| Previous changeset 2:a8f207b43f64 (2021-12-13) Next changeset 4:081139509124 (2023-04-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit 16a919905f336e34e237388c1921d0f4f8a368af |
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modified:
homer_findMotifsGenome.xml macros.xml tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/demoDB/background.fa test-data/demoDB/bg_list.tabular test-data/demoDB/data/accession/worm.description test-data/demoDB/data/accession/worm2gene.tsv test-data/demoDB/data/config.txt test-data/demoDB/data/promoters/worm.base test-data/demoDB/data/promoters/worm.base.gene test-data/demoDB/data/promoters/worm.cgbins test-data/demoDB/data/promoters/worm.cgfreq test-data/demoDB/data/promoters/worm.gcbins test-data/demoDB/data/promoters/worm.mask test-data/demoDB/data/promoters/worm.pos test-data/demoDB/data/promoters/worm.redun test-data/demoDB/data/promoters/worm.seq test-data/demoDB/homerResults_fasta.html test-data/demoDB/homerResults_id.html test-data/demoDB/knownResults_fasta.html test-data/demoDB/knownResults_id.html test-data/demoDB/peaks_id.html test-data/demoDB/target.fa test-data/demoDB/target_list.tabular test-data/homer_promoters.loc |
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| diff -r a8f207b43f64 -r 4fe92af4542b homer_findMotifsGenome.xml --- a/homer_findMotifsGenome.xml Mon Dec 13 15:14:25 2021 +0000 +++ b/homer_findMotifsGenome.xml Thu Apr 06 16:22:23 2023 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="homer_findMotifsGenome" name="findMotifsGenome" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05" license="MIT"> +<tool id="homer_findMotifsGenome" name="findMotifsGenome" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> <description/> <macros> <import>macros.xml</import> @@ -138,7 +138,7 @@ <inputs> <param name="input" type="data" format="bed,encodepeak,tabular" label="Peak file"/> <conditional name="genome"> - <param name="source" type="select" label="Will you select a reference genome from your history or use a installed genome?"> + <param name="source" type="select" label="Will you select a reference genome from your history or use an installed genome?"> <option value="preparsed">Preparsed (fasta is available and has been preparsed to specific size)</option> <option value="installed">Installed (fasta is available but will be preparsed as run time)</option> <option value="history">From History (fasta will be preparsed at run time)</option> |
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| diff -r a8f207b43f64 -r 4fe92af4542b macros.xml --- a/macros.xml Mon Dec 13 15:14:25 2021 +0000 +++ b/macros.xml Thu Apr 06 16:22:23 2023 +0000 |
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| @@ -4,7 +4,8 @@ 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> + <token name="@VERSION_SUFFIX@">3</token> + <token name="@PROFILE@">20.05</token> <xml name="xrefs"> <xrefs> <xref type="bio.tools">homer</xref> @@ -12,7 +13,7 @@ </xml> <xml name="requirements"> <requirements> - <requirement type="package" version="4.11">homer</requirement> + <requirement type="package" version="@TOOL_VERSION@">homer</requirement> </requirements> </xml> <xml name="choose_center"> @@ -41,6 +42,15 @@ </when> </conditional> </xml> + <xml name="geneid_input"> + <param name="organism" type="select" label="What is the organism DB to be used?"> + <options from_data_table="homer_promoters"> + <filter type="sort_by" column="organism"/> + <validator type="no_options" message="No pre-installed organism DBs are available. Contact your galaxy administrator."/> + </options> + </param> + <param name="target_set" type="data" format="tabular" label="List of gene identifiers for the positive set"/> + </xml> <xml name="citation"> <citations> <citation type="doi">10.1016/j.molcel.2010.05.004</citation> |
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| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/background.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/background.fa Thu Apr 06 16:22:23 2023 +0000 |
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| b'@@ -0,0 +1,340 @@\n+>NR_062133\n+GGACGCTCAACATTTTTGTCCAAACTGTGGGTCTTTGTTGGCTGTTAGGACGAGAGCCTAGAGTCTGAGATAAAAGCAATGACGTTCTGAAGCGCACGAC\n+AACAACCGGGTTTGGCAACGAGCTGTGGCTAGCCGAGGACCCGGCAGATGTCGGACGCTTCGTATTTTTAATGTACAAATTGNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCTTCAGCAAGTTGTTTTGAAAAAAAGTTTATTGTATAATTGGT\n+TCTTTTGTGCACGTCAGGGGTGAGAACAAAAAATAATGATTTGTGTTCGA\n+>NR_056762\n+AGGATGGAAACAAGTATTTAAAACTAACGACACAACGAGTGGCTCATACAAAAAGTTTATTACTTCTTAAGGCCAATTGGCAACGAAAAATCATTCTTGA\n+AAATTATTTTGAGACCAGTGATGTATATCTAGCAAAGTAACTAAATAGGATACAGTATTCATCGACGCAGAATTAACCGTATAAAATTCATCGCATCATC\n+TTCTTCTTCTTGATCATCGTTGTCAAACTCTGGAACATGATCCCAATTTTCCTCTGTATCGCCTTCTTGTAATTCGTTTTGAAACGTAATTCCTTCTCGT\n+TGAATTCCGAAAAAGCGTCGTGGTTCACGAGTCATGCTGATATATTCCCA\n+>NR_052859\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGCCTACAATAATTGTTTTTTATGTCAAACTCTTCAGAAACCCTTAA\n+AAATCTTCCAAATTGTTCAATAAAACCATAATTTCCCTCCATAAAACATATGTCGAAGATAAAAATGGTACCAACAATCGTCGTACTGTTCCTCCTGCTT\n+TGCCAATCCTAACCGTCAATTAGAAAAGTGACGGAGGAGAGGGATATATAGAAAAGATGTGCGAAAATTATAGAGGATGTGTATGTGACAGTAAACGTCT\n+CTTTAGAACATCCCCTGCCACGTGGCAAGCCTGGGGTCTACTTGACATTG\n+>NR_052313\n+ACTAATCGATAACGGGGAGAATGCGCGCAAGTTCGTGGACTGTAATTTGGAAGACGCTGTCCTTGTGCTGCTTGCCACGCGGCAAATGACAGTGCTTCAG\n+CATTCGTTGGAGGTTAGTTGGTGGCTGAAAAATCAATAAAATTAATAATCATTTTCAGATTCTCGGAAGACTCTCCGATTGGTCCACAACTTGTCGGGAG\n+AATTTGTGTGAATCAAATACGATTGACGTGTGCCTTCAGCTCATACCAGATGGGGATATTTTAACGCAAAAGTAGGTGGCAGCAGACATTTCACGACTTA\n+TAGCAGCCGACATTTCTGGGGTCTAACATGACATAGCTAGCAACCTGCAC\n+>NM_059827\n+TGGAAATGTTTGCTTCCTATTACTCTTTATGTGTTTTAAAACTTGTTTTATTAATTAAAATTTATGTAATAGCTTGTTTATCATTGAATTAAAACAGGTA\n+TTATTAAATTAAACTGGAAATATCCGGCGTGTTTGTTTCTTCCAAAAATGTTTTCTCCACTCACCGCAGAGCCTCCCGGAAAACTTGNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCGTTTCTTGGAATTTTCTCTTAGTTTTTCCAAAATTCAGCTTAAATTTAATGTTTTTTTCAGAAGGAA\n+ATGAACCAAGATGCAGTTGCGAAAGCCTTGTTGGGAATGGCGGAGGCACT\n+>NR_061358\n+CCATTGGGATCCGAGTATTGTTTTCTGGTATGCCGTATGTTTTTTACGAAAAAATACTGAACAGAAAATATGAAAACTACTTCAATAAATATTGTTGTAT\n+TCTATATATTGTATTCTCGTTAGTATTTGTGCCACTAAGGCATGCCTAATTAATTATTTCAATTTAATGTTTTTAATAACGACTGGNNNNNNNNNNNNNN\n+NNNNNNNNCTGAAACTTACTTTTTTTTGAAGTCTCGATTTTAAAACAAAAACCACACTGTTTCACATTATTCACTTAAACCTGAATAATTTTAAAATCAT\n+TGATGTTACTCGTAATTTTACACCTAAACATTTGTATGTAAATAGTTCAT\n+>NM_076270\n+GTCCGGTTTCTGACCTTCTTCGGAAGTGCACGCACTTCTTTTGCGTATGTCGCATGTATCGTTAGGTTTTCAAAATGGTCCGTTGGGATGTTTAGAATGG\n+GATATATTTCAAAAAATTTGGAAAAATGAACATGAAAAGAGACATGAGTGAAGAGGGCGTTCCCGGTCTTGAAAAAGAAACTGAGTAGTTGAAATAGAGA\n+CCGGAAAAAAAGAAAGAAAAAACTTCACTTAGCGCATCTGAATACGTTGTGCACATACCAACATATTCACTAGACAAATGTCATTTACGAGAAGAAGAAG\n+ATGGTTATTCTGAGTCATCATAAACGATCACCGCCACTTTTAATGAGGCT\n+>NR_072779\n+TCTTGATCATCTTTAAAATGTCTCCATTGTTTTGAATCGTCCAGTTGAATTAATTTTTGCCCCCTGCTCCATTACGCACAATATTTAGCACTATGAATCT\n+CGCTATTAACATTCCTACCCGGCCCGTTCTACTATCTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCGAAATTGAATAACTTCAATG\n+TTTTTTTTTAATAAACAGAACTTTAAATATTCTTCAAACAAAAAAAAGTTTTAAAAATGTTCAAAATCCCGATGGAGCGATTTTTCAAAGGTGTGACCTC\n+GTACACTACACATACTACGTGACAATGACATATGACGTAGGGGGCGAGAA\n+>NR_054986\n+CCTATTTTTCGCATAATTTCTTGTGAGCTCAGGTGTTTCGAGTTTTTCCAGCTCTACTGTCTACATGCTATAAGTCTTCCTGATTTATAGTTGGAATTCC\n+AGTATCCAATTTTTTGTAACAACACAAAAATAGTTCGAAATATGTAAGAGATCGATAATCAGACGTTCAGCTAACAATTATTATTGTATATAAACCCATA\n+GAAGCAGTATAAGCCAAAATTGTTCAAAAAAATTGCAAACTCTAAAAATTTTACTGTTTCACTCTAATGATGTAATGTGCAAAAAACATCATTTTAGTAG\n+TTCTGACACGACATTTACGAGTTGTTAAGTCAAAGTTTTAATAGCAAAAG\n+>NM_001027488\n+AATGATGAAAAAAGTGTTAATCCGAATGTCAAATCTCCCCCACTATCACCAGCTTACCGGAAATTTTTTGAATTTCCGTTGAGAAGAGAAAAAGTAAGGA\n+AATGTTGAAAATAAGCTGCAATTGGTACACTTCGCCAACGCATTGCAGCTAGTTATGCGTGTAATTTTAATATCATGTGATTCTATTTTTTATGTTTCTC\n+ATTTTTTGTTACATTGTCACTGTGTGACACCATTTGCTCTGAAATTTCTTTTCTTCTTTTTGTTGTAAAATTCTCTATCATTTTCAGTGATATATCAGAA\n+ATGTTACGATGGTTTCACGTAGAAGACGAGAAGACTTTCCTGTTTGGAAT\n+>NR_101537\n+ATTTAAGCAAAATACCCAAAAACTCTACCCTCCCTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAAATCAAAATATTCGGTATCAGCA\n+GCATAAATAACATCTATAGAACATTTTTTGACCTTGCCAATCCGAAATCCGCAATTTTGATGACTCCAGAATCTGAAACCAGAATATTCTGAGGCTTCAG\n+ATCACGGTGAACAATCCGTCGGAGATGACAATACGATAGAGCTGATAGAAGTTGCCACATG'..b'AGGAAAAAGTTTAGAAGTGTCTTGTTGTACGGAAATTTG\n+GAGAGAAATTGAAAATTTGATCAACTGATTTTTGGTTTGATCTGGTTTTTTAACTCCTGAACATTTTAAAATGATTGGAAATAATAAAACAATAGAACAG\n+ATTTTTTCTAGATTGTCGCTTAAAAATTGCTAAATTAATTATTTTATGAAATCACTGTTTCAAAACATTCGTTTTGGTGATAACTATTTTCAACCAACAA\n+TGTTTGAAGCAAATTGCGCAATTTTTTTTCAATCTGGGTGAAATGATTTT\n+>NM_064774\n+ACCACTGGTATTTCTTTTTACCAATTCGTACCATCCTCACCCCAAAAAAACCGATCAGAATAGTAGATTTTCCGCCTGATTTGTGTGTGTTTTGCCTATT\n+TATTATCGATATTATTCATTGAAATTTCCCCCCTTTGACCCCCATTTTTTTTGCAACGATACTCTTTCCATGAATTATATTGACGGAGTTGTAGCTGCAA\n+TTTTTATCCGATTTTCTGAAAATTTTTGGCGAATGTCGTTTTTAATATCTTTAAAACTCCATTTTTATCTGTAAAATCTATAATTTTAGCACCCAAAAAA\n+ATGCCAGCAGAGCCACAAAAATCCACAGAAGCCGGCAGCGTGGCACCGGA\n+>NR_067531\n+CATTGAAAATAGGGAAAATATCACAAAAATAGAAAAAAGAAAATTTAAATTTGAAATTAAATTTAGAAGCTAGATTCTGAAGAATCGGATCTCATCTTTT\n+TTGCAGCTGGGCCTTCAGAACATCCACTTTGTTCAGATGATTGTCCTGAATTACTGGAGCAAGTGATTCTTCTGCTGATTTTTGGAAAACTTCTTTTTCT\n+ACGTGTGGAAGTAGGGAACTTGGTGCTGAAAATAAAGTTTTTAATTTTTTCTGTTTCAGATTTCTGATAAAAGTCAGAGAAATTTAGTGATCTACTTTAA\n+TAAAACTAACCAATTCTCTCTTTCTTCTTCCAAATCTTCAAGCCATGGAT\n+>NR_067391\n+TGACCTTTTAAAAAACACTGCACTAGCTTTTCATTTTTTATAAACACAATTAGGGTCCAAACAAATTGAGTTCAGAAAATATTGTTTTTTTTTTCAAAAA\n+AAATTTGCTGTTCCAAAGAAATTATAAAGCCACTTGGGAAATACGCATGCGATGTATGCGATTTGTACATTTCGAAAAATTATTTGAGAAGAGAGTATCA\n+GTTTTTTTAAATTCTTATTTTAGGCACACATTATTACTTAAAATTTGAAAATTTTACATTTACTGATAGTTATTATTATCGAATGTTTATATTTGAGTTA\n+TTTGAGTTATTGCAGGTGTGTGGCTACTTTTGGAACATTTTGTTGAATGA\n+>NR_064800\n+CAGAATTAAAGCCCACGGGCGCACAACTACAGTACTCCTACAGTAACCTTGTAGAAATATATTTTTCGAGTAGCTCGATTGTTTTGTTGCAGCCGATCTC\n+TCCCGGATACAGTTTTGTGCTGCCACATTTAAAAACTGCGAAAACCCGGCAGATGTCGGGCGCTGGGAAAGAATTAGACAAAAAGGCTAGATTTCTCGGC\n+CCAGTTACTTGTCGGCTGCACACTTTTGTTCCTTGACATAACAGTTTTTTTTCACTGTTTCATCAGTTTTGTAAATGTTTTTCATTCTTTGCAGTTGTAT\n+TCAAATATCCTTGTTGACTAACTCACATTCGCAACCAAAAAAGCGTTTCC\n+>NR_055240\n+NNNNNNNNNNNNTATGATAAATGAAATTATTGAAACATGAGATAATGTTCTTCAAATGATGTGCCTAGTTACATAAAACCTGTTTCAGACTCGCTTAAAT\n+TTTTTGGCTAATTCCCATGATTTATTTATTTATTTATTCATCATGGAAACAAAAAGAATATGATTTCTTGTAAATTGTTATTTTACTTTTTCTCACAGAA\n+GCTTCAAAAGCTTCAGAGCAAATGACAAAGTTGCAAAATGATTTGAGTATTTTCTGTTTCAAATTTTCAATAACTAAAACTTTTGCAACAAAGTTTTTAT\n+TTTTTCTTCAGGTTCATAAGAAATTTGCATTCTGCAGGTTATTAAAACAG\n+>NR_069706\n+AAATGTGCACTAAATATTGGTGCACATTGGACGGACAAAGTGCTGTGCGGCAGTTGACAATTTTGGCATTGACGGGTTTTTTTTTGAATTTTTTCAAAAA\n+ATTGTTGTTAGAGCAAACTAGTTTTGCGAAAATTAACAAATTTCACTTTTGTTTTAAAGATTTGGCTAGTGATTTTTTGTTGAAAAATCTCTTCACCTAC\n+TAGGTTTAAGGTTTAAGTTTTGAAATTTAAAAGTGGACATTTTGCAACGAAGAACACATCTACTAGTTGAAATTTAAGGAAATTAGGTTGATGGTATTGT\n+TGGAAAGGATCTTTGAAGGTTTATGACTAGCCTAATAATACAAAATTATT\n+>NR_067486\n+ATATTTTTCGGAAGTTCGATATTTTTCAACAATAGTGTTCATGAGCGTTCATTCCTGTATGTTGAGATTCTATAAATATAATTTCGTGTATCTGACTTCG\n+GTATCAAATTTCCAGGATATCGAAATGTCTGGAAGGTTTGGCATGTAAATTTGAAGGCACACGCTATTTTTCTGAGTGGGTCTCGCCGCGAAACATGTAG\n+AACTTAGTGTCGCTTTTCTACGAATAATATTATTTCCTAATTTATACAAAAAAAACTGTTTCAACTTTCATTTAAAAATGGTAGAATGCATTTTTTTCAG\n+TTGTTTCGTCGCAGCACGCTTTAATAAATTTGAAAACAAAAACCTCTTTC\n+>NM_069722\n+TTGGTAATTTACCAAAACTACAGTTAAACTGAGAATTTTAATAAACTTTTAAATTGTTATATTTTCTAAATGATGTTCAACACTTCATATTTCAATCTTC\n+CCTTCTCACTTTCTAGAAATACGAAGAACAAATCACAATTTCTGTGAAACCTCTCTCAAAACCCGTGTTAAGTTCAGTGCTCATTTTCAGTTCCGTAATG\n+TCTCATAAAATCGCCGTAAAAGTGTTTCGTGTTATCACCTCGTGTCTGAAAAGCATAAAAACTCATCTGAAAATCAACATTTTGTGCCACAAACCCAAGA\n+ATGTGGTCGTTAACTCTTAGCTTCTCCCTCGTCTTTTTGACATTTGTTCA\n+>NR_063336\n+AGTAAGAGCAACTACATTTCATCAAAAAAAACCATATAAAACTGCAAAAACTTGGAGAAAAATTGTCTGTGTATAAAAAATTGCGGTTTCAGGACCAGTA\n+TAGAATATTTCCAAATCATCTCGAGTTTGATTAGAAACTTGGGGCAGCTTAACAGTTAAAATTTAAATTCTATTACTAATTTTACTTGCATGGAAATTGT\n+GAAAACGTATTTCAAGCAATCAATAACTATTCCAAAAGTAGTTTTAAAAAATTACTGTTTCACTATAATATCAAAGAAATAATTTAAATTTGGAGAAAAT\n+TGATTTGAAAAGAAATTCACAAATGTTTAAAATTCAACTTATCAGAAGAA\n+>NM_001029192\n+TTTTAAACAGTATCAAGTGAGGGTGTAAATACCTGGTTGGTGTCAGCCGGCGACGACCTTCTTGTCTCCGGAGAGAAGAGCTGCGTCTGAATACCTTTTC\n+GAGTGTTGTACGCAAAACTTTTCAAGTAGTGGAGGTCTTGGTAGCCCATCCTACTTGTTCATCTATGAGCGCTCTTTCATTCAAACTGTCCACCGTTTTT\n+TTCTTCTTCCTTGTTAGTGTTTCCTTTCAAATTCGATTTTGTGAAAATTTCAGCACCATTTTCTAAAAGCTTCATCAAATAACAAAAACATTTTTAGACA\n+ATGCCCTATCGTGCAGAGCTAAAACGTCCCGATTTGAAAGGCTCATTTCC\n' 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| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/bg_list.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/bg_list.tabular Thu Apr 06 16:22:23 2023 +0000 |
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| @@ -0,0 +1,79 @@ +13204479 +13198459 +13191966 +13189564 +172598 +13203659 +180673 +13224290 +13209673 +13206478 +13195162 +185825 +3565798 +24104712 +171853 +13193708 +266652 +177485 +174105 +13194942 +13193456 +185519 +13197724 +13190736 +13193728 +13202087 +173658 +179137 +13207423 +179557 +189331 +179732 +13200806 +13217996 +13199284 +3896823 +172133 +188632 +13194998 +13200004 +191464 +174485 +13186517 +24104913 +177948 +24104749 +13201278 +190555 +13224709 +13200468 +187147 +179509 +172774 +13199751 +13204783 +176400 +13214270 +7040179 +3565973 +13222557 +175585 +173573 +184951 +13207346 +176209 +13191484 +6418844 +13217489 +13210773 +175186 +13210106 +13209952 +13207233 +13195426 +13215667 +13210057 +178041 +13205726 +180727 |
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| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/accession/worm.description --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/accession/worm.description Thu Apr 06 16:22:23 2023 +0000 |
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| @@ -0,0 +1,100 @@ +GeneID Unigene RefSeq Ensembl name alias orf chromosome description type +13206415 NR_064002 21ur-4655 - CELE_Y105C5A.437 - ncRNA ncRNA +13192190 NR_052929 Y77E11A.18 - CELE_Y77E11A.18 - ncRNA ncRNA +13205826 NR_063434 21ur-2817 - CELE_Y105C5A.430 - ncRNA ncRNA +13204810 NR_062450 21ur-833 - CELE_Y73F8A.138 - ncRNA ncRNA +13204564 NR_062214 21ur-7076 - CELE_Y73F8A.575 - ncRNA ncRNA +185688 Cel.18491 NM_060137 F42H11.1 - CELE_F42H11.1 - hypothetical protein protein-coding +13193193 NR_053268 21ur-14710 - CELE_T08B6.40 - ncRNA ncRNA +13207184 NR_064753 21ur-12409 - CELE_Y105C5B.845 - ncRNA ncRNA +3565853 Cel.29934 NM_001026043 C40H1.9 - CELE_C40H1.9 - hypothetical protein protein-coding +175579 Cel.10790 NM_065499 C28A5.6 - CELE_C28A5.6 - hypothetical protein protein-coding +13206434 NR_064019 21ur-9453 - CELE_Y105C5A.982 - ncRNA ncRNA +3896775 clec-69 - CELE_F56D6.15 - pseudo pseudo +188085 Cel.14467 NM_062428 T05A7.7 - CELE_T05A7.7 - hypothetical protein protein-coding +178946 NR_000460 CD4.10 - CELE_CD4.10 - ncRNA ncRNA +179411 Cel.39151 NM_001269256 C08B6.8 - CELE_C08B6.8 - Probable oligoribonuclease protein-coding +13206365 NR_063953 21ur-13842 - CELE_Y105C5A.724 - ncRNA ncRNA +13213220 NR_068896 F13H6.16 - CELE_F13H6.16 - ncRNA ncRNA +186367 Cel.845 NM_075857 F56C3.9 - CELE_F56C3.9 - Uncharacterized protein protein-coding +13209600 NR_067056 21ur-13635 - CELE_Y51H4A.677 - ncRNA ncRNA +13194638 NR_054502 21ur-4645 - CELE_H35B03.4 - ncRNA ncRNA +13204479 NR_062133 21ur-2192 - CELE_Y40H7A.54 - ncRNA ncRNA +13198459 NR_056762 21ur-13274 - CELE_M18.10 - ncRNA ncRNA +13191966 NR_052859 F29C4.10 - CELE_F29C4.10 - ncRNA ncRNA +13189564 NR_052313 D1044.13 - CELE_D1044.13 - ncRNA ncRNA +172598 Cel.4960 NM_059827 mau-2 - CELE_C09H6.3 - Maternal uncoordinated protein 2 protein-coding +13203659 NR_061358 21ur-14851 - CELE_Y41E3.446 - ncRNA ncRNA +180673 Cel.17944 NM_076270 F47F2.1 - CELE_F47F2.1 - cAMP-dependent protein kinase, catalytic subunit-like protein-coding +13224290 NR_072779 K09E9.11 - CELE_K09E9.11 - ncRNA ncRNA +13209673 NR_067125 21ur-7588 - CELE_Y51H4A.592 - ncRNA ncRNA +13206478 NR_064063 21ur-3061 - CELE_Y105C5A.100 - ncRNA ncRNA +13195162 NR_054986 21ur-6358 - CELE_K02B2.27 - ncRNA ncRNA +185825 F46A8.9 - CELE_F46A8.9 - pseudo pseudo +3565798 Cel.29917 NM_001027488 K04C2.7 - CELE_K04C2.7 - hypothetical protein protein-coding +24104712 NR_101537 anr-45 - CELE_K03E5.8 - ncRNA ncRNA +171853 Cel.18297 NM_058660 rpl-1 - CELE_Y71F9AL.13 - 60S ribosomal protein L10a;Ribosomal protein protein-coding +13193708 NR_053707 21ur-10684 - CELE_W03F8.39 - ncRNA ncRNA +266652 Cel.12614 NM_070191 mam-3 - CELE_K09B11.10 - MAM (Meprin, A5-protein, PTPmu) domain protein protein-coding +177485 Cel.11628 NM_068710 ZC477.2 - CELE_ZC477.2 - hypothetical protein protein-coding +174105 NM_062964 rpy-1 - CELE_C18H9.7 - 43 kDa receptor-associated protein of the synapse homolog protein-coding +13194942 NR_054788 21ur-4374 - CELE_C06E7.45 - ncRNA ncRNA +13193456 NR_053482 21ur-9776 - CELE_C09B9.55 - ncRNA ncRNA +185519 Cel.3982 NM_074947 srh-174 - CELE_F40D4.1 - Serpentine Receptor, class H protein-coding +13197724 NR_056512 K04D7.13 - CELE_K04D7.13 - ncRNA ncRNA +13190736 NR_052598 T23G5.11 - CELE_T23G5.11 - ncRNA ncRNA +13193728 NR_053722 21ur-7386 - CELE_W03F8.62 - ncRNA ncRNA +13202087 NR_059860 21ur-11012 - CELE_Y57G11B.142 - ncRNA ncRNA +173658 Cel.14131 NM_062049 clec-123 - CELE_Y25C1A.1 - C-type LECtin protein-coding +179137 NM_072537 C54F6.5 - CELE_C54F6.5 - hypothetical protein protein-coding +13207423 NR_064976 21ur-10260 - CELE_Y105C5B.891 - ncRNA ncRNA +179557 Cel.19449 NM_073455 mxl-1 - CELE_T19B10.11 - MaX-Like protein-coding +189331 Cel.28984 NM_058653 W10C8.3 - CELE_W10C8.3 - hypothetical protein protein-coding +179732 Cel.2017 NM_073761 lin-25 - CELE_F56H9.5 - Protein lin-25 protein-coding +13200806 NR_058631 21ur-15409 - CELE_F02H6.49 - ncRNA ncRNA +13217996 C47A10.t4 - CELE_C47A10.t4 - tRNA tRNA +13199284 NR_057197 21ur-14882 - CELE_F52D4.16 - ncRNA ncRNA +3896823 Cel.33071 NM_001038411 cnc-9 - CELE_R13D7.11 - CaeNaCin (Caenorhabditis bacteriocin) protein-coding +172133 Cel.8139 NM_059112 fhod-1 - CELE_C46H11.11 - Formin HOmology Domain protein-coding +188632 Cel.29141 NM_066228 T20B12.5 - CELE_T20B12.5 - hypothetical protein protein-coding +13194998 srv-23 - CELE_H04M03.10 - pseudo pseudo +13200004 NR_057881 21ur-7113 - CELE_C27H2.102 - ncRNA ncRNA +191464 Cel.13743 NM_064140 ZK930.4 - CELE_ZK930.4 - hypothetical protein protein-coding +174485 Cel.39094 NM_063595 C06C3.4 - CELE_C06C3.4 - hypothetical protein protein-coding +13186517 sra-5 - CELE_AH6.9 - pseudo pseudo +24104913 NM_001307295 T21D12.14 - CELE_T21D12.14 - hypothetical protein protein-coding +177948 Cel.12370 NM_069551 zim-2 - CELE_T07G12.10 - Zinc finger In Meiosis protein-coding +24104749 NR_101576 K10D3.10 - CELE_K10D3.10 - ncRNA ncRNA +13201278 NR_059084 21ur-9623 - CELE_Y67A10A.243 - ncRNA ncRNA +190555 Cel.98 NM_066238 Y69F12A.1 - CELE_Y69F12A.1 - hypothetical protein protein-coding +13224709 NR_072940 T08G2.6 - CELE_T08G2.6 - ncRNA ncRNA +13200468 NR_058324 21ur-2521 - CELE_F52B11.27 - ncRNA ncRNA +187147 NM_001318264 K08D9.4 - CELE_K08D9.4 - hypothetical protein protein-coding +179509 Cel.3784 NM_073375 F32D8.5 - CELE_F32D8.5 - hypothetical protein protein-coding +172774 Cel.29728 NM_060113 calm-1 - CELE_F30A10.1 - CALMyrin (Calcium and Integrin Binding protein) homolog protein-coding +13199751 NR_057638 21ur-3538 - CELE_B0513.32 - ncRNA ncRNA +13204783 NR_062428 21ur-232 - CELE_Y73F8A.211 - ncRNA ncRNA +176400 Cel.18047 NM_066790 alg-4 - CELE_ZK757.3 - Putative protein tag-76 protein-coding +13214270 NR_069154 T27E4.12 CELE_T27E4.22|T27E4.22 CELE_T27E4.12 - ncRNA ncRNA +7040179 Cel.37810 NM_001136302 F49B2.7 - CELE_F49B2.7 - hypothetical protein protein-coding +3565973 Cel.30300 NM_001029452 sssh-1 - CELE_F31F6.8 - Protein quiver protein-coding +13222557 NR_072003 F57C7.7 - CELE_F57C7.7 - ncRNA ncRNA +175585 Cel.19565 NM_065510 ins-17 - CELE_F56F3.6 - Insulin-like peptide 17 protein-coding +173573 Cel.20284 NM_061802 C33C12.4 - CELE_C33C12.4 - hypothetical protein protein-coding +184951 NM_001368429 F26A1.13 - CELE_F26A1.13 - hypothetical protein protein-coding +13207346 NR_064902 21ur-6362 - CELE_Y105C5B.979 - ncRNA ncRNA +176209 Cel.10581 NM_001129220 polk-1 - CELE_F22B7.6 - DNA polymerase kappa protein-coding +13191484 NR_052780 Y56A3A.39 - CELE_Y56A3A.39 - ncRNA ncRNA +6418844 Cel.37682 NM_001129654 F09F9.5 - CELE_F09F9.5 - Uncharacterized protein protein-coding +13217489 Y32B12B.t1 - CELE_Y32B12B.t1 - tRNA tRNA +13210773 NR_068161 21ur-2726 - CELE_Y116A8C.179 - ncRNA ncRNA +175186 Cel.7065 NM_064774 cox-17 - CELE_F40G9.2 - Cytochrome OXidase assembly protein protein-coding +13210106 NR_067531 21ur-11271 - CELE_Y43D4A.125 - ncRNA ncRNA +13209952 NR_067391 21ur-1073 - CELE_Y51H4A.342 - ncRNA ncRNA +13207233 NR_064800 21ur-1461 - CELE_Y105C5B.128 - ncRNA ncRNA +13195426 NR_055240 21ur-13780 - CELE_H16O14.51 - ncRNA ncRNA +13215667 NR_069706 ZK836.8 - CELE_ZK836.8 - ncRNA ncRNA +13210057 NR_067486 21ur-7835 - CELE_Y43D4A.89 - ncRNA ncRNA +178041 Cel.13662 NM_069722 B0035.13 - CELE_B0035.13 - hypothetical protein protein-coding +13205726 NR_063336 21ur-12263 - CELE_Y105C5A.1125 - ncRNA ncRNA +180727 Cel.772 NM_001029192 ham-2 - CELE_C07A12.1 - Uncharacterized protein protein-coding |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/accession/worm2gene.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/accession/worm2gene.tsv Thu Apr 06 16:22:23 2023 +0000 |
| b |
| b'@@ -0,0 +1,701 @@\n+NR_062133\t13204479\t\tNR_062133\t\tCELE_Y40H7A.54\t21ur-2192\n+CELE_Y40H7A.54\t13204479\t\tNR_062133\t\tCELE_Y40H7A.54\t21ur-2192\n+21ur-2192\t13204479\t\tNR_062133\t\tCELE_Y40H7A.54\t21ur-2192\n+13204479\t13204479\t\tNR_062133\t\tCELE_Y40H7A.54\t21ur-2192\n+13198459\t13198459\t\tNR_056762\t\tCELE_M18.10\t21ur-13274\n+CELE_M18.10\t13198459\t\tNR_056762\t\tCELE_M18.10\t21ur-13274\n+NR_056762\t13198459\t\tNR_056762\t\tCELE_M18.10\t21ur-13274\n+21ur-13274\t13198459\t\tNR_056762\t\tCELE_M18.10\t21ur-13274\n+13191966\t13191966\t\tNR_052859\t\tCELE_F29C4.10\tF29C4.10\n+NR_052859\t13191966\t\tNR_052859\t\tCELE_F29C4.10\tF29C4.10\n+CELE_F29C4.10\t13191966\t\tNR_052859\t\tCELE_F29C4.10\tF29C4.10\n+F29C4.10\t13191966\t\tNR_052859\t\tCELE_F29C4.10\tF29C4.10\n+D1044.13\t13189564\t\tNR_052313\t\tCELE_D1044.13\tD1044.13\n+CELE_D1044.13\t13189564\t\tNR_052313\t\tCELE_D1044.13\tD1044.13\n+13189564\t13189564\t\tNR_052313\t\tCELE_D1044.13\tD1044.13\n+NR_052313\t13189564\t\tNR_052313\t\tCELE_D1044.13\tD1044.13\n+NP_492228\t172598\tCel.4960\tNM_059827\t\tCELE_C09H6.3\tmau-2\n+mau-2\t172598\tCel.4960\tNM_059827\t\tCELE_C09H6.3\tmau-2\n+SCC4_CAEEL\t172598\tCel.4960\tNM_059827\t\tCELE_C09H6.3\tmau-2\n+CAB03867\t172598\tCel.4960\tNM_059827\t\tCELE_C09H6.3\tmau-2\n+172598\t172598\tCel.4960\tNM_059827\t\tCELE_C09H6.3\tmau-2\n+O17581\t172598\tCel.4960\tNM_059827\t\tCELE_C09H6.3\tmau-2\n+Cel.4960\t172598\tCel.4960\tNM_059827\t\tCELE_C09H6.3\tmau-2\n+CELE_C09H6.3\t172598\tCel.4960\tNM_059827\t\tCELE_C09H6.3\tmau-2\n+NM_059827\t172598\tCel.4960\tNM_059827\t\tCELE_C09H6.3\tmau-2\n+13203659\t13203659\t\tNR_061358\t\tCELE_Y41E3.446\t21ur-14851\n+21ur-14851\t13203659\t\tNR_061358\t\tCELE_Y41E3.446\t21ur-14851\n+NR_061358\t13203659\t\tNR_061358\t\tCELE_Y41E3.446\t21ur-14851\n+CELE_Y41E3.446\t13203659\t\tNR_061358\t\tCELE_Y41E3.446\t21ur-14851\n+NP_508672\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+CCD71419\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+Q95ZT2\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+F47F2.1\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+NP_508671\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+Q20541\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+Cel.17944\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+CCD71417\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+NM_171660\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+KAPC2_CAEEL\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+CELE_F47F2.1\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+NM_076270\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+CCD71418\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+Q8MQ39\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+180673\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+Q7JP68\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+NP_741759\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+NM_076271\t180673\tCel.17944\tNM_076270\t\tCELE_F47F2.1\tF47F2.1\n+NR_072779\t13224290\t\tNR_072779\t\tCELE_K09E9.11\tK09E9.11\n+13224290\t13224290\t\tNR_072779\t\tCELE_K09E9.11\tK09E9.11\n+K09E9.11\t13224290\t\tNR_072779\t\tCELE_K09E9.11\tK09E9.11\n+CELE_K09E9.11\t13224290\t\tNR_072779\t\tCELE_K09E9.11\tK09E9.11\n+21ur-7588\t13209673\t\tNR_067125\t\tCELE_Y51H4A.592\t21ur-7588\n+13209673\t13209673\t\tNR_067125\t\tCELE_Y51H4A.592\t21ur-7588\n+NR_067125\t13209673\t\tNR_067125\t\tCELE_Y51H4A.592\t21ur-7588\n+CELE_Y51H4A.592\t13209673\t\tNR_067125\t\tCELE_Y51H4A.592\t21ur-7588\n+21ur-3061\t13206478\t\tNR_064063\t\tCELE_Y105C5A.100\t21ur-3061\n+NR_064063\t13206478\t\tNR_064063\t\tCELE_Y105C5A.100\t21ur-3061\n+13206478\t13206478\t\tNR_064063\t\tCELE_Y105C5A.100\t21ur-3061\n+CELE_Y105C5A.100\t13206478\t\tNR_064063\t\tCELE_Y105C5A.100\t21ur-3061\n+13195162\t13195162\t\tNR_054986\t\tCELE_K02B2.27\t21ur-6358\n+21ur-6358\t13195162\t\tNR_054986\t\tCELE_K02B2.27\t21ur-6358\n+NR_054986\t13195162\t\tNR_054986\t\tCELE_K02B2.27\t21ur-6358\n+CELE_K02B2.27\t13195162\t\tNR_054986\t\tCELE_K02B2.27\t21ur-6358\n+185825\t185825\t\t\t\tCELE_F46A8.9\tF46A8.9\n+F46A8.9\t185825\t\t\t\tCELE_F46A8.9\tF46A8.9\n+CELE_F46A8.9\t185825\t\t\t\tCELE_F46A8.9\tF46A8.9\n+3565798\t3565798\tCel.29917\tNM_001027488\t\tCELE_K04C2.7\tK04C2.7\n+CELE_K04C2.7\t3565798\tCel.29917\tNM_001027488\t\tCELE_K04C2.7\tK04C2.7\n+CCD72620\t3565798\tCel.29917\tNM_001027488\t\tCELE_K04C2.7\tK04C2.7\n+Q4TTC8_CAEEL\t3565798\tCel.29917\t'..b'99\t\tCELE_C28A5.6\tC28A5.6\n+CAA83602\t175579\tCel.10790\tNM_065499\t\tCELE_C28A5.6\tC28A5.6\n+C28A5.6\t175579\tCel.10790\tNM_065499\t\tCELE_C28A5.6\tC28A5.6\n+G5EC33\t175579\tCel.10790\tNM_065499\t\tCELE_C28A5.6\tC28A5.6\n+Cel.10790\t175579\tCel.10790\tNM_065499\t\tCELE_C28A5.6\tC28A5.6\n+G5EC33_CAEEL\t175579\tCel.10790\tNM_065499\t\tCELE_C28A5.6\tC28A5.6\n+13206434\t13206434\t\tNR_064019\t\tCELE_Y105C5A.982\t21ur-9453\n+CELE_Y105C5A.982\t13206434\t\tNR_064019\t\tCELE_Y105C5A.982\t21ur-9453\n+21ur-9453\t13206434\t\tNR_064019\t\tCELE_Y105C5A.982\t21ur-9453\n+NR_064019\t13206434\t\tNR_064019\t\tCELE_Y105C5A.982\t21ur-9453\n+CELE_F56D6.15\t3896775\t\t\t\tCELE_F56D6.15\tclec-69\n+3896775\t3896775\t\t\t\tCELE_F56D6.15\tclec-69\n+clec-69\t3896775\t\t\t\tCELE_F56D6.15\tclec-69\n+188085\t188085\tCel.14467\tNM_062428\t\tCELE_T05A7.7\tT05A7.7\n+CCD69225\t188085\tCel.14467\tNM_062428\t\tCELE_T05A7.7\tT05A7.7\n+CELE_T05A7.7\t188085\tCel.14467\tNM_062428\t\tCELE_T05A7.7\tT05A7.7\n+NM_062428\t188085\tCel.14467\tNM_062428\t\tCELE_T05A7.7\tT05A7.7\n+NP_494829\t188085\tCel.14467\tNM_062428\t\tCELE_T05A7.7\tT05A7.7\n+Q22208_CAEEL\t188085\tCel.14467\tNM_062428\t\tCELE_T05A7.7\tT05A7.7\n+Cel.14467\t188085\tCel.14467\tNM_062428\t\tCELE_T05A7.7\tT05A7.7\n+T05A7.7\t188085\tCel.14467\tNM_062428\t\tCELE_T05A7.7\tT05A7.7\n+Q22208\t188085\tCel.14467\tNM_062428\t\tCELE_T05A7.7\tT05A7.7\n+CD4.10\t178946\t\tNR_000460\t\tCELE_CD4.10\tCD4.10\n+NR_000460\t178946\t\tNR_000460\t\tCELE_CD4.10\tCD4.10\n+178946\t178946\t\tNR_000460\t\tCELE_CD4.10\tCD4.10\n+CELE_CD4.10\t178946\t\tNR_000460\t\tCELE_CD4.10\tCD4.10\n+C08B6.8\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+179411\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+CCD31032\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+Q17819\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+CAA96590\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+G3MU09\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+NP_001256185\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+ORN_CAEEL\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+NM_001269256\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+Cel.39151\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+G3MU09_CAEEL\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+CELE_C08B6.8\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+NM_001269257\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+NP_001256186\t179411\tCel.39151\tNM_001269256\t\tCELE_C08B6.8\tC08B6.8\n+21ur-13842\t13206365\t\tNR_063953\t\tCELE_Y105C5A.724\t21ur-13842\n+NR_063953\t13206365\t\tNR_063953\t\tCELE_Y105C5A.724\t21ur-13842\n+CELE_Y105C5A.724\t13206365\t\tNR_063953\t\tCELE_Y105C5A.724\t21ur-13842\n+13206365\t13206365\t\tNR_063953\t\tCELE_Y105C5A.724\t21ur-13842\n+F13H6.16\t13213220\t\tNR_068896\t\tCELE_F13H6.16\tF13H6.16\n+NR_068896\t13213220\t\tNR_068896\t\tCELE_F13H6.16\tF13H6.16\n+13213220\t13213220\t\tNR_068896\t\tCELE_F13H6.16\tF13H6.16\n+CELE_F13H6.16\t13213220\t\tNR_068896\t\tCELE_F13H6.16\tF13H6.16\n+186367\t186367\tCel.845\tNM_075857\t\tCELE_F56C3.9\tF56C3.9\n+NP_508258\t186367\tCel.845\tNM_075857\t\tCELE_F56C3.9\tF56C3.9\n+O61761_CAEEL\t186367\tCel.845\tNM_075857\t\tCELE_F56C3.9\tF56C3.9\n+CCD69814\t186367\tCel.845\tNM_075857\t\tCELE_F56C3.9\tF56C3.9\n+NM_075857\t186367\tCel.845\tNM_075857\t\tCELE_F56C3.9\tF56C3.9\n+CELE_T24H10.9\t13186367\t\tNR_051518\t\tCELE_T24H10.9\t21ur-13301\n+13186367\t13186367\t\tNR_051518\t\tCELE_T24H10.9\t21ur-13301\n+O61761\t186367\tCel.845\tNM_075857\t\tCELE_F56C3.9\tF56C3.9\n+Cel.845\t186367\tCel.845\tNM_075857\t\tCELE_F56C3.9\tF56C3.9\n+NR_051518\t13186367\t\tNR_051518\t\tCELE_T24H10.9\t21ur-13301\n+F56C3.9\t186367\tCel.845\tNM_075857\t\tCELE_F56C3.9\tF56C3.9\n+CELE_F56C3.9\t186367\tCel.845\tNM_075857\t\tCELE_F56C3.9\tF56C3.9\n+21ur-13301\t13186367\t\tNR_051518\t\tCELE_T24H10.9\t21ur-13301\n+21ur-13635\t13209600\t\tNR_067056\t\tCELE_Y51H4A.677\t21ur-13635\n+NR_067056\t13209600\t\tNR_067056\t\tCELE_Y51H4A.677\t21ur-13635\n+CELE_Y51H4A.677\t13209600\t\tNR_067056\t\tCELE_Y51H4A.677\t21ur-13635\n+13209600\t13209600\t\tNR_067056\t\tCELE_Y51H4A.677\t21ur-13635\n+CELE_H35B03.4\t13194638\t\tNR_054502\t\tCELE_H35B03.4\t21ur-4645\n+NR_054502\t13194638\t\tNR_054502\t\tCELE_H35B03.4\t21ur-4645\n+13194638\t13194638\t\tNR_054502\t\tCELE_H35B03.4\t21ur-4645\n+21ur-4645\t13194638\t\tNR_054502\t\tCELE_H35B03.4\t21ur-4645\n' |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/config.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/config.txt Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -0,0 +1,16 @@ +# Homer Configuration File (automatically generated) +# +# This file is updated from the Homer website and contains information about data available for +# use with the program. +# +# Each section has the same format, which is <tab> separated values specifying: +# package name <tab> version <tab> description <tab> url <tab> optional parameters (, separated) +# +SOFTWARE +homer v4.11.1 Code/Executables, ontologies, motifs for HOMER http://homer.ucsd.edu/homer/data/software/homer.v4.11.1.zip ./ +ORGANISMS +worm v6.3 Caenorhabditis elegans (worm) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/worm.v6.3.zip data/accession/ 6239,NCBI Gene +PROMOTERS +worm v5.5 worm promoters (worm) http://homer.ucsd.edu/homer/data/promoters/worm.v5.5.zip data/promoters/ worm,ce10,refseq,-2000,2000 +GENOMES +SETTINGS |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/promoters/worm.base --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/promoters/worm.base Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -0,0 +1,83 @@ +NR_064002 +NR_052929 +NR_063434 +NR_062450 +NM_060137 +NR_053268 +NR_064753 +NM_001026043 +NM_065499 +NM_062428 +NR_000460 +NM_001269256 +NR_068896 +NM_075857 +NR_067056 +NR_062133 +NR_056762 +NR_052859 +NR_052313 +NM_059827 +NR_061358 +NM_076270 +NR_072779 +NR_054986 +NM_001027488 +NR_101537 +NM_058660 +NR_053707 +NM_070191 +NM_068710 +NM_062964 +NR_054788 +NR_053482 +NM_074947 +NR_056512 +NR_052598 +NR_053722 +NR_059860 +NM_062049 +NM_072537 +NR_064976 +NM_073455 +NM_058653 +NM_073761 +NR_058631 +NR_057197 +NM_001038411 +NM_059112 +NM_066228 +NR_057881 +NM_064140 +NM_063595 +NM_069551 +NR_101576 +NR_059084 +NM_066238 +NR_072940 +NR_058324 +NM_073375 +NM_060113 +NR_057638 +NR_062428 +NM_066790 +NR_069154 +NM_001136302 +NM_001029452 +NR_072003 +NM_065510 +NM_061802 +NM_001129220 +NR_052780 +NM_001129654 +NR_068161 +NM_064774 +NR_067531 +NR_067391 +NR_064800 +NR_055240 +NR_069706 +NR_067486 +NM_069722 +NR_063336 +NM_001029192 |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/promoters/worm.base.gene --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/promoters/worm.base.gene Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -0,0 +1,99 @@ +13206415 +13192190 +13205826 +13204810 +13204564 +185688 +13193193 +13207184 +3565853 +175579 +13206434 +3896775 +188085 +178946 +179411 +13206365 +13213220 +186367 +13209600 +13194638 +13204479 +13198459 +13191966 +13189564 +172598 +13203659 +180673 +13224290 +13209673 +13206478 +13195162 +185825 +3565798 +24104712 +171853 +13193708 +266652 +177485 +174105 +13194942 +13193456 +185519 +13197724 +13190736 +13193728 +13202087 +173658 +179137 +13207423 +179557 +189331 +179732 +13200806 +13217996 +13199284 +3896823 +172133 +188632 +13194998 +13200004 +191464 +174485 +13186517 +24104913 +177948 +24104749 +13201278 +190555 +13224709 +13200468 +187147 +179509 +172774 +13199751 +13204783 +176400 +13214270 +7040179 +3565973 +13222557 +175585 +173573 +184951 +13207346 +176209 +13191484 +6418844 +13217489 +13210773 +175186 +13210106 +13209952 +13207233 +13195426 +13215667 +13210057 +178041 +13205726 +180727 |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/promoters/worm.cgbins --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/promoters/worm.cgbins Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -0,0 +1,85 @@ +NR_064002 2 +NR_052929-HOMER3 2 +NR_052929-HOMER2 3 +NR_052929 5 +NR_063434 0 +NR_062450 1 +NM_060137 4 +NR_053268 1 +NR_064753 2 +NM_001026043 1 +NM_065499 3 +NM_062428 3 +NR_000460 3 +NM_001269256 3 +NR_068896 5 +NM_075857 1 +NR_067056 1 +NR_062133 5 +NR_056762 4 +NR_052859 2 +NR_052313 4 +NM_059827 2 +NR_061358 2 +NM_076270 4 +NR_072779 3 +NR_054986 2 +NM_001027488 2 +NR_101537 3 +NM_058660 4 +NR_053707 2 +NM_070191 3 +NM_068710 1 +NM_062964 3 +NR_054788 1 +NR_053482 2 +NM_074947 2 +NR_056512 2 +NR_052598 3 +NR_053722 3 +NR_059860 2 +NM_062049 3 +NM_072537 0 +NR_064976 2 +NM_073455 1 +NM_058653 3 +NM_073761 2 +NR_058631 1 +NR_057197 1 +NM_001038411 3 +NM_059112 2 +NM_066228 1 +NR_057881 3 +NM_064140 3 +NM_063595 3 +NM_069551 2 +NR_101576 5 +NR_059084 1 +NM_066238 4 +NR_072940 3 +NR_058324 1 +NM_073375 3 +NM_060113 2 +NR_057638 2 +NR_062428 1 +NM_066790 4 +NR_069154 4 +NM_001136302 4 +NM_001029452 4 +NR_072003 4 +NM_065510 3 +NM_061802 2 +NM_001129220 5 +NR_052780 3 +NM_001129654 3 +NR_068161 1 +NM_064774 3 +NR_067531 0 +NR_067391 1 +NR_064800 4 +NR_055240 0 +NR_069706 1 +NR_067486 4 +NM_069722 2 +NR_063336 0 +NM_001029192 3 |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/promoters/worm.cgfreq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/promoters/worm.cgfreq Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -0,0 +1,85 @@ +NR_064002 0.020057 0.282857 0.445714 0.505714 350 +NR_052929-HOMER3 0.028881 0.358423 0.534050 0.483871 279 +NR_052929-HOMER2 0.034384 0.388571 0.471429 0.448571 350 +NR_052929 0.054795 0.486486 0.500000 0.635135 74 +NR_063434 0.008596 0.277143 0.548571 0.545714 350 +NR_062450 0.015337 0.323171 0.469512 0.445122 328 +NM_060137 0.040115 0.337143 0.528571 0.494286 350 +NR_053268 0.018750 0.326087 0.580745 0.565217 322 +NR_064753 0.022923 0.294286 0.514286 0.522857 350 +NM_001026043 0.017192 0.300000 0.468571 0.482857 350 +NM_065499 0.031519 0.302857 0.408571 0.482857 350 +NM_062428 0.031519 0.368571 0.402857 0.462857 350 +NR_000460 0.038462 0.443038 0.544304 0.531646 79 +NM_001269256 0.036810 0.329268 0.445122 0.475610 328 +NR_068896 0.054441 0.451429 0.434286 0.491429 350 +NM_075857 0.011905 0.266272 0.378698 0.455621 169 +NR_067056 0.014327 0.280000 0.454286 0.465714 350 +NR_062133 0.051095 0.438406 0.539855 0.442029 276 +NR_056762 0.045845 0.360000 0.482857 0.522857 350 +NR_052859 0.027027 0.383838 0.511785 0.538721 297 +NR_052313 0.048711 0.451429 0.528571 0.482857 350 +NM_059827 0.023026 0.333333 0.460784 0.441176 306 +NR_061358 0.021472 0.274390 0.454268 0.478659 328 +NM_076270 0.042980 0.388571 0.562857 0.505714 350 +NR_072779 0.038835 0.353698 0.456592 0.527331 311 +NR_054986 0.020057 0.308571 0.491429 0.508571 350 +NM_001027488 0.025788 0.334286 0.462857 0.454286 350 +NR_101537 0.038835 0.395498 0.514469 0.569132 311 +NM_058660 0.045845 0.408571 0.428571 0.408571 350 +NR_053707 0.020057 0.260000 0.511429 0.480000 350 +NM_070191 0.037249 0.382857 0.402857 0.482857 350 +NM_068710 0.011461 0.322857 0.448571 0.514286 350 +NM_062964 0.031519 0.340000 0.502857 0.500000 350 +NR_054788 0.019672 0.287582 0.506536 0.506536 306 +NR_053482 0.020057 0.342857 0.540000 0.454286 350 +NM_074947 0.022923 0.362857 0.491429 0.534286 350 +NR_056512 0.025788 0.394286 0.508571 0.514286 350 +NR_052598 0.034384 0.388571 0.540000 0.505714 350 +NR_053722 0.031519 0.294286 0.511429 0.531429 350 +NR_059860 0.025788 0.277143 0.451429 0.505714 350 +NM_062049 0.030201 0.277592 0.481605 0.531773 299 +NM_072537 0.008596 0.322857 0.388571 0.454286 350 +NR_064976 0.022923 0.305714 0.482857 0.514286 350 +NM_073455 0.014327 0.302857 0.422857 0.451429 350 +NM_058653 0.037249 0.454286 0.440000 0.517143 350 +NM_073761 0.026706 0.369822 0.514793 0.517751 338 +NR_058631 0.014327 0.248571 0.491429 0.517143 350 +NR_057197 0.017192 0.285714 0.511429 0.505714 350 +NM_001038411 0.031519 0.382857 0.442857 0.534286 350 +NM_059112 0.022923 0.300000 0.411429 0.505714 350 +NM_066228 0.011461 0.305714 0.474286 0.534286 350 +NR_057881 0.036923 0.374233 0.598160 0.524540 326 +NM_064140 0.035484 0.375000 0.535256 0.500000 312 +NM_063595 0.031519 0.308571 0.448571 0.522857 350 +NM_069551 0.022923 0.300000 0.425714 0.428571 350 +NR_101576 0.057307 0.442857 0.451429 0.482857 350 +NR_059084 0.014327 0.234286 0.500000 0.500000 350 +NM_066238 0.040230 0.372493 0.426934 0.484241 349 +NR_072940 0.034384 0.468571 0.508571 0.514286 350 +NR_058324 0.014327 0.294286 0.497143 0.500000 350 +NM_073375 0.031519 0.362857 0.477143 0.502857 350 +NM_060113 0.022923 0.431429 0.382857 0.517143 350 +NR_057638 0.020231 0.273775 0.452450 0.409222 347 +NR_062428 0.011461 0.271429 0.494286 0.468571 350 +NM_066790 0.043750 0.363354 0.562112 0.509317 322 +NR_069154 0.040115 0.402857 0.465714 0.542857 350 +NM_001136302 0.042373 0.476793 0.468354 0.582278 237 +NM_001029452 0.040115 0.362857 0.397143 0.451429 350 +NR_072003 0.048711 0.494286 0.548571 0.511429 350 +NM_065510 0.039216 0.402597 0.457792 0.490260 308 +NM_061802 0.022901 0.284091 0.511364 0.575758 264 +NM_001129220 0.057307 0.388571 0.508571 0.508571 350 +NR_052780 0.037249 0.411429 0.471429 0.562857 350 +NM_001129654 0.031519 0.385714 0.397143 0.542857 350 +NR_068161 0.011461 0.271429 0.520000 0.465714 350 +NM_064774 0.034384 0.365714 0.425714 0.505714 350 +NR_067531 0.005731 0.314286 0.497143 0.480000 350 +NR_067391 0.014327 0.268571 0.485714 0.445714 350 +NR_064800 0.040115 0.411429 0.451429 0.491429 350 +NR_055240 0.002967 0.263314 0.473373 0.476331 338 +NR_069706 0.014327 0.308571 0.520000 0.428571 350 +NR_067486 0.042980 0.328571 0.465714 0.457143 350 +NM_069722 0.025788 0.334286 0.434286 0.522857 350 +NR_063336 0.008596 0.260000 0.562857 0.554286 350 +NM_001029192 0.037249 0.408571 0.440000 0.471429 350 |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/promoters/worm.gcbins --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/promoters/worm.gcbins Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -0,0 +1,85 @@ +NR_064002 2 +NR_052929-HOMER3 4 +NR_052929-HOMER2 4 +NR_052929 6 +NR_063434 2 +NR_062450 3 +NM_060137 3 +NR_053268 3 +NR_064753 2 +NM_001026043 3 +NM_065499 3 +NM_062428 4 +NR_000460 5 +NM_001269256 3 +NR_068896 6 +NM_075857 2 +NR_067056 2 +NR_062133 5 +NR_056762 4 +NR_052859 4 +NR_052313 6 +NM_059827 3 +NR_061358 2 +NM_076270 4 +NR_072779 4 +NR_054986 3 +NM_001027488 3 +NR_101537 4 +NM_058660 5 +NR_053707 2 +NM_070191 4 +NM_068710 3 +NM_062964 3 +NR_054788 2 +NR_053482 3 +NM_074947 4 +NR_056512 4 +NR_052598 4 +NR_053722 2 +NR_059860 2 +NM_062049 2 +NM_072537 3 +NR_064976 3 +NM_073455 3 +NM_058653 6 +NM_073761 4 +NR_058631 1 +NR_057197 2 +NM_001038411 4 +NM_059112 3 +NM_066228 3 +NR_057881 4 +NM_064140 4 +NM_063595 3 +NM_069551 3 +NR_101576 5 +NR_059084 1 +NM_066238 4 +NR_072940 6 +NR_058324 2 +NM_073375 4 +NM_060113 5 +NR_057638 2 +NR_062428 2 +NM_066790 4 +NR_069154 5 +NM_001136302 6 +NM_001029452 4 +NR_072003 6 +NM_065510 5 +NM_061802 2 +NM_001129220 4 +NR_052780 5 +NM_001129654 4 +NR_068161 2 +NM_064774 4 +NR_067531 3 +NR_067391 2 +NR_064800 5 +NR_055240 2 +NR_069706 3 +NR_067486 3 +NM_069722 3 +NR_063336 2 +NM_001029192 5 |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/promoters/worm.mask --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/promoters/worm.mask Thu Apr 06 16:22:23 2023 +0000 |
| b |
| b'@@ -0,0 +1,85 @@\n+NR_064002\tNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAAGTTTTGATTGATGTTTTTTTCTAATTTTAGTTGAATACAGTTTCACCATACTGTTAAATAAACTGGGTTTTTCCGATTCAGCACTCGTAGTTGGAATATGATTTCGTGATTTTTATTTCAAAAATTGAAGTTTTGTTTGAATATTGGGTTCTCCAGATGTTTTTTCTTATATGTTAAAAGAAGAGTTTAAGTTACAAGTGAATCAAGTTGTTAGTTTGTGTTGTTACGAAAAACAAATTGTTTGAAAACCAACAAAAATGACATGTTTCTAAACTTTGTTAAACTGAATAAACGTATGGGTTAAAGGTTTTATACCATTCTTTCAGATTGTTCCTAAATGACTGTAATAGTGAAACATATGAGACGTCAAAAACAACTTTGGAACATTAAACGGCGAATGAATACTTTTGAGTTGATATGAATAAATTGAAACAACAAAATTATGTTTGCAGTGAATGAGTTTTCACTACGGCTTGCTAACTTCATCTTGTTAAGAATGAGAAAGTTAACGTTTCTAAACCCTTATATCACATGTGCCGTGAAGTTTGAATTCCCAAATGCCCCCGAAGAATCTAAATTGTTGAAATGGTGACTTTTTCAGTTTTTAAATTTGTGCATTTTTTTAATGACGGTGCAACATTCTATCAGAAAATTTTGCAGGGATACTACATCTCGGGTGTTTGGCATGAAAACGGTATCAAAGTTTCAATTTGAGTAATCGTTAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCTGATCATAGCATATCTCTGAAACATTATTTTTTTTCTAAAAAAAACCCGCACTTTTTGGCTTCAACGCAAAATATAGTTTTTGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTTCACCAAATGCATTTGAGTGTACAAATTATGATTTTATGGTTTTTCCTACATCTTCCATTAGTTTTTCATTTTTCCCTGACAAAATTTGTTTGAATTGTAATTCTGAAAACTCTTTGAAAATCAGCAAGTTAAATACCCATTTTTTTCACCTTTTCGTAAATATTTTTTAAAATCCAATCCCTTCAATTCGACAAAATTCGCCAACAGTGTCATATTTTTAAGTTTCTGTATAATGCGCTCAATATAGGCAGAAAATTCAAATTTTGCGAAAAAACAAAAATTTCTAGAAAAAATTCTGCTGTTTCAAACAGTTTTCATCAGTATTGACTTCAAAAATTTTATTGATGCTTCGAGCGGATAGTTAATTTCCAAAATAACTGTTTTTATGTGAATCCAGTTATAAACTATCGGTTAATGCAGTCCAATTTAAAAAAAGTGAACAGTAGAGCATTTTAAGGCAAAAAACGAATTATCCACGAAATTATTATTAATTTTTTTGTCGTTTCAAGCTGTTTTAAACAGCATTAATTGAACAATTATATCATTTGCATATCCTATAAAGCCATTGTTTTCAATTTATCCTAGATTACTATAGTTGGTAGAAAAACATTAAAATCCAATAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAATCAAAAAAGCAAAATAAATAATGCAATTCTATTCATCGGAAAAAAATCCGGAAAAATATTTAATCGCTGTTTCATATATTTTGTAAATAAACCAGTTCCACTTTTTTGACCAATGACGTAAAAATACTTTCTAACGGAAAATTACTATAGACAGCGCCTTCCAACGTTTAGAACAGTTTTACCGGATTTTTTAACATATGAATGTTTGAACAAGGAACTGGAAAATCCAAATATTTGTTTTTAAAAAATAGCCCAGAATTTGTTTTATTTTTATGAAGAAAATACACATTTTCAATTTTTTTCAGACTTAGGAGCTTCTCGCAAAATCGATAAAGCCAACAAAAAACGGCCAAAATATTTGAGGGCTTCAGGGTTAATTCTTGTTTTTAAGATGCTAATTTTGATCGTGAAATTTCAAACTAATACAAAAAATGATCAGAAAATATTTATCTACAATTTATTGTTTATCAATTTTGAAATTTCTGTTTTCCACGGTTGCTAGAGATACCGCAATATTTGATTTTTCAGGTGACAATGTATTGGGCTGCTAGTTTGCGTCGTAAAAAACATTTAATTGAACAGAAATGTTGAGCAAATATCTTTTAACAAATGTAATAATAAGCTAACAGTGAAATAGTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAACCGCTTCGTTGTACAAATTCGTGCAAATTATTGAAAAAATAGTGCAAAGTGGATGATTTTTAAATTCCGAATAACAATTACAGTTTCAAAAATAATATTTCAACTTTGCAAAAAAAAAATTATGTAACAACCAGATGAGTCCCATAGTGTTGGTTTTTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGCTTGAATCGGGAAGTAAAGTAAAACGCTTTCGAAAATGAAAAAAATAGCAAAAAAAATTTTGAAACATTGAAGCGAAAGTGTGAAAAAAAAGAATTAAAAAATGCATGGCTAAACACTTGACGTCGATGAAATACATACGAAAATTGTTCATTCAAAACATGGGTTGGAAAAATTCTTTTTTTTTTGCTCTATAATAATACTGTTTTGGTGAGCTATCAAAAGTTTGATACAAATCAGTGAAATTAGTTTGATTGTTCTATGGAAAGTATCCGATCAAATAGTTTTTCCAAAATTTCCGTTAAAATCTAAGTGCTCTTTATTACGTTGCACCATACACCATAATTATGGAACCAACAAAAAAAATGTTTCAAAAAATTGCCCTTTGCATACGTCAAAGCACTTCAGGCTGTATGAAATGAATTCTCCTGGACTGAATAAAAAAAACTGAACTTTGTACTCAATATAGCGAAGATCTTTAAAAAAGTGTGCTACTTGAAAACACAGTGAAACAGGTTTGTTTTATGATTCAAGTTTTCGAATTTATATCGCAAGATAAAAATCAAACAGTCGTGATTTTACAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN'..b'GCATACTTCAACATTTTAGAGGTTCAAACATGCAAACTCAGTTTTCTCCGCTTTTCGACTCTAAATATTATTAAATATTGCAAAAGTTTCATTATGATACTTAGACGTTTTAGCACAAAAGGCGTGGTTTTGAACCATTTCACTAAGTCCAAAAACTAAAAATCGCAACAATTGTAATATGCTAATACATATATGAATAGGAGCATTCTCTATTTGAATGTCTAATTGATGCAAATATGTGGACCATAAAAGTATGTTCCTAGGTTCTTCAAACATTCTTTCCAATACCTGTTAGTCCTGCTAAAATTGAAAACTTCTAAAAAATGTTCATTTCCATTTCCCTTTTTTCTCATATGTTCCTCCTACTTGCCCACCTAGACCTCTTGTCACTTTGCGTTCACCTGTCTGTCTTTTGATGTAGTATATGGAACAGTTTTCTTATCCATTCGCTATATCTCCATTACCTTACTCGCCTCTTGTTTCTTTTCTCTCGGAGATATATACCAGATAGACATTTGGCGGGAAAAGGCAAGATGTGCTATGATAGCTACTGATTATGTAGCCGTCAAGAAAAGGAACGCGACCTGTACGCGGGAGGAGGTGAATCCTTATTATACGAGCGCCTGGACACACGGCCAAGGCCAATCCCTGTTCGTGCCGAGAATCTCAACGGGGTAAGATTCACACTCTTATCCGTCACCGCTCTACAATTACTGTAGTTGCTGCGGCGTGTGTAGGCCCAAAAAAATAATACAGATAGATAGAAACTCAACAGTCATACTCAACATTTTCAAAATTTTGGTAGTGTGTGCCCAATTAAAATAGCACATTGAATAGAGATAGTTGAACTTGTTGATGCGGATCGAGAAAACCGGCCTCAAAGCATTGTGTGATTATGGGGTCGAATGGCAGTCAGAAGAGAGGGGGAGCGGGAGCGAGAGAGAGACAAAAATTCGAATATAATAGCGATGTTGGATAGTTTATTCTAGCATTGCGCAACCCGAATCAATTTTACAAAACTGGTTTTGTTGTGGTCGTCCAATAAGAAAAAAGAACACGAGAATCGAAGATGCGCGCAATCCTCAACTCAAGCAATCATGCTGTCTATGGTTTGAGGGCTTTTTTGGTGTATCCCTCGCGTCATTCTATTTTTTTTTGGGTCAGCCGTGTTTGGTAGAAGTTTCCCAACTGTTATTCGCTTGTGTTCTATACTAAAAAAAAGCTTGAACAGCTTGCCCACATCTGTTCCTAAGAGCATCGTGCTTCTATCTAAGACTCGCTTCCAACTTTTTTTTTTCAAAATTGAGAAAGCTAATCAACTCGCAATTGCTAGCCAAAATTGTTGCCACTTACTATCCCGACTGTGCTTGATGCCATTCCCCTCACCCCGTGCGTCCCGTCGCTCACTATCTCTATTCTGCATGGTATGCCCCGCCTCCAAAAATCGGGTAGGCGGGGGGAGTCATAGCCTTCAGCTCGTTCTTGCACTACTGCTTGCCATTTTGTTAGTCCAAGAGCACAGGTCACCGGATTACTGTAGTATTCATTTTAAGATTGCAGAAGCCGTGTGACAAATTTCGATTTTGAATGTTCTGTTATTTTCTCACTTCCTCCTCTCGAGCACTCTTACCTTCCCCGCCATACTTGAGCTACTGTAATGCATTGTCCAATCGCTGCTATGTATGCTTTTTCGCTACTTTTAAACAGTATCAAGTGAGGGTGTAAATACCTGGTTGGTGTCAGCCGGCGACGACCTTCTTGTCTCCGGAGAGAAGAGCTGCGTCTGAATACCTTTTCGAGTGTTGTACGCAAAACTTTTCAAGTAGTGGAGGTCTTGGTAGCCCATCCTACTTGTTCATCTATGAGCGCTCTTTCATTCAAACTGTCCACCGTTTTTTTCTTCTTCCTTGTTAGTGTTTCCTTTCAAATTCGATTTTGTGAAAATTTCAGCACCATTTTCTAAAAGCTTCATCAAATAACAAAAACATTTTTAGACAATGCCCTATCGTGCAGAGCTAAAACGTCCCGATTTGAAAGGCTCATTTCCCTGCTCGATTTGCCAAAAAGTATTCTGCCACAGTTCGTCTCTGAGTCGTCACCGGATGCAGGCTCACTTTAAAAGCTACACCTGTACCACTTGCAACAACGAAATTCCAAGTAAGTTTGAAAATGCAAGTTTGAGAAAAAAAAGAGAAATAGATGAATCAGAGTAGCAGGAGCTTGACTAACAATAGGGGAGAAAGAGCGAAACAATTTATGCCGCTATTGATGTTTTCACAGTTTTGTATCATGTTTTATCATATGATAATAAGAAAAAAGAGAGGGAAACTTAACTCGAGAACATAGCTATTGTTGAATTGTACGGAACTTATTCTATTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGGTTCTAGGTGATGTTTAACTTTCTAATTTATTTTTTCAAAATTGAATTAAAATTCTGAACGAATGTTCTATTTCCTGCTGCATTTAGTTTCTGTCTTCTACCAGTTTATTGCATTTCTACATTTTTCTAATCTCCCTCCCAATACATTTATTTGATCGGAAGTCTCCATAATCTGAAATGCGCGAAAGCTCAGTGGCATTGTTTACTGACAAGCTTAAACTCAACTCACACCCTCCGATTAGCACGTGGCTATATTGGGCATGTGTCAAACAAGGTTGATACAGTCTCCTTCTTTCCGCCAAAAAATTACATTGGTTATCTAAATATTGACACCCTTTCCAACTACTACTGTATTCTTAATTGTAGACATCTATATGGCATGGCAAACTGAATGAGGAGGTGTGCAAATACCGAGATAGCTCCGACTGTCAATTAGGAGTATCTATTTAGTAATATCTGTTAAGCTTTTAAAACAACCATGTGCACTTTTGGACTAGTAGCAAAAAGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATTATTGACAGTCAAAAAGTGGCAATAACTGTGTTCTTGCCACTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGAATATTTATATTTGAAAAATATGTAGGCGACTGTTTATCGACGACTTTCAAAAAAGTAATTACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTAGCGTCGTTTGGCAAATTCGGCGTTATTTTTTTTCAATTTCCCACTGGAGCGTCTCCAGCTATAATGGAAAGCAGTATCATGTATTAAATAATAACAAATTGACTCTAATATTTGTGCAAGAATCTTTTGAAAAGACACCTCTGACCATATTACGCCACAGTTTTACAATAACACGTCTGCTATTTGCATTGTCTAATTGCCCCATCTTTCCATCCCGAGCGGCTTCCTAAGAGAGCGAGAGGCATAAATAACCGACGGTATGTATGTATTACTTAATGGTTTCTTTTCTTGGAATGGAAGGTAGGATGAACCTCCAAGGTCAGTCATTTGATGACCATCCATCAGCTAATTGTTGGCACGCCACTGTCGCTAAGTGAGCTTGAGAGCGAAGAATAGGGCCAGCGCGCGGGCAAAGTAAAAAAAAAACCACCGATTGTCTTCTTTCCCCATCTTCCGCAACAAAAATTGCAACCTCTTCTTTTTCTACCACCTTTCCAACATTACAATTTATTGGTTGTTCACTCGCCGTCAATCATTTGTTACGGTTCGCTGAGCATGGGGGTCGTTCAAGAAACTTTCGGCCAAAGCACCCAGCTTTTTTCACACCTTACTTCACCGCTCGCCTATACGTGGAATCCATACGGCGGCATGTTAGCAGGCAGATCAACAGGATTTGTTATATTACTCGTGCGCAATCCAACAATAAGCGGATCAACCAGTAGAATACCGAAACATAACATGAAAATGTTTTACAGCCTGACCCCTGCGTTTGTCGTTTTTTTTTGTGTTACTGCTTTGTCG\n' |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/promoters/worm.pos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/promoters/worm.pos Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -0,0 +1,85 @@ +NR_064002 chrIV 15730234 15734234 0 +NR_052929 chrIII 1652496 1656496 1 +NR_052929-HOMER2 chrIII 93973 97973 1 +NR_052929-HOMER3 chrII 11063272 11067272 0 +NR_063434 chrIV 15582788 15586788 0 +NR_062450 chrIV 15294372 15298372 0 +NM_060137 chrI 9574349 9578349 0 +NR_053268 chrIV 4881676 4885676 1 +NR_064753 chrIV 15911881 15915881 0 +NM_001026043 chrIII 9317957 9321957 0 +NM_065499 chrIII 4427471 4431471 1 +NM_062428 chrII 4679319 4683319 1 +NR_000460 chrV 5595434 5599434 1 +NM_001269256 chrV 10132674 10136674 0 +NR_068896 chrV 6357694 6361694 1 +NM_075857 chrX 1391982 1395982 1 +NR_067056 chrIV 16615511 16619511 0 +NR_062133 chrIV 15217414 15221414 1 +NR_056762 chrIV 12120603 12124603 1 +NR_052859 chrIV 144729 148729 0 +NR_052313 chrIII 5514279 5518279 1 +NM_059827 chrI 8123802 8127802 0 +NR_061358 chrIV 14967730 14971730 0 +NM_076270 chrX 3882243 3886243 0 +NR_072779 chrX 15625971 15629971 1 +NR_054986 chrIV 5950304 5954304 1 +NM_001027488 chrIII 6880201 6884201 0 +NR_101537 chrI 3409467 3413467 1 +NM_058660 chrI 2874304 2878304 1 +NR_053707 chrIV 5177815 5181815 0 +NM_070191 chrIV 13443242 13447242 1 +NM_068710 chrIV 7106210 7110210 0 +NM_062964 chrII 6703402 6707402 1 +NR_054788 chrIV 5855979 5859979 0 +NR_053482 chrIV 5045232 5049232 0 +NM_074947 chrV 17176733 17180733 0 +NR_056512 chrIV 10187131 10191131 0 +NR_052598 chrIII 9240647 9244647 1 +NR_053722 chrIV 5193437 5197437 0 +NR_059860 chrIV 14551805 14555805 1 +NM_062049 chrII 3112293 3116293 0 +NM_072537 chrV 7527098 7531098 0 +NR_064976 chrIV 15973505 15977505 1 +NM_073455 chrV 11242821 11246821 0 +NM_058653 chrI 2831255 2835255 1 +NM_073761 chrV 12647940 12651940 0 +NR_058631 chrIV 14223531 14227531 0 +NR_057197 chrIV 13709454 13713454 1 +NM_001038411 chrV 7398166 7402166 1 +NM_059112 chrI 5066831 5070831 1 +NM_066228 chrIII 7365047 7369047 1 +NR_057881 chrIV 13946882 13950882 1 +NM_064140 chrII 11904521 11908521 0 +NM_063595 chrII 9371538 9375538 0 +NM_069551 chrIV 10553629 10557629 0 +NR_101576 chrI 7137383 7141383 1 +NR_059084 chrIV 14347712 14351712 0 +NM_066238 chrIII 7454884 7458884 0 +NR_072940 chrX 17199767 17203767 0 +NR_058324 chrIV 14098665 14102665 1 +NM_073375 chrV 10892908 10896908 0 +NM_060113 chrI 9472771 9476771 1 +NR_057638 chrIV 13866443 13870443 1 +NR_062428 chrIV 15285030 15289030 1 +NM_066790 chrIII 9889243 9893243 1 +NR_069154 chrV 9089601 9093601 1 +NM_001136302 chrI 14303058 14307058 0 +NM_001029452 chrX 14874096 14878096 0 +NR_072003 chrX 10592053 10596053 0 +NM_065510 chrIII 4475490 4479490 1 +NM_061802 chrII 2164466 2168466 1 +NM_001129220 chrIII 8626416 8630416 1 +NR_052780 chrIII 11886455 11890455 0 +NM_001129654 chrX 4115927 4119927 0 +NR_068161 chrIV 17047732 17051732 1 +NM_064774 chrIII 188996 192996 0 +NR_067531 chrIV 16786239 16790239 1 +NR_067391 chrIV 16716013 16720013 0 +NR_064800 chrIV 15921688 15925688 0 +NR_055240 chrIV 6061520 6065520 1 +NR_069706 chrV 12219404 12223404 1 +NR_067486 chrIV 16770082 16774082 1 +NM_069722 chrIV 11304681 11308681 1 +NR_063336 chrIV 15564688 15568688 1 +NM_001029192 chrX 4552668 4556668 0 |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/promoters/worm.redun --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/promoters/worm.redun Thu Apr 06 16:22:23 2023 +0000 |
| b |
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| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/data/promoters/worm.seq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/data/promoters/worm.seq Thu Apr 06 16:22:23 2023 +0000 |
| b |
| b'@@ -0,0 +1,85 @@\n+NR_064002\tNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAAGTTTTGATTGATGTTTTTTTCTAATTTTAGTTGAATACAGTTTCACCATACTGTTAAATAAACTGGGTTTTTCCGATTCAGCACTCGTAGTTGGAATATGATTTCGTGATTTTTATTTCAAAAATTGAAGTTTTGTTTGAATATTGGGTTCTCCAGATGTTTTTTCTTATATGTTAAAAGAAGAGTTTAAGTTACAAGTGAATCAAGTTGTTAGTTTGTGTTGTTACGAAAAACAAATTGTTTGAAAACCAACAAAAATGACATGTTTCTAAACTTTGTTAAACTGAATAAACGTATGGGTTAAAGGTTTTATACCATTCTTTCAGATTGTTCCTAAATGACTGTAATAGTGAAACATATGAGACGTCAAAAACAACTTTGGAACATTAAACGGCGAATGAATACTTTTGAGTTGATATGAATAAATTGAAACAACAAAATTATGTTTGCAGTGAATGAGTTTTCACTACGGCTTGCTAACTTCATCTTGTTAAGAATGAGAAAGTTAACGTTTCTAAACCCTTATATCACATGTGCCGTGAAGTTTGAATTCCCAAATGCCCCCGAAGAATCTAAATTGTTGAAATGGTGACTTTTTCAGTTTTTAAATTTGTGCATTTTTTTAATGACGGTGCAACATTCTATCAGAAAATTTTGCAGGGATACTACATCTCGGGTGTTTGGCATGAAAACGGTATCAAAGTTTCAATTTGAGTAATCGTTAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNCTCTGATCATAGCATATCTCTGAAACATTATTTTTTTTCTAAAAAAAACCCGCACTTTTTGGCTTCAACGCAAAATATAGTTTTTGCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTTTCACCAAATGCATTTGAGTGTACAAATTATGATTTTATGGTTTTTCCTACATCTTCCATTAGTTTTTCATTTTTCCCTGACAAAATTTGTTTGAATTGTAATTCTGAAAACTCTTTGAAAATCAGCAAGTTAAATACCCATTTTTTTCACCTTTTCGTAAATATTTTTTAAAATCCAATCCCTTCAATTCGACAAAATTCGCCAACAGTGTCATATTTTTAAGTTTCTGTATAATGCGCTCAATATAGGCAGAAAATTCAAATTTTGCGAAAAAACAAAAATTTCTAGAAAAAATTCTGCTGTTTCAAACAGTTTTCATCAGTATTGACTTCAAAAATTTTATTGATGCTTCGAGCGGATAGTTAATTTCCAAAATAACTGTTTTTATGTGAATCCAGTTATAAACTATCGGTTAATGCAGTCCAATTTAAAAAAAGTGAACAGTAGAGCATTTTAAGGCAAAAAACGAATTATCCACGAAATTATTATTAATTTTTTTGTCGTTTCAAGCTGTTTTAAACAGCATTAATTGAACAATTATATCATTTGCATATCCTATAAAGCCATTGTTTTCAATTTATCCTAGATTACTATAGTTGGTAGAAAAACATTAAAATCCAATAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAATCAAAAAAGCAAAATAAATAATGCAATTCTATTCATCGGAAAAAAATCCGGAAAAATATTTAATCGCTGTTTCATATATTTTGTAAATAAACCAGTTCCACTTTTTTGACCAATGACGTAAAAATACTTTCTAACGGAAAATTACTATAGACAGCGCCTTCCAACGTTTAGAACAGTTTTACCGGATTTTTTAACATATGAATGTTTGAACAAGGAACTGGAAAATCCAAATATTTGTTTTTAAAAAATAGCCCAGAATTTGTTTTATTTTTATGAAGAAAATACACATTTTCAATTTTTTTCAGACTTAGGAGCTTCTCGCAAAATCGATAAAGCCAACAAAAAACGGCCAAAATATTTGAGGGCTTCAGGGTTAATTCTTGTTTTTAAGATGCTAATTTTGATCGTGAAATTTCAAACTAATACAAAAAATGATCAGAAAATATTTATCTACAATTTATTGTTTATCAATTTTGAAATTTCTGTTTTCCACGGTTGCTAGAGATACCGCAATATTTGATTTTTCAGGTGACAATGTATTGGGCTGCTAGTTTGCGTCGTAAAAAACATTTAATTGAACAGAAATGTTGAGCAAATATCTTTTAACAAATGTAATAATAAGCTAACAGTGAAATAGTCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCAACCGCTTCGTTGTACAAATTCGTGCAAATTATTGAAAAAATAGTGCAAAGTGGATGATTTTTAAATTCCGAATAACAATTACAGTTTCAAAAATAATATTTCAACTTTGCAAAAAAAAAATTATGTAACAACCAGATGAGTCCCATAGTGTTGGTTTTTANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGCTTGAATCGGGAAGTAAAGTAAAACGCTTTCGAAAATGAAAAAAATAGCAAAAAAAATTTTGAAACATTGAAGCGAAAGTGTGAAAAAAAAGAATTAAAAAATGCATGGCTAAACACTTGACGTCGATGAAATACATACGAAAATTGTTCATTCAAAACATGGGTTGGAAAAATTCTTTTTTTTTTGCTCTATAATAATACTGTTTTGGTGAGCTATCAAAAGTTTGATACAAATCAGTGAAATTAGTTTGATTGTTCTATGGAAAGTATCCGATCAAATAGTTTTTCCAAAATTTCCGTTAAAATCTAAGTGCTCTTTATTACGTTGCACCATACACCATAATTATGGAACCAACAAAAAAAATGTTTCAAAAAATTGCCCTTTGCATACGTCAAAGCACTTCAGGCTGTATGAAATGAATTCTCCTGGACTGAATAAAAAAAACTGAACTTTGTACTCAATATAGCGAAGATCTTTAAAAAAGTGTGCTACTTGAAAACACAGTGAAACAGGTTTGTTTTATGATTCAAGTTTTCGAATTTATATCGCAAGATAAAAATCAAACAGTCGTGATTTTACAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN'..b'GCATACTTCAACATTTTAGAGGTTCAAACATGCAAACTCAGTTTTCTCCGCTTTTCGACTCTAAATATTATTAAATATTGCAAAAGTTTCATTATGATACTTAGACGTTTTAGCACAAAAGGCGTGGTTTTGAACCATTTCACTAAGTCCAAAAACTAAAAATCGCAACAATTGTAATATGCTAATACATATATGAATAGGAGCATTCTCTATTTGAATGTCTAATTGATGCAAATATGTGGACCATAAAAGTATGTTCCTAGGTTCTTCAAACATTCTTTCCAATACCTGTTAGTCCTGCTAAAATTGAAAACTTCTAAAAAATGTTCATTTCCATTTCCCTTTTTTCTCATATGTTCCTCCTACTTGCCCACCTAGACCTCTTGTCACTTTGCGTTCACCTGTCTGTCTTTTGATGTAGTATATGGAACAGTTTTCTTATCCATTCGCTATATCTCCATTACCTTACTCGCCTCTTGTTTCTTTTCTCTCGGAGATATATACCAGATAGACATTTGGCGGGAAAAGGCAAGATGTGCTATGATAGCTACTGATTATGTAGCCGTCAAGAAAAGGAACGCGACCTGTACGCGGGAGGAGGTGAATCCTTATTATACGAGCGCCTGGACACACGGCCAAGGCCAATCCCTGTTCGTGCCGAGAATCTCAACGGGGTAAGATTCACACTCTTATCCGTCACCGCTCTACAATTACTGTAGTTGCTGCGGCGTGTGTAGGCCCAAAAAAATAATACAGATAGATAGAAACTCAACAGTCATACTCAACATTTTCAAAATTTTGGTAGTGTGTGCCCAATTAAAATAGCACATTGAATAGAGATAGTTGAACTTGTTGATGCGGATCGAGAAAACCGGCCTCAAAGCATTGTGTGATTATGGGGTCGAATGGCAGTCAGAAGAGAGGGGGAGCGGGAGCGAGAGAGAGACAAAAATTCGAATATAATAGCGATGTTGGATAGTTTATTCTAGCATTGCGCAACCCGAATCAATTTTACAAAACTGGTTTTGTTGTGGTCGTCCAATAAGAAAAAAGAACACGAGAATCGAAGATGCGCGCAATCCTCAACTCAAGCAATCATGCTGTCTATGGTTTGAGGGCTTTTTTGGTGTATCCCTCGCGTCATTCTATTTTTTTTTGGGTCAGCCGTGTTTGGTAGAAGTTTCCCAACTGTTATTCGCTTGTGTTCTATACTAAAAAAAAGCTTGAACAGCTTGCCCACATCTGTTCCTAAGAGCATCGTGCTTCTATCTAAGACTCGCTTCCAACTTTTTTTTTTCAAAATTGAGAAAGCTAATCAACTCGCAATTGCTAGCCAAAATTGTTGCCACTTACTATCCCGACTGTGCTTGATGCCATTCCCCTCACCCCGTGCGTCCCGTCGCTCACTATCTCTATTCTGCATGGTATGCCCCGCCTCCAAAAATCGGGTAGGCGGGGGGAGTCATAGCCTTCAGCTCGTTCTTGCACTACTGCTTGCCATTTTGTTAGTCCAAGAGCACAGGTCACCGGATTACTGTAGTATTCATTTTAAGATTGCAGAAGCCGTGTGACAAATTTCGATTTTGAATGTTCTGTTATTTTCTCACTTCCTCCTCTCGAGCACTCTTACCTTCCCCGCCATACTTGAGCTACTGTAATGCATTGTCCAATCGCTGCTATGTATGCTTTTTCGCTACTTTTAAACAGTATCAAGTGAGGGTGTAAATACCTGGTTGGTGTCAGCCGGCGACGACCTTCTTGTCTCCGGAGAGAAGAGCTGCGTCTGAATACCTTTTCGAGTGTTGTACGCAAAACTTTTCAAGTAGTGGAGGTCTTGGTAGCCCATCCTACTTGTTCATCTATGAGCGCTCTTTCATTCAAACTGTCCACCGTTTTTTTCTTCTTCCTTGTTAGTGTTTCCTTTCAAATTCGATTTTGTGAAAATTTCAGCACCATTTTCTAAAAGCTTCATCAAATAACAAAAACATTTTTAGACAATGCCCTATCGTGCAGAGCTAAAACGTCCCGATTTGAAAGGCTCATTTCCCTGCTCGATTTGCCAAAAAGTATTCTGCCACAGTTCGTCTCTGAGTCGTCACCGGATGCAGGCTCACTTTAAAAGCTACACCTGTACCACTTGCAACAACGAAATTCCAAGTAAGTTTGAAAATGCAAGTTTGAGAAAAAAAAGAGAAATAGATGAATCAGAGTAGCAGGAGCTTGACTAACAATAGGGGAGAAAGAGCGAAACAATTTATGCCGCTATTGATGTTTTCACAGTTTTGTATCATGTTTTATCATATGATAATAAGAAAAAAGAGAGGGAAACTTAACTCGAGAACATAGCTATTGTTGAATTGTACGGAACTTATTCTATTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGGGTTCTAGGTGATGTTTAACTTTCTAATTTATTTTTTCAAAATTGAATTAAAATTCTGAACGAATGTTCTATTTCCTGCTGCATTTAGTTTCTGTCTTCTACCAGTTTATTGCATTTCTACATTTTTCTAATCTCCCTCCCAATACATTTATTTGATCGGAAGTCTCCATAATCTGAAATGCGCGAAAGCTCAGTGGCATTGTTTACTGACAAGCTTAAACTCAACTCACACCCTCCGATTAGCACGTGGCTATATTGGGCATGTGTCAAACAAGGTTGATACAGTCTCCTTCTTTCCGCCAAAAAATTACATTGGTTATCTAAATATTGACACCCTTTCCAACTACTACTGTATTCTTAATTGTAGACATCTATATGGCATGGCAAACTGAATGAGGAGGTGTGCAAATACCGAGATAGCTCCGACTGTCAATTAGGAGTATCTATTTAGTAATATCTGTTAAGCTTTTAAAACAACCATGTGCACTTTTGGACTAGTAGCAAAAAGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATTATTGACAGTCAAAAAGTGGCAATAACTGTGTTCTTGCCACTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTGAATATTTATATTTGAAAAATATGTAGGCGACTGTTTATCGACGACTTTCAAAAAAGTAATTACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGTAGCGTCGTTTGGCAAATTCGGCGTTATTTTTTTTCAATTTCCCACTGGAGCGTCTCCAGCTATAATGGAAAGCAGTATCATGTATTAAATAATAACAAATTGACTCTAATATTTGTGCAAGAATCTTTTGAAAAGACACCTCTGACCATATTACGCCACAGTTTTACAATAACACGTCTGCTATTTGCATTGTCTAATTGCCCCATCTTTCCATCCCGAGCGGCTTCCTAAGAGAGCGAGAGGCATAAATAACCGACGGTATGTATGTATTACTTAATGGTTTCTTTTCTTGGAATGGAAGGTAGGATGAACCTCCAAGGTCAGTCATTTGATGACCATCCATCAGCTAATTGTTGGCACGCCACTGTCGCTAAGTGAGCTTGAGAGCGAAGAATAGGGCCAGCGCGCGGGCAAAGTAAAAAAAAAACCACCGATTGTCTTCTTTCCCCATCTTCCGCAACAAAAATTGCAACCTCTTCTTTTTCTACCACCTTTCCAACATTACAATTTATTGGTTGTTCACTCGCCGTCAATCATTTGTTACGGTTCGCTGAGCATGGGGGTCGTTCAAGAAACTTTCGGCCAAAGCACCCAGCTTTTTTCACACCTTACTTCACCGCTCGCCTATACGTGGAATCCATACGGCGGCATGTTAGCAGGCAGATCAACAGGATTTGTTATATTACTCGTGCGCAATCCAACAATAAGCGGATCAACCAGTAGAATACCGAAACATAACATGAAAATGTTTTACAGCCTGACCCCTGCGTTTGTCGTTTTTTTTTGTGTTACTGCTTTGTCG\n' |
| b |
| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/homerResults_fasta.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/homerResults_fasta.html Thu Apr 06 16:22:23 2023 +0000 |
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| b'@@ -0,0 +1,637 @@\n+<HTML><HEAD><TITLE>.// - Homer de novo Motif Results</TITLE></HEAD>\n+<BODY>\n+<H1>Homer <i>de novo</i> Motif Results (.//)</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 = 15<BR/>\n+Total background sequences = 68<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(0.59,0,0,0.001,0,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,0,48.95)">G</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.271,2,48.9)">A</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.727,1,35.35)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,27,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,25,48.95)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.223,25,48.9)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.775,26,37.75)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" 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transform="matrix(0.65,0,0,'..b'276,48.9)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.997,277,48.85)">A</text>\n+ \n+ </g>\n+</svg>\n+</TD><TD>1e-3</TD><TD>-7.120e+00</TD><TD>40.00%</TD><TD>4.41%</TD><TD>82.9bp (107.9bp)</TD><TD>RLR1?/SacCer-Promoters/Homer(0.799)<BR/><A target="_blank" HREF="homerResults/motif10.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif10.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif10.motif">motif file (matrix)</A></TD></TR>\n+<TR><TD>11\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(0.53,0,0,0.001,2,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.072,0,48.95)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.325,1,45.35)">T</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.602,0,29.1)">G</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,25,49)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.180,26,48.95)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.217,27,39.95)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.602,25,29.1)">G</text>\n+ \n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,50,49)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.010,51,48.95)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.108,52,48.45)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.881,50,43.05)">C</text>\n+ \n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,76,49)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.108,75,48.95)">C</text>\n+ <text fill="#00BB00" x="0" y="0" 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transform="matrix(0.55,0,0,0.109,150,48.5)">G</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.227,152,43.05)">A</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.654,151,31.7)">T</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,175,49)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.118,176,48.95)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.217,177,43.05)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.664,175,32.2)">G</text>\n+ \n+ </g>\n+</svg>\n+</TD><TD>1e-2</TD><TD>-5.714e+00</TD><TD>26.67%</TD><TD>1.47%</TD><TD>125.4bp (0.0bp)</TD><TD>brk/dmmpmm(Papatsenko)/fly(0.807)<BR/><A target="_blank" HREF="homerResults/motif11.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif11.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif11.motif">motif file (matrix)</A></TD></TR>\n+</TABLE>\n+<P></P>\n+</BODY></HTML>\n' |
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| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/homerResults_id.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/homerResults_id.html Thu Apr 06 16:22:23 2023 +0000 |
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| b'@@ -0,0 +1,637 @@\n+<HTML><HEAD><TITLE>.// - Homer de novo Motif Results</TITLE></HEAD>\n+<BODY>\n+<H1>Homer <i>de novo</i> Motif Results (.//)</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 = 15<BR/>\n+Total background sequences = 68<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(0.59,0,0,0.001,0,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,0,48.95)">G</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.271,2,48.9)">A</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.727,1,35.35)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,27,49)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,25,48.95)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.223,25,48.9)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.775,26,37.75)">T</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" 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y="0" transform="matrix(0.55,0,0,0.602,0,29.1)">G</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,25,49)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.180,26,48.95)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.217,27,39.95)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.602,25,29.1)">G</text>\n+ \n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,50,49)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.010,51,48.95)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.108,52,48.45)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.881,50,43.05)">C</text>\n+ \n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,76,49)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.108,75,48.95)">C</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.217,77,43.55)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.674,75,32.7)">G</text>\n+ \n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,100,49)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,101,48.95)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.009,102,48.9)">A</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.989,100,48.45)">C</text>\n+ \n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.001,127,49)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.001,125,48.95)">G</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.001,126,48.9)">T</text>\n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.997,125,48.85)">C</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.010,150,49)">C</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.109,150,48.5)">G</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.227,152,43.05)">A</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.654,151,31.7)">T</text>\n+ \n+ <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.001,175,49)">C</text>\n+ <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.118,176,48.95)">T</text>\n+ <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.217,177,43.05)">A</text>\n+ <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.664,175,32.2)">G</text>\n+ \n+ </g>\n+</svg>\n+</TD><TD>1e-2</TD><TD>-5.714e+00</TD><TD>26.67%</TD><TD>1.47%</TD><TD>125.4bp (0.0bp)</TD><TD>POL006.1_BREu/Jaspar(0.723)<BR/><A target="_blank" HREF="homerResults/motif11.info.html">More Information</A> | <A target="blank" HREF="homerResults/motif11.similar.html">Similar Motifs Found</A></TD><TD><A target="_blank" HREF="homerResults/motif11.motif">motif file (matrix)</A></TD></TR>\n+</TABLE>\n+<P></P>\n+</BODY></HTML>\n' |
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| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/knownResults_fasta.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/knownResults_fasta.html Thu Apr 06 16:22:23 2023 +0000 |
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| @@ -0,0 +1,95 @@ +<HTML><HEAD><TITLE>./ - Homer Known Motif Enrichment Results</TITLE></HEAD> +<BODY> +<H1>Homer Known Motif Enrichment Results (./)</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 = 15, Total Background Sequences = 68</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> +<TR><TD>1</TD><TD> +<svg width="380" height="50"> + <g font-family="Arial" font-weight="bold" font-size="66.5"> + <text fill="#F9A500" x="0" y="0" 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transform="matrix(0.59,0,0,0.033,275,49)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.035,276,47.35)">T</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.065,277,45.6)">A</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.867,275,42.35)">G</text> + + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.028,301,49)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.048,300,47.6)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.136,300,45.2)">G</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.788,302,38.4)">A</text> + + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.039,326,49)">T</text> + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.041,325,47.05)">C</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.053,325,45)">G</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.867,327,42.35)">A</text> + + <text fill="#0000EE" x="0" y="0" transform="matrix(0.59,0,0,0.175,350,49)">C</text> + <text fill="#DD0000" x="0" y="0" transform="matrix(0.65,0,0,0.190,351,40.25)">T</text> + <text fill="#F9A500" x="0" y="0" transform="matrix(0.55,0,0,0.222,350,30.75)">G</text> + <text fill="#00BB00" x="0" y="0" transform="matrix(0.53,0,0,0.412,352,19.65)">A</text> + + </g> +</svg> + +</TD><TD>Bcl6(Zf)/Liver-Bcl6-ChIP-Seq(GSE31578)/Homer</TD><TD>1e-2</TD><TD>-5.538e+00</TD><TD>1.0000</TD><TD>9.0</TD><TD>60.00%</TD><TD>14.0</TD><TD>20.59%</TD><TD><A target="_blank" HREF="knownResults//known1.motif">motif file (matrix)</A></TD> +<TD><A HREF="knownResults//known1.logo.svg">svg</A></TD> +</TR> +</TABLE></BODY></HTML> |
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| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/knownResults_id.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/knownResults_id.html Thu Apr 06 16:22:23 2023 +0000 |
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| @@ -0,0 +1,11 @@ +<HTML><HEAD><TITLE>./ - Homer Known Motif Enrichment Results</TITLE></HEAD> +<BODY> +<H1>Homer Known Motif Enrichment Results (./)</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 = 15, Total Background Sequences = 68</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 a8f207b43f64 -r 4fe92af4542b test-data/demoDB/target.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/target.fa Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -0,0 +1,75 @@ +>NR_064002 +CTACATCTTCCATTAGTTTTTCATTTTTCCCTGACAAAATTTGTTTGAATTGTAATTCTGAAAACTCTTTGAAAATCAGCAAGTTAAATACCCATTTTTT +TCACCTTTTCGTAAATATTTTTTAAAATCCAATCCCTTCAATTCGACAAAATTCGCCAACAGTGTCATATTTTTAAGTTTCTGTATAATGCGCTCAATAT +AGGCAGAAAATTCAAATTTTGCGAAAAAACAAAAATTTCTAGAAAAAATTCTGCTGTTTCAAACAGTTTTCATCAGTATTGACTTCAAAAATTTTATTGA +TGCTTCGAGCGGATAGTTAATTTCCAAAATAACTGTTTTTATGTGAATCC +>NR_052929 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCACACCCCGACCCCAAATAACTAG +GTTGGGTCCCGCCACGAAAACTTTGGTTTAAAGGCGCACAACTCATTAAA +>NR_063434 +AAAAAAACTGACAGAAAAAGAAAAGTCTTGCCTAGAATGTACTAGGCTAGATTGTAGATAGGTAGGCAGGCACCAGTGCCTAAAATGCAAAATAAAAGTT +CAAGGTTTTTTGCTTCAAATGTTTCGAGTTTAATAAAATCACAAACTTTTGGGATAAATAAAAAACCAGTTTTTTTGTTAATTTCTATTTGTTACACACA +AAAATGGCATAAAAAATACACGGTCACACACTATAAATTTGAAGTTTTTATTAACTGTTTCACTGTGGTTTTTTAAATTTCAACATTTTATAAAATTTAT +TCATAAATCAATCCATGTACGAAAACCAAATAGTCAAAAAAAGCTGAAAA +>NR_062450 +AGGCAGGTACATCTTCTGGCGCCTGCCAGTCGCCTACTCATTTGCAGTTTTTTGTGAAATTTGGTGTCAGTAGAGATTTACTAGTTTTCAAATTTTTTTT +TGGTAACTGAGTTAGCGAATAGAAAAGTTCGCAAGGTAGGCAAGAATTTTTATCTCCACATTATGCAACTCATGTACTCATTATTTGCAGAAATATTGAA +TAAATACGCTGAAATACTTGAAATTAGATTCNNNNNNNNNNNNNNNNNNNNNNCAGTTTCACAAAGTTATTTAATAAGTTCTTAGATTTTTAATTTTTAC +TGGAAGATCCTGGATTTTAACTGGTCATTCAAATTTCTGATGTTACTATA +>NM_060137 +CAAAAGTGAAATTTGTAAAACTTACAATGTTAAGTTGCGCGTCCAAGAGTAAAAGTTGCGAAATAACAAGGTTTTGGAAGGTAATGATTATTTTGATGCG +TTTCTATTTTATTTAATTTTTTTAGAACACGCAGTTTATTGGATGACAAATCGAAAAATAGGCTTGCATGTAATGTACTAATAGGAAAAATGCGCTAATA +ATTTAAACAAGCATTATTCTTATTACACGTGCAACGCTTCACAAAAAACCTTTCAATAAAGAGCTTGTCAACTGCAAGTTTGCGACTATCGACGCTATCA +ATGGACGTTCAAGATATCATTGGAATTGCTTTGATCTTGGCAACTGCCGG +>NR_053268 +GCATGATTTGTCACATTTTCTGGACAGCAAAGGGAAGATCNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTATTTCAGTAATTTTACTTCAAATTTCACGA +AAAATATAAGCAAGAAACGGAGAAATAAATCACTATCTCGTAGATCAATCTACATTAAGCAAAATACAAAACCTTATTTTCCGCTCAAATTGCACAAAAC +CTAATTTTCTAGAAGCTGTTAAAATGTGAATACAAGGAACAATAACAAAAGATATTGTTTCGGTAGCTATACGAAAAAGGAAGGAAATTCATCAAATAGC +TGTCTAGAGTGGGGATAAGAGACAGAAGAATGTGATTCAGAACTGCAAAT +>NR_064753 +ATATGCCTAAAAAAAGCTAATATGCCTAAAACTTTGAAATTGTTTTTCGTGGCTTATGAATAAAATTTAGTAATTACAGTTCCGGTGCGTTATCATTAGA +TGAGTGGTTAAAACATACTGTTTTGTGTAACTGCCTTTAAGGCAACCTACGCCTGTCTTGCACCTAGAGCTTTTCTATACGCAAAAAAAATAATATTTGC +AGTGTTTATAACGCGAACACCACTTTCGAAAATTATGCCTATTTGAAAAAAAATCCACTGTTTCAATAGGTTATCAATTGATGAAGCAAAAGAAAATAAT +TATTCAATGATAGTTACAATTAAACCAATAAAATGTATTTAATACATATT +>NM_001026043 +ACTGAACCTGAAATTTGAACAAATATTTCTAAAAAAAAGCTGGTAAAAGTAAAAGTAATTATTTGTTGAAAAGATTTCAGTAAACCTAAAGTTTAGTGTT +CTAGTCAACCAACAGGTCTGTTTGAATAGATGAGTACATACACACAACGTGGTATTCATATAAAACTTGTTTTTCTTCATTCTTATCACTTTCTCATTGA +CCATTAGTCTTGAAGAGTTGATCGAAAAGAAGAGCCGTCCTGGTATCATTTTATCATTTATTGTACTCATCATTGTTGAATTTTCTCCAAACGATCAAAA +ATGATAGTTTTATTTCTGCTTTTTCTTATTTCGCTCGGAATTTATCCATT +>NM_065499 +TAAGTACTATTCACACACAATTATCTATTTTCAGCTGCAATTCATGTACCGAAACGAGCTACACACGTATATGTGAGAGATCGACATAATTTTCATACAC +GTTCTCTATTTTTATCCGCTCCCAATTTTCAAAAAATTTGGTGTATTATTTTGTTCCAATTATAATAAAATTATCTACGCTTAAACTGTTTTATTTCTTA +CTTGACATTCCCTTTAATTTCAAAGTTCAATAATTTAAACTTTCACGTCCTTAGGCCTAACACTTCTTCTTGTATAGTTTTAATTTATTTCTTGATTAGA +ATGGATTTTCCTTTCGAATATGTGGAACGAGCGATCACTTATCCAAGTTT +>NM_062428 +CCGAGAATCTCTTCCCAATTTACGGTTCATCACCTGTTCATTCTCTTCCCACAACCTAACCGGATTCGTCACATAATTGCTCTCGCCTGTCATTCTGTTA +CTTTCTGTCTCTTTTCCGACTACTCACTTGTCAACAAGTTTCTCTTGTTGAGGTTACGTAATTCTTCTCCATAATTTTCGACAAATTTGGTGTTTTTTGT +GGTTTCGTTTTCTCAAGAGGTGTAATTATTTTCGAACCTCTCGTGGTCTCAAGATTTGGTCAGTTAATTGAGAAGCAAGAAAAACACATTTCAAGAAAGG +ATGCCAATATTGAAAAATGTTTTTCAATTTTTGACAGTTACAAGCTTTAT +>NR_000460 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGGATCCCGTTCATTTGTCAGAAGAAAAG +TCTTTTGAGCTAAGCAGCTCGACCATGGTCTTCAACGGAGATCAAGACAA +>NM_001269256 +TTGAATTTTTATCCGTTTTTCTTGAAAGTTTTTCTGGATGTAAAATGTTTTTTTGAGAAAAATTAACAATTCATAGTGNNNNNNNNNNNNNNNNNNNNNN +GTTAAACTCTAAATTTCGATACCTACATGTTATCTGTTCTTTTTTACGCATTTGGAAACGCGGGTATTTAATATATTATGAAAAACAGTCTACGTATTGC +CTAATATGATTATTTTTCCTCATCTTCATCCGCAATGTTTTCAGAGTGCATGCTAGGAGCTCTTTTAAAGTCAATCAATATACCTATCAGCCGACGCGCA +ATGTCTACACTCTACCATACCTGTGACAAAATCGAGCAACGAATCATTTG +>NR_068896 +TGTGGCTATTTCGGAAATACGCGGTCAGTCTGTGGACTCCACTTATTGCCATTACTTCTTCTCTAGAGTTGTTTACACTAAAACTTAATTTCTCGGAAAG +TAGTTATATACTGTTCACTTTTTTCTGCATTGTTGAATGGTCTTTTTCGGTCACACGGGCGCCGATATGACGTGGTGGCAACATCAACATGTAGCACAAG +TAACCTGACCCCTGAGCGCCGAGCCAACGACCGGTCTTTGACGACCTTCTTCTATTCATTGATGCTCTATTCAAACACATTCTCTCCCCCTTCGGCTCCC +AGTTTCACGTACGAGAAAAAGAAAGGCGCCGAGTTTCAAGAGTCTATCTC +>NM_075857 +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTTTTTTCCTTTTTTTGTAT +TTTTTTTCTTGGCGAAAAAAAAACTTTTTCTTGATTCAGTTTTATCTATATTTTTTTTAATTTTCTCACACCACTGATTCAAAACATTTTTTTTAGGAAA +ATGACTCAACAAAAAATGCACATGTTCTCCACTGAAACTGCTCTTCGGAA +>NR_067056 +CTTTCTTTATAAAAACTGTCAAATTAAAAATGTCTCGCTAGTCCTCTCATATAGTTGAGAAAATTAAAAAATTTTGGAATTAGTTATTCTTTTGAATCAG +TTCCAGAAAAATCAAAAATGAATCCGTAGAATTGTTTTTTGGTTTTTTTTCCCATTTAGCTTTCCTGGCTCCGTCCAAACTCTGTACTTTGTCGGAAAAT +TTGCAAAATGGAGCTGTGTAAAGTGAATTTTTGTATTCCATTTGGTATAATTTACTGTTTCAAATTGCACCTGGAACTATTCAATCCATTTTTAAATCAA +TAAGTAAAAAACTCGAACATTTTAAATTTTTGTTCAAAATATTGTTTGTT |
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| diff -r a8f207b43f64 -r 4fe92af4542b test-data/demoDB/target_list.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/demoDB/target_list.tabular Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -0,0 +1,20 @@ +13206415 +13192190 +13205826 +13204810 +13204564 +185688 +13193193 +13207184 +3565853 +175579 +13206434 +3896775 +188085 +178946 +179411 +13206365 +13213220 +186367 +13209600 +13194638 |
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| diff -r a8f207b43f64 -r 4fe92af4542b test-data/homer_promoters.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/homer_promoters.loc Thu Apr 06 16:22:23 2023 +0000 |
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| @@ -0,0 +1,7 @@ +# homer_preparse.loc +# This is a *.loc file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for promoter DBs distributed by Homer. +# The file should include an one line entry for each set and has 5 text columns seperated by TABS. +# +# <value> <dbkey> <organism> <path> <organism_version> <promoter_version> +worm demo_ov0_pv0 worm ${__HERE__}/demoDB/data v0 v0 |
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| diff -r a8f207b43f64 -r 4fe92af4542b tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Mon Dec 13 15:14:25 2021 +0000 +++ b/tool_data_table_conf.xml.sample Thu Apr 06 16:22:23 2023 +0000 |
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| @@ -2,11 +2,16 @@ <!-- Locations of all fasta files under genome directory --> <table name="all_fasta" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/all_fasta.loc" /> + <file path="tool-data/all_fasta.loc"/> </table> <!-- Locations of preparsed genomes --> <table name="homer_preparse" comment_char="#"> <columns>value, dbkey, mask, size, name, path, path_fasta, version</columns> - <file path="tool-data/homer_preparse.loc" /> + <file path="tool-data/homer_preparse.loc"/> + </table> + <!-- Built-in homer promoter and ID DBs (dir of <env>/share/data, 1 per organism) --> + <table name="homer_promoters" comment_char="#"> + <columns>value, dbkey, organism, path, organism_version, promoter_version</columns> + <file path="tool-data/homer_promoters.loc"/> </table> </tables> |
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| diff -r a8f207b43f64 -r 4fe92af4542b tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Mon Dec 13 15:14:25 2021 +0000 +++ b/tool_data_table_conf.xml.test Thu Apr 06 16:22:23 2023 +0000 |
| b |
| @@ -2,11 +2,16 @@ <!-- Locations of preparsed genomes --> <table name="homer_preparse" comment_char="#"> <columns>value, dbkey, mask, size, name, path, path_fasta, version</columns> - <file path="${__HERE__}/test-data/homer_preparse.loc" /> + <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" /> + <file path="${__HERE__}/test-data/all_fasta.loc"/> + </table> + <!-- Built-in homer promoter and ID DBs (dir of <env>/share/data, 1 per organism) --> + <table name="homer_promoters" comment_char="#"> + <columns>value, dbkey, organism, path, organism_version, promoter_version</columns> + <file path="${__HERE__}/test-data/homer_promoters.loc"/> </table> </tables> |