+\t2\tgene_id "ENSMUSG00000001819"; gene_version "4"; transcript_id "ENSMUST00000001872"; transcript_version "4"; exon_number "2"; gene_name "Hoxd13"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000013304"; havana_gene_version "2"; transcript_name "Hoxd13-201"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS16139"; havana_transcript "OTTMUST00000032142"; havana_transcript_version "2"; protein_id "ENSMUSP00000001872"; protein_version "4"; tag "basic"; transcript_support_level "1";\n'..b'vana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; transcript_support_level "1";\n+chr2\thavana\texon\t74711929\t74712316\t.\t+\t.\tgene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "1"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000690059"; exon_version "2"; transcript_support_level "1";\n+chr2\thavana\texon\t74722553\t74722631\t.\t+\t.\tgene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "2"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00001456804"; exon_version "1"; transcript_support_level "1";\n+chr2\thavana\texon\t74723332\t74723367\t.\t+\t.\tgene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "3"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00001459290"; exon_version "1"; transcript_support_level "1";\n+chr2\thavana\texon\t74725463\t74725597\t.\t+\t.\tgene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "4"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000766717"; exon_version "1"; transcript_support_level "1";\n+chr2\thavana\texon\t74725845\t74725978\t.\t+\t.\tgene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "5"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000795268"; exon_version "1"; transcript_support_level "1";\n+chr2\thavana\texon\t74726876\t74726932\t.\t+\t.\tgene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "6"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000795377"; exon_version "1"; transcript_support_level "1";\n+chr2\thavana\texon\t74728359\t74728868\t.\t+\t.\tgene_id "ENSMUSG00000101174"; gene_version "8"; transcript_id "ENSMUST00000144040"; transcript_version "8"; exon_number "7"; gene_name "Hoxd4"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; havana_gene "OTTMUSG00000019164"; havana_gene_version "17"; transcript_name "Hoxd4-203"; transcript_source "havana"; transcript_biotype "processed_transcript"; havana_transcript "OTTMUST00000040121"; havana_transcript_version "16"; exon_id "ENSMUSE00000723430"; exon_version "2"; transcript_support_level "1";\n' |
| b |
| diff -r 000000000000 -r db456c398880 tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -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. +# |
| b |
| diff -r 000000000000 -r db456c398880 tool-data/homer_preparse.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/homer_preparse.loc.sample Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,25 @@ +# homer_preparse.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Homer preparsed genomes. +# The file should include an one line entry for each index set. +# The path points to the "directory" for the set, not a specific file. +# It has six text columns seperated by TABS. +# +# <unique_preparse_id> <dbkey> <mask> <size> <display_name> <directory_path> <path_fasta> <version> +# +# So, for example, if you had phiX174 preparsed with 200bp stored in: +# +# /tmp/phix_200 +# +# containing phiX174.fasta.200.* files, such as: +# -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.cgbins +# -rw-r--r-- 1 ldelisle ldelisle 249K Jul 9 10:14 phiX174.fasta.200.cgfreq +# -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.gcbins +# -rw-r--r-- 1 ldelisle ldelisle 169K Jul 9 10:14 phiX174.fasta.200.pos +# -rw-r--r-- 1 ldelisle ldelisle 955K Jul 9 10:14 phiX174.fasta.200.seq +# +# then the homer_preparse.loc entry could look like this: +# +# phiX174_200 phiX174 False 200 phiX174 (200bp) /tmp/phix_200 /tmp/phiX174.fasta 4.11 +# +# |
| b |
| diff -r 000000000000 -r db456c398880 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +<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> + <!-- Locations of preparsed genomes --> + <table name="homer_preparse" comment_char="#"> + <columns>value, dbkey, mask, size, name, path, path_fasta, version</columns> + <file path="tool-data/homer_preparse.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r db456c398880 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Dec 13 15:13:33 2021 +0000 |
| b |
| @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of preparsed genomes --> + <table name="homer_preparse" comment_char="#"> + <columns>value, dbkey, mask, size, name, path, path_fasta, version</columns> + <file path="${__HERE__}/test-data/homer_preparse.loc" /> + </table> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/all_fasta.loc" /> + </table> +</tables> |
