# HG changeset patch # User jbrayet # Date 1442923243 14400 # Node ID fb38cedce83e55592dc90f7f7aea29774264f4a3 # Parent 2db939186e37ad51693d2a4bbc9e798571229ce5 Uploaded diff -r 2db939186e37 -r fb38cedce83e matrixScan_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matrixScan_wrapper.xml Tue Sep 22 08:00:43 2015 -0400 @@ -0,0 +1,268 @@ + + + Scan a DNA sequence with a profile matrix + + python + + + matrixScan_wrapper.py -sequence $sequenceFile -matrix $matrixFile -outGalaxy $txtFile -matrix_format $matrix_format -n_treatment $n_treatment -markov $markov + #if $background_method_condition.background_method == "bgfile": + -organism $background_method_condition.serverChoice.organism + -server $background_method_condition.serverChoice.server + -background $background_method_condition.background + #else: + -server $background_method_condition.organism + #end if + #if $scanning_options_condition.scanning_options == "yes": + -origin $scanning_options_condition.origin + -return $scanning_options_condition.return + -uth $scanning_options_condition.pval + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +.. class:: infomark + +Scan a DNA sequence with a profile matrix. + +------ + +*Example with transfac matrix and fasta file*:: + + AC m1 + XX + ID m1 + XX + DE m1 m1; from JASPAR + P0 A C G T + 1 4 16 0 0 + 2 19 0 1 0 + 3 0 20 0 0 + 4 0 0 20 0 + 5 0 0 0 20 + 6 0 0 20 0 + XX + CC program: jaspar + CC matrix.nb: 1 + CC min.prior: 0.25 + CC alphabet.size: 4 + CC max.bits: 2 + CC total.information: 6.56407409450406 + CC information.per.column: 1.09401234908401 + CC max.possible.info.per.col: 1.38629436111989 + CC consensus.strict: CACGTG + CC consensus.strict.rc: CACGTG + CC consensus.IUPAC: CACGTG + CC consensus.IUPAC.rc: CACGTG + CC consensus.regexp: CACGTG + CC consensus.regexp.rc: CACGTG + CC residues.content.crude.freq: a:0.1917|c:0.3000|g:0.3417|t:0.1667 + CC G+C.content.crude.freq: 0.641666666666667 + CC residues.content.corrected.freq: a:0.1944|c:0.2976|g:0.3373|t:0.1706 + CC G+C.content.corrected.freq: 0.634920634920635 + XX + // + + >mm9_chr3_121848111_121848740_+ + tggggtgggttccaggacagccaggactgtcacacaaagaaaccttgtctcaaaaaaaca + aaaCAAAAAACAAAACAAAACCAAGCAAGCAAGCAAACATGGGCTTAAATctggatacag + tggcctttatttctagttccagtgactgggagactgaaacaagagagtcacttgagtaca + ggagtgcaaggctagcttgagcaatatagtaagactatctcaaaaTGTGAATTtagatca + acagaattgacatcaagaaaaatactgatatcactcaaagcaatctacagattcaacaca + atctccatcaacatgacaatgacttccatcaGCATGACAATGACTCCATCAACATGCCAA + TGGGCCCCATCAACATAACAATGACCCCTATCATCATGACAATGATCCCCATCAACATGA + CAATGACCTCCATCAACATGACAATTACTCCTGTCAACATGCCAATtgttggggttcaga + agtcaccctgcaaaccacaagaacactaatctcagtcaagcagggatggtttactgaacg + tatatccaaagactgagtgaccaagggaacagctcagactctagagctgaaagctagctg + tgcgctggacatttctcggggccaactta + >mm9_chr14_86795691_86796311_+ + CTCAAGGAGGATCCAGAAGTTGGCAGTTTCTGAGGCGAGTCCCATATTCCTCCCCTAAGG + GGTCAGGATTTTTCAGGTCTGGGCTCTTCTTGTTCTTTTGACAGCGACATTAATAATTGT + ACCAGCTCTCCCCTGGCAGGGCCGCACCACAGAGTAAAGCCTGGAGTAGGAGCTGTGCCC + AGCGCAATAATACCAGTTAAATAAGTACGTTCATTACCTCCCAACAGTCAAGGAGTTTAA + AATCCGTCAATTCACCCCACATGAGGGAGATTATGTGATTTACATGTTAAAGTGCCCCTG + TGGTTTGATTTGCATAGCAAAGACTTTGGGGGCACAGAAACAAAGCATCCGCATGCATGA + CAAGAGGACTATTAGCATAGAGAGAGCAGGTTTTCCGACAGCCCAGCCTGGCAAACAATG + CTGCACCTTCGCTGCTCGCTGGAGTTTATAGGATTTGACAGTTTCTCATCTGAGGGAGGA + GAAGGTTAGGGAGTTGGGGTGGAATGAGGTTCGCTAGATTGGCTGTCTGCCTTAAGCACA + ATAATTTGTCTTTCTCTGAAGACCTCCCCTCCTCTTATCACCTTTATCGTTTCTTTCTGA + TGTTCATTCAAAGACGTCTT + +------ + +*Results with threshold (sites + pval) 0.0001*:: + + #seq_id ft_type ft_name strand start end sequence weight Pval ln_Pval sig + mm9_chr3_121848111_121848740_+ limit START_END D 1 629 . 0 0 0 0 + mm9_chr14_86795691_86796311_+ limit START_END D 1 620 . 0 0 0 0 + mm9_chr15_84452311_84453000_+ limit START_END D 1 689 . 0 0 0 0 + mm9_chr1_134118761_134119120_+ limit START_END D 1 359 . 0 0 0 0 + mm9_chr17_35640731_35641360_+ limit START_END D 1 629 . 0 0 0 0 + mm9_chr18_66052791_66053190_+ limit START_END D 1 399 . 0 0 0 0 + mm9_chr6_125165051_125165561_+ limit START_END D 1 510 . 0 0 0 0 + mm9_chr16_35588051_35588520_+ limit START_END D 1 469 . 0 0 0 0 + mm9_chr2_51927461_51927981_+ limit START_END D 1 520 . 0 0 0 0 + mm9_chr2_51927461_51927981_+ site m1 D 106 111 CACGTG 9.1 7.2e-05 -9.545 4.145 + mm9_chr2_51927461_51927981_+ site m1 R 106 111 CACGTG 9.1 7.2e-05 -9.545 4.145 + mm9_chr3_18523921_18524271_+ limit START_END D 1 350 . 0 0 0 0 + mm9_chr17_29324151_29324630_+ limit START_END D 1 479 . 0 0 0 0 + mm9_chr5_111009921_111010390_+ limit START_END D 1 469 . 0 0 0 0 + mm9_chr14_37727831_37728360_+ limit START_END D 1 529 . 0 0 0 0 + mm9_chr11_77707171_77707751_+ limit START_END D 1 580 . 0 0 0 0 + mm9_chr14_50067391_50067801_+ limit START_END D 1 410 . 0 0 0 0 + + + + @article{Medina-Rivera22042015, + author = {Medina-Rivera, Alejandra and Defrance, Matthieu and Sand, Olivier and Herrmann, Carl and Castro-Mondragon, Jaime A. and Delerce, Jeremy and Jaeger, Sébastien and Blanchet, Christophe and Vincens, Pierre and Caron, Christophe and Staines, Daniel M. and Contreras-Moreira, Bruno and Artufel, Marie and Charbonnier-Khamvongsa, Lucie and Hernandez, Céline and Thieffry, Denis and Thomas-Chollier, Morgane and van Helden, Jacques}, + title = {RSAT 2015: Regulatory Sequence Analysis Tools}, + year = {2015}, + doi = {10.1093/nar/gkv362}, + URL = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.abstract}, + eprint = {http://nar.oxfordjournals.org/content/early/2015/04/21/nar.gkv362.full.pdf+html}, + journal = {Nucleic Acids Research} + } + + +