| Next changeset 1:034d5b66e97a (2015-11-18) |
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Commit message:
Uploaded |
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added:
mdust.xml mdust_wrapper.py test-data/masked-seq-mdust.fsa test-data/seq-mdust.fsa tool_dependencies.xml |
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| diff -r 000000000000 -r cc6db1ee2d48 mdust.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mdust.xml Mon Oct 05 11:05:21 2015 -0400 |
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| @@ -0,0 +1,87 @@ +<?xml version="1.0"?> +<tool id="mdust" name="mdust" version="1.0"> + <description>fast and symmetric DUST implementation to mask low-complexity DNA sequences</description> + <requirements> + <requirement type="package" version="1.0">mdust</requirement> + </requirements> + <command interpreter="python"> + mdust_wrapper.py -i ${input_file} -v ${cutoff} -w ${wsize} -m ${masking_letter.masking_letter_selector} -f ${output_type.output_type_selector} + + #if str( $output_type.output_type_selector) == "default" + -o ${output_masked_fasta} + #end if + + #if str( $output_type.output_type_selector) == "tab" + -o ${output_tab} + #end if + + #if str( $output_type.output_type_selector) == "bed" + -o ${output_bed} + #end if + </command> + <inputs> + <param name="input_file" type="data" format="fasta" label="Input fasta file" help=""/> + <param name="cutoff" type="integer" value="28" label="cutt-off" help="cut-off" /> + <param name="wsize" type="integer" value="3" label="set maximum word size" help="word-size" /> + <conditional name="masking_letter"> + <param name="masking_letter_selector" type="select" label="Choose your masking type" help="Select the masking letter (N,X or lowercase)" > + <option value="N" selected="True">N (default)</option> + <option value="X">X</option> + <option value="L">lowercase</option> + </param> + </conditional> + <conditional name="output_type"> + <param name="output_type_selector" type="select" label="Choose your output type" help="select your output"> + <option value="default" selected="True">masked file (default)</option> + <option value="tab">output masking coordinates only (tab delimited)</option> + <option value="bed">output masking coordinates only (bed format)</option> + </param> + </conditional> + </inputs> + <outputs> + <data format="fasta" name="output_masked_fasta" label="masked.${input_file.name}"> + <filter>( output_type['output_type_selector'] == 'default' )</filter> + </data> + <data format="tabular" name="output_tab" label="${input_file.name}.tab"> + <filter>( output_type['output_type_selector'] == 'tab' )</filter> + </data> + <data format="bed" name="output_bed" label="${input_file.name}.bed"> + <filter>( output_type['output_type_selector'] == 'bed' )</filter> + </data> + </outputs> + <tests> + <test> + <param name="input_file" value="seq-mdust.fsa" /> + <output name="output_masked_fasta" file="masked-seq-mdust.fsa" ftype="fasta" /> + </test> + </tests> + <help><![CDATA[ +mdust new implementation of the DUST module that uses the same function to assign a complexity score to a sequence, but uses a different rule by which high-scoring sequences are masked. + +----- + +**Usage:** :: + + mdust [<fasta-file>] [-w <wsize>] [-v <cut-off>] [-m N|X|L] [-c] + if no <fasta-file> is given, a multi-fasta stream is expected at stdin + -v default <cut-off> value is 28 (lower values might mask more, + but possibly still useful sequence; > 64 will rarely mask poly-triplets) + -w set maximum word size to <wsize> (default 3) + -m if fasta output is not disabled by -c, set the masking letter type: + N ('N', default), X ('X'), L (make lowercase) + -c output masking coordinates only: + seq_name, seqlength, mask_start, mask_end (tab delimited) + +----- + +**Reference:** :: + + A fast and symmetric DUST implementation to mask low-complexity DNA sequences. + Morgulis A, Gertz EM, Schäffer AA, Agarwala R. + J Comput Biol. 2006 Jun;13(5):1028-40. + PMID:16796549 + + +]]> + </help> +</tool> |
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| diff -r 000000000000 -r cc6db1ee2d48 mdust_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mdust_wrapper.py Mon Oct 05 11:05:21 2015 -0400 |
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| @@ -0,0 +1,113 @@ +#!/usr/bin/env python + +import subprocess +import tempfile +import sys +import os +import re +from optparse import OptionParser + + +class MdustWrapper(object): + + def __init__(self): + self._options = None + + def stop_err(self, msg): + sys.stderr.write("%s\n" % msg) + sys.exit() + + def setAttributesFromCmdLine(self): + description = "mdust_wrapper" + description += "\nWrapper for mdust\n" + description += "example: mdust_wrapper.py -i seq.fasta -v 27\n" + parser = OptionParser(description = description, version = "0.1") + parser.add_option("-i", "--input", dest = "FastaFile", action = "store", type = "string", help = "Input Fasta File name [compulsory] [format: Fasta]", default = "") + parser.add_option("-o", "--output", dest = "outFile", action = "store", type = "string", help = "output File name [compulsory] [format: fasta,tab or bed]", default = "") + parser.add_option("-v", "--cutoff", dest = "cutoff", action = "store", type = "int", help = "cutoff", default = 28) + parser.add_option("-w", "--wsize", dest = "wsize", action = "store", type = "int", help = "window size", default = 3) + parser.add_option("-m", "--maskingletter", dest = "maskingletter", action = "store", type = "string", help = "masking letter", default = "N") + parser.add_option("-f", "--format", dest = "format", action = "store", type = "string", help = "format", default = "default") + options = parser.parse_args()[0] + self._setAttributesFromOptions(options) + + + def _setAttributesFromOptions(self, options): + self._options = options + + if self._options.FastaFile == "": + raise Exception("Missing input file, please provide fasta file with -i file !") + if self._options.outFile == "": + raise Exception("Missing output file, please provide output file with -o file !") + + + def run(self): + + prg = "mdust" + args = "" + args += " %s" % self._options.FastaFile + args += " -v %d" % self._options.cutoff + args += " -w %d" % self._options.wsize + args += " -m %s" % self._options.maskingletter + if self._options.format == "tab" or self._options.format == "bed": + args += " -c " + cmd = "%s %s" %(prg, args) + + try: + tmp_err = tempfile.NamedTemporaryFile().name + tmp_out = "outfile" + tmp_stderr = open( tmp_err, 'wb' ) + tmp_stdout = open( tmp_out, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr ) + returncode = proc.wait() + tmp_stderr.close() + # get stderr, allowing for case where it's very large + tmp_stderr = open( tmp_err, 'rb' ) + tmp_stdout = open( tmp_out, 'rb' ) + + stderr = '' + stdout = '' + buffsize = 1048576 + try: + while True: + stdout += tmp_stdout.read( buffsize ) + if not stdout or len( stdout ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stdout.close() + + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + if stderr: + raise Exception, stderr + except Exception, e: + self.stop_err( 'Error with mdust :\n' + str( e ) ) + + if self._options.format == 'bed': + with open(tmp_out,"r") as fin: + with open(self._options.outFile, "w") as fout: + lineNumber = 0 + for line in fin: + lineNumber += 1 + m = re.search(r"^(\S+)\t(\d+)\t(\d+)\t(\d+)$", line) + if m is not None: + fout.write("%s\t%d\t%d\n" % (m.group(1), int(m.group(3))-1, int(m.group(4)))) + if m is None: + raise Exception("\nLine %d '%s' does not has a mdust format." % (lineNumber, line)) + else: + os.rename(tmp_out,self._options.outFile) + + + + +if __name__ == "__main__": + iWrapper = MdustWrapper() + iWrapper.setAttributesFromCmdLine() + iWrapper.run() |
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| diff -r 000000000000 -r cc6db1ee2d48 test-data/masked-seq-mdust.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/masked-seq-mdust.fsa Mon Oct 05 11:05:21 2015 -0400 |
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| b'@@ -0,0 +1,5000 @@\n+>seqmdust\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNcaccctcaccctCGgtcgtacggcgtgacaatgtctccagaatcgatttggtcttg\n+acgaaagcagcgcacatagcacttccggatgattttgtcgcatgctttgtcaaacacgac\n+gtccgtaagtactagctcgttcggcctagctttcgcgcccgtctgctgctcgctcttccg\n+caagaattgacgcagaacgacgcgccgcttctgggtatcgaactcgataatttgggctgg\n+ctggagccggtcctcgtcaaggtcgtcattccattcgcggacgaggacggtgtcaccaat\n+tgcatatttgctccggcactcgtcgaatataggaacgtcatgcttgcactggcacctaaa\n+gtcgcttgcttgaattgcaacgaagtcgtatgtgtcttgctcgtaaactgtgcggaactt\n+ctggcgcacaaagtgtcctccctgctaatatggatccttggcatactaacatacgtctgc\n+cttaaagcgcgccttcggatacgcgagaagtccaacacgaggactcgagagagatacttc\n+cgcaaaaacgacagagaacacagatacaactactctgttatcgactccgacaatacaagc\n+atttcgtagaacacgagagggctaactacgcaaaagacgatctctttagcgtctggaaaa\n+cccgatacgaaatagcaagacaacgggagatcaataaggtacctaggaatacaaatagct\n+accttagtcgatttccatggagctcgccaggaaaacacagaataggaggaagacgcgctt\n+taactagtgccttctatactatcctattaggacacggatacctaaagtcctatctctatc\n+gctttggacacgtaacgacgccagactgcccttgcggacgacgagaaacagcagaacacc\n+tcgtatgtagctgccctatctacgatgtatttaggccactaccgctacgacaagcacaat\n+ctctactagaaatagtagaagataaggaactccggaaacacctcactacctttctctcgg\n+acacaaagattgcttctaggtcctggcacctagcaagaggcgaagacgagaccgtctagc\n+ctacactccttttacttttccttatttgtctttctttaaagtccttcgatactagctggc\n+tactatcctaggcacgggtctttccctaaggtcaagagatacgagagaacaacgattgta\n+catagatagactgctgtcgcgagacagccgtcctacatagtcatagactcctacaggacg\n+taaatGGaacaaacaaacaaacaaacaaatacgtctgccttatctaagacgcaatctagg\n+tcgagagccgatgtgccgcagctgcagttgtcggacaagaagagctcattcgcaaaaggg\n+taataggctttgccaagtgtagtgtcctttggctcgtacagccagagaacatcgagcgaa\n+gtacaatctttgcgagtgtgcacgttctaaacataggcataccatgcgtgcgctttgatc\n+ccctatttggtactgacatccggcgcgacgcatacgacatcccctgtgttcaccgtgact\n+gctttgttcccctcttgagattcgcttcggctcatactcctaggcgttaaggtttgcatt\n+ggcggtgcactcggagatgctcgtcgcggcgtcagtctgagccttacttttagctcatcc\n+gacttcttcagcacatttcggtccgtgatcgtccgctcttccagctggttaccgaagtac\n+atatgtcgaaagcactggtagacaaaaggcgtgacgatcgttcgcaactccttgtttggc\n+tgcgctgggatagctgtaagattatagggatcgacttcaccctagatcggttgtcggcac\n+aatccagactctttgtcatcgatatcccagcattctttccaaaggaagccgacatttgcg\n+gcaatggtcgtgcggaagtctttgagtttgcattcagctagccattagttaaagctagta\n+ttatcgccgtagagtctagttagctattggtaaaatcgtctgcggaaatgtccaagggta\n+acctgctggttgctgaggaggtagtcgacgaagtgcttcccgaactgtgctagctaaagg\n+aacggctcgtagaatcgacgatattccggtgcaggcgttcccagctcgtaccaatgacta\n+aacagagcggacgctttcgactacagcttcgattaaatgcagatgctactggcaaaatct\n+gtaaagtccaggtcgccgtacctactgatagccaagatctcgaactgcacgccctacatg\n+tagcgcttttcgttgcctgccgatagaatgccatcgaaacagaactctgcatagtttgat\n+tgccgcagtttctcaagagtgacgaggtccgatgcgcgtcgtccgtccgctatgtatacc\n+gagaattgatcgagtttgaaagtagcacattccggagtttcggtgctagcagacttcgca\n+gctgcgaagaagcctgcactcaagtctaggcttgcttcgacctcgtttacaggttgcaaa\n+ggaggtttgtatccgtagtaagcgcttctcggaaatgctggtcctacaatggagatgtgg\n+cttaagtagcgaagctgccgtcgtttcccggaacgagctgtggccccaggctctgctcta\n+gtagcaggctcgtcccctagttctgtttcggtcgctggaggagtgagtgcagtcctgagc\n+cttcgttgtctgggcgtgcgtagtgggccctagtccttaacttcccgatctccgactgtt\n+tggcttgtctgctcctcgcccaattctatcttatactaaaccgctctctgcactccatct\n+tcttcttgttgtttcgactcgcctcggtcctgctcagaagccgcaggactgattacaatc\n+gcattgcttagggaagctctagtgcgcaaaatgtctatctacaattgtccattctgaagc\n+cgcggcttcttggaaggcctcgaagtaggtcctaccacaatgttgtcctcgtcatcctga\n+atgacaatcgtgtcgccgctgatccgtctcttcatggttgccgtgctacttaatgccgtc\n+gtgtgcgaggtagtaatagggttaagaatgccgctgtcttgctacaaaggcgccatgttc\n+ttttcgttgctcgaagcagtccgtccgcggtaagtgtgccaaatcgcacaatgcaagtgc\n+tagagctgcaagtgaagtccaagagtgaatgcactaactatttaccttgcaagccgtgca\n+cgcagtgtaatgatctgccgaagcaaagaagaaatagcagaccaagatatccgcaaaaca\n+aatatccgtagaggtaaaaaggaatgcgcgcaacttgccagtaaaacgttgcttcgtgag\n+gtagttaatgaagtgtagtctggaagctttgaagtgcgaccaaggatgttctagccattg\n+acttttgaccgcgcctgcacctcaatgcccgtaatggccgccatcgcgaatggcatatgt\n+tagcgctgttaaattcaaatagtagaagtgagatggattatattcgagattacttatgta\n+cgcctacttgagggcggtggcatgtaacccgagtcttcgcttaagtgttgttacgaacgc\n+ttgaggtcctcctcgactgttccttgtccggctacggcatcgcgctgggcccaggcctct\n+cgtattcggggtttggcgtccctcgctcttttgtatgctcggagagggcggctcaaaagt\n+'..b'CAGCCAAGCAGCAGCCAAAGTACGACGCAC\n+AAACCAGGATGATTCACCATCAAAGCAAACAAATATGAGGTTCAACGAGAGGTGTGAGGT\n+ATAATGACTTCGAGCATGAGCCGGTGCTTGGCCCTTCTCGAGTATGCTCGTGCCATCTGC\n+TGTCCTTTTCGAAGATATTGCATGTGCATGAACATTTCTGGAGAAGGGCCTCGCTGAGAT\n+CACACGGCTCGAACTTGAACCAGATAATGCTGGCGATAAAGAATCATGCTCTTCCCCTAC\n+AGTCCAATCCCTACGAGCGAGGACTAACCCATCTAGGTATACACAACGGCAAAAGCGAAG\n+CGACCATGCCAGATCTCGACTCGAGAGATGTCGAGAAGAATGCCCTGGATTCACCTGAGA\n+TGCACGGTCCGGAGTCGGCCACATCCTCCACCGCCTCAGAAGGCCGCTCAAGGAACTTCC\n+TCAGCAGCGTCAAGCAGTCCGTCGTACACGACAACTTCGAGGCTCGCGGCGTCCAACGAG\n+TACTCCCAGCCGAGCGCAATCCGACATCCACATTTGGCTTTCTCCAAATCATGCTTATGT\n+GGATGAGCATCAACATGACCGCCGTCGTGATCGTCCTGGGCTTCCTCGGGCCCATCACTT\n+TCTCCTTATCCTTCAAAGATGCCTCTCTCCTTGCAGTCTTCGGCGCAATAGTTGGAGCGA\n+CGCCGGTCGCCTACATCGCCACTTTCGGCCCTCGCTCCGGCAACCGCACCATGATCCTCA\n+CCCGATACATCACCGGTTGGTGGCCATCCAAAGTCATCGTCATTCTCACACTCATCATCC\n+TCATGGGCTACGTCCTCCTCGACGCCGTTATTGGCGGTCAGATCCTCTCAGCCGTCAGTC\n+CCAACGCTTCCCTCAGCGTCATAGTCGGCATCGTCATCGTCTGCATCCTCACCTGGATCG\n+TGACCGCATTCGGCTATTGTGTCTTCCATCACTTCGAGCGCTACGCCTGGATCCCCTCCC\n+TCATCGTCATTTGTCTCCTCATCGGCGTCTCCGCTCCAAAATGGAATCTCGAACCAGGTC\n+CCGCTCTCCCACCTCGCACCCTCGCCGGCAACCGCCTCTCCTTCTTCTCTCTTTGTCTCG\n+CCGCCGAAATCACCTACGCCGAATCGGGAGCCGACATGTTTGTCTACTATCCATCCACCA\n+CTTCCCGCACAAAAGTCTTTCTCTCCACCCTCGCTGGTCTCACCCTCTCCTCCGCCATCG\n+CCCTCATCACCGGTATTGGCCTCGGCTCCGGCACTCTCACCGATCCAGCCTGGTCCTCCG\n+CCTACTCCGTCTCCGCAGGTGCCCTCATCGTTGAAGCATTCCGTCCACTCGGTGGATTCG\n+GCTCATTCTGCAGCGTTCTCGTTGCACTGGGTATAGTCGCAAATATGGTCCTGCCGACCT\n+ACGCTTCAGGAGTGGACTTCCAAGCGTTCGGCCGATGGTTCGAAAGGGTCCCGCGGATCG\n+TGTGGAATACCGTTGCGCTGGTCGTACCGATGATTGGAGCAATCGCAGGACGAGAACACC\n+TGGCGGAGATCTTCTCCAACTTCCTGGCATTGATGGGTTATTGGGTGTCTATCTGGATTG\n+CGATCGTGGTGGAAGAGCACATCTTGTTCCGAAAGATGGGAGGCAAGGGTTGGAAGTGGG\n+AGGACTGGAATGACAGGACGAAGCTCCCTATCGGTATTGCGGCGGGCGTTGCGTTCCTTG\n+TGGGATGGGTTGGAGCGATTATGGGTATGTCGCAGGTCTGGTATGTGGGACCGTTGGCGA\n+AGCTGGTCAGTGAGCAGGGAGCGGATATCGGGAATTATGTTGGGTTTTCGTGGGCGTTGG\n+TGGTGTATCCGCCTTTGAGGTGGGTGGAGCTGAGGTGGGTTGGGAGATAGGAGGGCAGAT\n+GGAGGATGGAGGAAGTCGGTGGACAGATCAAGGCGGAGAATCGGAGGTTGTGAAGCCCTC\n+GAGTTGTGGCTCGGGATGTGCCTGCGCTGTTTATCTTTGCGGCACTCAACTCCGCCAACA\n+GCATGCATTCGTGCGAGCAACGCAGACAAATTCAGCGTATCCTCTCGAGCATTGATATGG\n+CAAGCCCGAATACGCTCAACTCTGCGCCCTTCTCCGTTCATTCAACAGCATATACTCATA\n+CCGACATCAATATTCGTTATCATTATTTGCACAACTAGCGGTGAATCGCGATGAAGCCCG\n+ACTTACCTTAGTCATGCACTGCATCCGACATCGGGACGCGTATCGCCCGCATTCTTGGCA\n+CCTCCCCGGGCGCAAAATCCTGTTATCTTCCCGGCTGGCTCCCTCCTTCTTTTCATATGC\n+ACGCGTAATCCTCACCGTCTCTCCCTTTCACATTCACGCACCAGTTCACAATAACAATAT\n+TCACGCTTGACTTCACCTCACTTCACTGCCACCCCTCCCTACCTCACTCTTTCCCACTGC\n+TGCGCAGTCATGCCTCGCCCTCCAGACCACTACACCCACGCCCAATTCGAGCCCGTCGAG\n+TCGGACCACGCCGGCGAAACGGTCCAATGTCGCCACTGCCGCAACTGGACGGGTTCCATC\n+AAGACGCTTAATCGGAAAAAAGCTCATCTTCTCACGTGCACGCAGTATGCGCAGTGGCGG\n+GCGGCGGGGAATGGGCAGGATTTGGCGCCGCCGAATAAGTATCATAAGAGGGATAGTTCG\n+GTTATGGGTGGTGGGTGGGAGGGGCAGGGGGATGGGTCAGTGATCTTCTTTTGATGTTGT\n+GGTGTTTTGTGGTGGCTTGAAGATGGAATTGCGATGATTTGGGTTCTTTGTGATGTTGGT\n+GGAATGCTAACGGTGTTATTGCAGGAATACCTCTGGCTTCAATATGTCGCCGTTCAATGA\n+TACCCCGACGGTGGCTCGTGGCCGCAATCTTGATCTGACCAAGGTAGACATTGACAAGAT\n+GTTCCAATTCGCTGCAGTATACTGATCATGTACAGTACTTCTCCGAATTCTGGGACGACA\n+CCGCTTCGAACAAGGTCAGTGACTATCTACAGGATTTTACAGGCAATCTGTCTATTGTCA\n+CTTTCGTGATCCTCTGCATCTTCAGATCCAGCGCCACAAGTACTTACAAGTATCTACCAG\n+TGCATGCGAGTACGCTGCCTCTCCTGCGGCTTCGTCCGGGCAAAGAACACCACCCGCCAA\n+GTCGAACATCTTGCCAGCTGCGCCTCGTTCCTCAACAGCACCGAAGGTCAAGCCGCTGTC\n+GCGAACGGCGAACTCGAAATGACACCTGCCGCACCTCGCCAGTCTTTCGGAGGCGGGAAT\n+GACATCTGGCGTGGCGGTGCACCAAACCCGAATCTGCAAGTCAGCCAGACGCCAACTTCG\n+ACCAGCCGTGGTGGAGGAAGAGCCTATCCGATGCCGCCTCCTCCCAAAGCACCCTCCCTC\n+GTATCTCACCTCCTCAACAAGTTCCAGGAAAAGTTCAATGTTGCGACTCAACAGTCTTTC\n+CTCTCTCACGCCGGCTGCGGTACTCTGTCCCACGCAGCTCTCTGCTCCTGGCTCACACAG\n+CATGGCCACATTTCTCGAGCTATGATTGCCGCCATTGGATCACTCATCGCCAAAGTGTTC\n+CTGCCAGATGCCGCCAATACTCGCATTGCTACGCCATACCGTGCTCTGGACCTGCTCATC\n+TCCACGATCAGCAATCTTCGTAAAGAGATCGACTTCATCGAGAATACTAAGCGGAAGTAT\n+CGCTTGGACGCTGCGAGTGAGCCGCCGTCGCCGATGACGAAGGCATACGTCGATCTCTTG\n+GCGAGTGCTTCTGAGCCGAGAGCAGATCTGCTGGAGGGAATGGTAGCGCTGTGGGCGACC\n+GAGCATGTATGTTGACCACCTTTTCCGTTTCTGTGTTCGATGTCACTAACTCTATACCAG\n' 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| diff -r 000000000000 -r cc6db1ee2d48 test-data/seq-mdust.fsa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seq-mdust.fsa Mon Oct 05 11:05:21 2015 -0400 |
| b |
| b'@@ -0,0 +1,5000 @@\n+>seqmdust\n+ccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaa\n+ccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaa\n+ccctcaccctcaccctCGgtcgtacggcgtgacaatgtctccagaatcgatttggtcttg\n+acgaaagcagcgcacatagcacttccggatgattttgtcgcatgctttgtcaaacacgac\n+gtccgtaagtactagctcgttcggcctagctttcgcgcccgtctgctgctcgctcttccg\n+caagaattgacgcagaacgacgcgccgcttctgggtatcgaactcgataatttgggctgg\n+ctggagccggtcctcgtcaaggtcgtcattccattcgcggacgaggacggtgtcaccaat\n+tgcatatttgctccggcactcgtcgaatataggaacgtcatgcttgcactggcacctaaa\n+gtcgcttgcttgaattgcaacgaagtcgtatgtgtcttgctcgtaaactgtgcggaactt\n+ctggcgcacaaagtgtcctccctgctaatatggatccttggcatactaacatacgtctgc\n+cttaaagcgcgccttcggatacgcgagaagtccaacacgaggactcgagagagatacttc\n+cgcaaaaacgacagagaacacagatacaactactctgttatcgactccgacaatacaagc\n+atttcgtagaacacgagagggctaactacgcaaaagacgatctctttagcgtctggaaaa\n+cccgatacgaaatagcaagacaacgggagatcaataaggtacctaggaatacaaatagct\n+accttagtcgatttccatggagctcgccaggaaaacacagaataggaggaagacgcgctt\n+taactagtgccttctatactatcctattaggacacggatacctaaagtcctatctctatc\n+gctttggacacgtaacgacgccagactgcccttgcggacgacgagaaacagcagaacacc\n+tcgtatgtagctgccctatctacgatgtatttaggccactaccgctacgacaagcacaat\n+ctctactagaaatagtagaagataaggaactccggaaacacctcactacctttctctcgg\n+acacaaagattgcttctaggtcctggcacctagcaagaggcgaagacgagaccgtctagc\n+ctacactccttttacttttccttatttgtctttctttaaagtccttcgatactagctggc\n+tactatcctaggcacgggtctttccctaaggtcaagagatacgagagaacaacgattgta\n+catagatagactgctgtcgcgagacagccgtcctacatagtcatagactcctacaggacg\n+taaatGGaacaaacaaacaaacaaacaaatacgtctgccttatctaagacgcaatctagg\n+tcgagagccgatgtgccgcagctgcagttgtcggacaagaagagctcattcgcaaaaggg\n+taataggctttgccaagtgtagtgtcctttggctcgtacagccagagaacatcgagcgaa\n+gtacaatctttgcgagtgtgcacgttctaaacataggcataccatgcgtgcgctttgatc\n+ccctatttggtactgacatccggcgcgacgcatacgacatcccctgtgttcaccgtgact\n+gctttgttcccctcttgagattcgcttcggctcatactcctaggcgttaaggtttgcatt\n+ggcggtgcactcggagatgctcgtcgcggcgtcagtctgagccttacttttagctcatcc\n+gacttcttcagcacatttcggtccgtgatcgtccgctcttccagctggttaccgaagtac\n+atatgtcgaaagcactggtagacaaaaggcgtgacgatcgttcgcaactccttgtttggc\n+tgcgctgggatagctgtaagattatagggatcgacttcaccctagatcggttgtcggcac\n+aatccagactctttgtcatcgatatcccagcattctttccaaaggaagccgacatttgcg\n+gcaatggtcgtgcggaagtctttgagtttgcattcagctagccattagttaaagctagta\n+ttatcgccgtagagtctagttagctattggtaaaatcgtctgcggaaatgtccaagggta\n+acctgctggttgctgaggaggtagtcgacgaagtgcttcccgaactgtgctagctaaagg\n+aacggctcgtagaatcgacgatattccggtgcaggcgttcccagctcgtaccaatgacta\n+aacagagcggacgctttcgactacagcttcgattaaatgcagatgctactggcaaaatct\n+gtaaagtccaggtcgccgtacctactgatagccaagatctcgaactgcacgccctacatg\n+tagcgcttttcgttgcctgccgatagaatgccatcgaaacagaactctgcatagtttgat\n+tgccgcagtttctcaagagtgacgaggtccgatgcgcgtcgtccgtccgctatgtatacc\n+gagaattgatcgagtttgaaagtagcacattccggagtttcggtgctagcagacttcgca\n+gctgcgaagaagcctgcactcaagtctaggcttgcttcgacctcgtttacaggttgcaaa\n+ggaggtttgtatccgtagtaagcgcttctcggaaatgctggtcctacaatggagatgtgg\n+cttaagtagcgaagctgccgtcgtttcccggaacgagctgtggccccaggctctgctcta\n+gtagcaggctcgtcccctagttctgtttcggtcgctggaggagtgagtgcagtcctgagc\n+cttcgttgtctgggcgtgcgtagtgggccctagtccttaacttcccgatctccgactgtt\n+tggcttgtctgctcctcgcccaattctatcttatactaaaccgctctctgcactccatct\n+tcttcttgttgtttcgactcgcctcggtcctgctcagaagccgcaggactgattacaatc\n+gcattgcttagggaagctctagtgcgcaaaatgtctatctacaattgtccattctgaagc\n+cgcggcttcttggaaggcctcgaagtaggtcctaccacaatgttgtcctcgtcatcctga\n+atgacaatcgtgtcgccgctgatccgtctcttcatggttgccgtgctacttaatgccgtc\n+gtgtgcgaggtagtaatagggttaagaatgccgctgtcttgctacaaaggcgccatgttc\n+ttttcgttgctcgaagcagtccgtccgcggtaagtgtgccaaatcgcacaatgcaagtgc\n+tagagctgcaagtgaagtccaagagtgaatgcactaactatttaccttgcaagccgtgca\n+cgcagtgtaatgatctgccgaagcaaagaagaaatagcagaccaagatatccgcaaaaca\n+aatatccgtagaggtaaaaaggaatgcgcgcaacttgccagtaaaacgttgcttcgtgag\n+gtagttaatgaagtgtagtctggaagctttgaagtgcgaccaaggatgttctagccattg\n+acttttgaccgcgcctgcacctcaatgcccgtaatggccgccatcgcgaatggcatatgt\n+tagcgctgttaaattcaaatagtagaagtgagatggattatattcgagattacttatgta\n+cgcctacttgagggcggtggcatgtaacccgagtcttcgcttaagtgttgttacgaacgc\n+ttgaggtcctcctcgactgttccttgtccggctacggcatcgcgctgggcccaggcctct\n+cgtattcggggtttggcgtccctcgctcttttgtatgctcggagagggcggctcaaaagt\n+'..b'CAGCCAAGCAGCAGCCAAAGTACGACGCAC\n+AAACCAGGATGATTCACCATCAAAGCAAACAAATATGAGGTTCAACGAGAGGTGTGAGGT\n+ATAATGACTTCGAGCATGAGCCGGTGCTTGGCCCTTCTCGAGTATGCTCGTGCCATCTGC\n+TGTCCTTTTCGAAGATATTGCATGTGCATGAACATTTCTGGAGAAGGGCCTCGCTGAGAT\n+CACACGGCTCGAACTTGAACCAGATAATGCTGGCGATAAAGAATCATGCTCTTCCCCTAC\n+AGTCCAATCCCTACGAGCGAGGACTAACCCATCTAGGTATACACAACGGCAAAAGCGAAG\n+CGACCATGCCAGATCTCGACTCGAGAGATGTCGAGAAGAATGCCCTGGATTCACCTGAGA\n+TGCACGGTCCGGAGTCGGCCACATCCTCCACCGCCTCAGAAGGCCGCTCAAGGAACTTCC\n+TCAGCAGCGTCAAGCAGTCCGTCGTACACGACAACTTCGAGGCTCGCGGCGTCCAACGAG\n+TACTCCCAGCCGAGCGCAATCCGACATCCACATTTGGCTTTCTCCAAATCATGCTTATGT\n+GGATGAGCATCAACATGACCGCCGTCGTGATCGTCCTGGGCTTCCTCGGGCCCATCACTT\n+TCTCCTTATCCTTCAAAGATGCCTCTCTCCTTGCAGTCTTCGGCGCAATAGTTGGAGCGA\n+CGCCGGTCGCCTACATCGCCACTTTCGGCCCTCGCTCCGGCAACCGCACCATGATCCTCA\n+CCCGATACATCACCGGTTGGTGGCCATCCAAAGTCATCGTCATTCTCACACTCATCATCC\n+TCATGGGCTACGTCCTCCTCGACGCCGTTATTGGCGGTCAGATCCTCTCAGCCGTCAGTC\n+CCAACGCTTCCCTCAGCGTCATAGTCGGCATCGTCATCGTCTGCATCCTCACCTGGATCG\n+TGACCGCATTCGGCTATTGTGTCTTCCATCACTTCGAGCGCTACGCCTGGATCCCCTCCC\n+TCATCGTCATTTGTCTCCTCATCGGCGTCTCCGCTCCAAAATGGAATCTCGAACCAGGTC\n+CCGCTCTCCCACCTCGCACCCTCGCCGGCAACCGCCTCTCCTTCTTCTCTCTTTGTCTCG\n+CCGCCGAAATCACCTACGCCGAATCGGGAGCCGACATGTTTGTCTACTATCCATCCACCA\n+CTTCCCGCACAAAAGTCTTTCTCTCCACCCTCGCTGGTCTCACCCTCTCCTCCGCCATCG\n+CCCTCATCACCGGTATTGGCCTCGGCTCCGGCACTCTCACCGATCCAGCCTGGTCCTCCG\n+CCTACTCCGTCTCCGCAGGTGCCCTCATCGTTGAAGCATTCCGTCCACTCGGTGGATTCG\n+GCTCATTCTGCAGCGTTCTCGTTGCACTGGGTATAGTCGCAAATATGGTCCTGCCGACCT\n+ACGCTTCAGGAGTGGACTTCCAAGCGTTCGGCCGATGGTTCGAAAGGGTCCCGCGGATCG\n+TGTGGAATACCGTTGCGCTGGTCGTACCGATGATTGGAGCAATCGCAGGACGAGAACACC\n+TGGCGGAGATCTTCTCCAACTTCCTGGCATTGATGGGTTATTGGGTGTCTATCTGGATTG\n+CGATCGTGGTGGAAGAGCACATCTTGTTCCGAAAGATGGGAGGCAAGGGTTGGAAGTGGG\n+AGGACTGGAATGACAGGACGAAGCTCCCTATCGGTATTGCGGCGGGCGTTGCGTTCCTTG\n+TGGGATGGGTTGGAGCGATTATGGGTATGTCGCAGGTCTGGTATGTGGGACCGTTGGCGA\n+AGCTGGTCAGTGAGCAGGGAGCGGATATCGGGAATTATGTTGGGTTTTCGTGGGCGTTGG\n+TGGTGTATCCGCCTTTGAGGTGGGTGGAGCTGAGGTGGGTTGGGAGATAGGAGGGCAGAT\n+GGAGGATGGAGGAAGTCGGTGGACAGATCAAGGCGGAGAATCGGAGGTTGTGAAGCCCTC\n+GAGTTGTGGCTCGGGATGTGCCTGCGCTGTTTATCTTTGCGGCACTCAACTCCGCCAACA\n+GCATGCATTCGTGCGAGCAACGCAGACAAATTCAGCGTATCCTCTCGAGCATTGATATGG\n+CAAGCCCGAATACGCTCAACTCTGCGCCCTTCTCCGTTCATTCAACAGCATATACTCATA\n+CCGACATCAATATTCGTTATCATTATTTGCACAACTAGCGGTGAATCGCGATGAAGCCCG\n+ACTTACCTTAGTCATGCACTGCATCCGACATCGGGACGCGTATCGCCCGCATTCTTGGCA\n+CCTCCCCGGGCGCAAAATCCTGTTATCTTCCCGGCTGGCTCCCTCCTTCTTTTCATATGC\n+ACGCGTAATCCTCACCGTCTCTCCCTTTCACATTCACGCACCAGTTCACAATAACAATAT\n+TCACGCTTGACTTCACCTCACTTCACTGCCACCCCTCCCTACCTCACTCTTTCCCACTGC\n+TGCGCAGTCATGCCTCGCCCTCCAGACCACTACACCCACGCCCAATTCGAGCCCGTCGAG\n+TCGGACCACGCCGGCGAAACGGTCCAATGTCGCCACTGCCGCAACTGGACGGGTTCCATC\n+AAGACGCTTAATCGGAAAAAAGCTCATCTTCTCACGTGCACGCAGTATGCGCAGTGGCGG\n+GCGGCGGGGAATGGGCAGGATTTGGCGCCGCCGAATAAGTATCATAAGAGGGATAGTTCG\n+GTTATGGGTGGTGGGTGGGAGGGGCAGGGGGATGGGTCAGTGATCTTCTTTTGATGTTGT\n+GGTGTTTTGTGGTGGCTTGAAGATGGAATTGCGATGATTTGGGTTCTTTGTGATGTTGGT\n+GGAATGCTAACGGTGTTATTGCAGGAATACCTCTGGCTTCAATATGTCGCCGTTCAATGA\n+TACCCCGACGGTGGCTCGTGGCCGCAATCTTGATCTGACCAAGGTAGACATTGACAAGAT\n+GTTCCAATTCGCTGCAGTATACTGATCATGTACAGTACTTCTCCGAATTCTGGGACGACA\n+CCGCTTCGAACAAGGTCAGTGACTATCTACAGGATTTTACAGGCAATCTGTCTATTGTCA\n+CTTTCGTGATCCTCTGCATCTTCAGATCCAGCGCCACAAGTACTTACAAGTATCTACCAG\n+TGCATGCGAGTACGCTGCCTCTCCTGCGGCTTCGTCCGGGCAAAGAACACCACCCGCCAA\n+GTCGAACATCTTGCCAGCTGCGCCTCGTTCCTCAACAGCACCGAAGGTCAAGCCGCTGTC\n+GCGAACGGCGAACTCGAAATGACACCTGCCGCACCTCGCCAGTCTTTCGGAGGCGGGAAT\n+GACATCTGGCGTGGCGGTGCACCAAACCCGAATCTGCAAGTCAGCCAGACGCCAACTTCG\n+ACCAGCCGTGGTGGAGGAAGAGCCTATCCGATGCCGCCTCCTCCCAAAGCACCCTCCCTC\n+GTATCTCACCTCCTCAACAAGTTCCAGGAAAAGTTCAATGTTGCGACTCAACAGTCTTTC\n+CTCTCTCACGCCGGCTGCGGTACTCTGTCCCACGCAGCTCTCTGCTCCTGGCTCACACAG\n+CATGGCCACATTTCTCGAGCTATGATTGCCGCCATTGGATCACTCATCGCCAAAGTGTTC\n+CTGCCAGATGCCGCCAATACTCGCATTGCTACGCCATACCGTGCTCTGGACCTGCTCATC\n+TCCACGATCAGCAATCTTCGTAAAGAGATCGACTTCATCGAGAATACTAAGCGGAAGTAT\n+CGCTTGGACGCTGCGAGTGAGCCGCCGTCGCCGATGACGAAGGCATACGTCGATCTCTTG\n+GCGAGTGCTTCTGAGCCGAGAGCAGATCTGCTGGAGGGAATGGTAGCGCTGTGGGCGACC\n+GAGCATGTATGTTGACCACCTTTTCCGTTTCTGTGTTCGATGTCACTAACTCTATACCAG\n' |
| b |
| diff -r 000000000000 -r cc6db1ee2d48 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Oct 05 11:05:21 2015 -0400 |
| b |
| @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mdust" version="1.0"> + <install version="1.0"> + <actions> + <action type="download_by_url">ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/mdust.tar.gz</action> + <action type="shell_command">make</action> + <action type="move_file"> + <source>mdust</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |