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Commit message:
Upload ctat tools. |
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added:
ctat_edger_differential_expression.py ctat_edger_differential_expression.xml test-data/Sp.Trinity.fasta test-data/Sp.counts.matrix |
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| diff -r 000000000000 -r f36264827fb4 ctat_edger_differential_expression.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_edger_differential_expression.py Tue Jul 17 11:52:09 2018 -0400 |
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| @@ -0,0 +1,87 @@ +import sys, os, subprocess + +TRINITY_BASE_DIR = "" +if os.environ.has_key('TRINITY_HOME'): + TRINITY_BASE_DIR = os.environ['TRINITY_HOME']; +elif hasattr(os, 'symlink'): # symlink was implemented to always return false when it was not implemented in earlier versions of python. + # 2017-09-26 + # Cicada Dennis added looking for the location of the Trinity program using the Unix "which" utility. + # I tried using "command -v Trinity" but for some reason, I was getting a OS permission error with that. + # I also found distutils.spawn.find_executable() which might work, but already implemented the below. + try: + pipe1 = subprocess.Popen(["which", "Trinity"], stdout=subprocess.PIPE) + except: + msg = "You must set the environmental variable TRINITY_HOME to the base installation directory of Trinity before running {:s}.\n".format(sys.argv[0]) + sys.stderr.write(msg) + # t, v, tb = sys.exc_info() + # raise t, v, tb + # For some reason the above was giving a syntax error. + # A simple raise should reraise the existing exception. + raise + else: + TrinityPath, err_info = pipe1.communicate() + # FIX - probably should be checking err_info for errors... + # Determine the TRINITY_BASE_DIR from output1. + # If TrinityPath is a link, we need to dereference the link. + TrinityPath = TrinityPath.rstrip() # Need to strip off a newline. + # print "Trinity that was found is: {:s}".format(repr(TrinityPath)) + # print os.path.islink(TrinityPath) + TrinityPath = os.path.abspath(TrinityPath) + # msg = "The Absolute Trinity path that was found is: {:s}".format(TrinityPath) + # print msg + # print os.path.islink(TrinityPath) + while os.path.islink(TrinityPath): + # print "That path is a link." + TrinityPath = os.path.join(os.path.dirname(TrinityPath),os.readlink(TrinityPath)) + # print "The new path is: {:s}".format(TrinityPath) + # Take off the last part of the path (which is the Trinity command) + TRINITY_BASE_DIR = "/".join(TrinityPath.split("/")[0:-1]) +else: + sys.stderr.write("Either set TRINITY_HOME to the trinity base directory, " + \ + "or ensure that directory is in the PATH before running.") + sys.exit(1) + +usage= "usage: " + " $counts_matrix" + " $dispersion" + +if len(sys.argv)<2: + print "Require at least two parameters, " + usage +else: + print "All good- command going ahead" +print " " + +def run_command(cmd): + # 2017-10-02 + # Cicada Dennis put the subprocess command in a try/except statement. + # Errors were going undetected the way it was written previously. + print "Running command:\n\t" + cmd + try: + pipe = subprocess.Popen(cmd, shell=True, stderr=subprocess.PIPE, stdout=subprocess.PIPE) + cmd_stdout, cmd_stderr = pipe.communicate() + except: + msg = "ERROR while running command:\n\t" + cmd + sys.stderr.write(msg) + raise + + sys.stdout.write(cmd_stdout) + ret = pipe.returncode + if ret: + print "command died: " + str(ret) + sys.stderr.write(cmd_stderr) + sys.exit(ret) + else: + # Any error output is written to stdout instead of stderr, since no error has occurred. + sys.stderr.write(cmd_stderr) + return + +print "" + +countmatrix= "counts_matrix" + +cmd= "cp " + sys.argv[1] + " " + countmatrix +run_command(cmd) + +cmd= TRINITY_BASE_DIR + "/Analysis/DifferentialExpression/run_DE_analysis.pl "+ " --matrix "+ countmatrix + " --method edgeR " + " --output edgeR_results "+ " --dispersion " + sys.argv[2] + " --tar_gz_outdir" + +run_command(cmd) + +sys.exit(0) |
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| diff -r 000000000000 -r f36264827fb4 ctat_edger_differential_expression.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ctat_edger_differential_expression.xml Tue Jul 17 11:52:09 2018 -0400 |
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| @@ -0,0 +1,76 @@ +<tool id="ctat_edger_differential_expression" name="ctat_edger_differential_expression" version="1.0.0" profile="17.05"> + + <description>Identify Differentially Expressed Transcripts Using EdgeR</description> + <requirements> + <requirement type="package" version="2.7">python</requirement> + <requirement type="package">subprocess32</requirement> + <requirement type="package">bzip2</requirement> + <requirement type="package" version="1.3.0">rsem</requirement> + <requirement type="package" version="3">bioconductor-edger</requirement> + <requirement type="package" version="2">bioconductor-qvalue</requirement> + <requirement type="package" version="2.6.6">trinity</requirement> + </requirements> + <command detect_errors="exit_code"> + <![CDATA[ + python $__tool_directory__/ctat_edger_differential_expression.py + $counts_matrix + $dispersion + ]]> + </command> + <inputs> + + <param type="data" format="txt" name="counts_matrix" label="Matrix of RNA-Seq fragment counts for transcripts per condition" /> + <param type="data" format="fasta" name="transcripts_fasta_file" label="Transcripts fasta file corresponding to matrix" /> + <param type="float" name="dispersion" value="0.1" min="0" label="dispersion value" help="Dispersion value to be used in the negative binomial" /> + + </inputs> + <outputs> + <!-- + <data format="tar.gz" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" /> + --> + <data format="txt" name="EdgeR_Archive" label="${tool.name} on ${on_string}: EdgeR_Results.tar.gz" from_work_dir="edgeR_results.tar.gz" /> + + </outputs> + <tests> + <test> + <param name="counts_matrix" value="Sp.counts.matrix" /> + <!-- The transcripts_fasta_file does not seem to be used for anything. --> + <param name="transcripts_fasta_file" value="Sp.Trinity.fasta" /> + <param name="dispersion" value="0.1" /> + + <!-- One could create more detailed tests if the output files were explicitly + saved rather than placed into an archive. We had a case where the archive + was being created, but it was missing one of the files, or one of the + files was empty. There is no easy way to look into the archive file to + test this. + --> + <output name="EdgeR_Archive" > + <assert_contents> + <has_line_matching expression=".+" /> + <!-- The following is the magic number for all gzip files. --> + <has_text_matching expression="\x1F\x8B" /> + </assert_contents> + </output> + </test> + </tests> + <help> +.. class:: infomark + +edgeR is a Bioconductor package focusing on the analysis of digital gene expression data derived from RNA-Seq sequencing technologies. + +To learn more about edgeR read their paper_, visit their website_ , or read this user_ guide_ . +If you are following the Trinity RNA-seq protocol please go here_ for a galaxy tool walk through or the Nature Protocols publication_ . + +.. _paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2796818/ +.. _publication: http://www.nature.com/nprot/journal/v8/n8/full/nprot.2013.084.html +.. _user: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf +.. _guide: https://bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf +.. _website: http://bioinf.wehi.edu.au/edgeR/ +.. _here: https://github.com/trinityrnaseq/GalaxyTrinityProtocol/wiki + </help> + + <citations> + <citation type="doi">10.1038/nbt.1883</citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r f36264827fb4 test-data/Sp.Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Sp.Trinity.fasta Tue Jul 17 11:52:09 2018 -0400 |
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| b'@@ -0,0 +1,5256 @@\n+>TRINITY_DN75_c0_g1_i1 len=570 path=[548:0-569] [-1, 548, -2]\n+AAGGTTTAAGCAAAGTCCCGTTGCTAGCAATATGCCTACTTATGGAAGCTCTAACCGTAC\n+GGTTCAATCCCAAAAGCGCTCGATTCGGGACAAATATATACAAATGCCAAATGATTCTAC\n+GCAAGCTTCCCTTATGCCTTCTTATACCAGAAAAACTAGCAATGCATCAAAGAAACTTAC\n+TACTGAAGAAGATGAATTTTATGACTCAGAAGAAGAGCCTGAAGCCATAGTTCACAGGGA\n+TACATCGGCGTTAGAGAGAACTGTACTCAATTTTATAAACAGCAGTACTGCTAAGGAACT\n+CTCTGATACTGCTAGTTGCCCTTTGTCCCACTCGAAACTCCTTTTAGAGCATCGTCCTTT\n+CCAGACACTTGCCGAAGCTTGTATCATCAAACATCCTGATGACGTTCCTAGCAAACCTGG\n+TAGACGTGGAAGGCGTCGTGAAAAAAATCCTATGGGCCAAAAAATCGTCAATGCTTGTAT\n+GGAAACCATGGAAGGATATTATGCAATTGATAATCTAATTGCCAAATGCGAGTTTCTTGG\n+TAATCGTATATCTAAAGGTATGGCCTCGTG\n+>TRINITY_DN55_c0_g1_i1 len=2583 path=[2561:0-393 5289:394-417 2956:418-1586 5290:1587-1610 4149:1611-1646 5292:1647-1670 4209:1671-2169 5291:2170-2193 4732:2194-2582] [-1, 2561, 5289, 2956, 5290, 4149, 5292, 4209, 5291, 4732, -2]\n+GTTATTTATAACCCATTTCCCACTAAGTTCCTTTGTTGAACGCTTAAAAGATTGTTCATA\n+CGTTTGAACATATTTAAAATCACGTTATAGCTGAGAAGAAAACCCCTTTTCAAGTAATAA\n+AAGTATATTTAATTACTTATTTTACCCTTTATATTACGAACTGTACGACTTAACCGGTTT\n+TATCTATAAATTCCTTCATTTTTCTTTGTTTTCGTTTTCAATTTGATTTCATTACAAAAT\n+GTCGAACACAGAAACTTTCAAGTTTGAGGCTGAAATCAGCCAGTTGATGTCTTTAATCAT\n+CAACACTGTTTATTCTAACAAGGAAATTTTCCTTCGTGAGCTTATTTCCAACGCTTCCGA\n+TGCCTTGGACAAAATTCGTTATCAAAGCCTTTCCGATCCTCATGCCTTAGACGCTGAGAA\n+GGATCTTTTCATTCGCATTACTCCTGACAAGGAGAACAAAATCCTTAGCATTCGCGATAC\n+CGGTATTGGTATGACCAAGAATGACCTTATCAACAACCTTGGTGTTATCGCCAAGTCTGG\n+TACTAAGCAGTTTATGGAAGCTGCTGCTTCTGGTGCTGATATCTCCATGATTGGTCAATT\n+CGGTGTTGGTTTCTACTCTGCATACTTGGTTGCCGACAAGGTCCAAGTCGTAAGTAAGCA\n+TAATGACGATGAGCAATACATCTGGGAATCCTCTGCTGGTGGTAGCTTCACCGTCACTTT\n+GGACACCGATGGACCTCGCTTGTTACGTGGTACCGAGATTCGTCTCTTCATGAAAGAAGA\n+CCAACTTCAATACCTCGAGGAAAAGACTATCAAAGATACCGTCAAGAAACATAGTGAGTT\n+CATCTCTTACCCCATTCAATTAGTTGTTACCCGTGAGGTTGAGAAGGAGGTCCCTGAAGA\n+AGAAGAGACCGAAGAAGTTAAGAATGAAGAAGACGATAAGGCTCCTAAGATTGAGGAGGT\n+TGATGATGAATCTGAGAAGAAGGAGAAGAAGACCAAGAAGGTCAAGGAGACCACCACTGA\n+GACTGAGGAGTTGAACAAGACCAAGCCCATTTGGACTCGCAACCCCAGTGAAGTTACCAA\n+GGAAGAGTATGCCTCTTTCTACAAGTCTTTGACTAACGACTGGGAAGACCATTTGGCCGT\n+CAAGCACTTCAGCGTTGAAGGTCAATTGGAATTCCGTGCCATTCTTTTCGTCCCCCGCCG\n+CGCTCCTATGGACCTTTTTGAGGCCAAGCGTAAGAAGAACAACATCAAGCTCTATGTTCG\n+CCGTGTTTTCATTACCGACGACTGTGAAGAGTTGATTCCTGAATGGTTGGGTTTCATTAA\n+GGGTGTTGTTGATTCTGAGGACTTGCCCTTGAACTTGTCTCGTGAGATGCTTCAACAAAA\n+CAAGATCATGAAGGTTATTCGTAAGAACCTTGTCCGTCGTTGTCTTGATATGTTCAACGA\n+GATTGCCGAGGACAAGGAGAACTTCAAGACTTTCTACGATGCTTTCAGCAAGAATTTGAA\n+GCTTGGTATCCATGAGGATGCTGCTAACCGCCCTGCTTTAGCCAAGCTTTTGCGTTACAA\n+CTCCCTTAACTCCCCTGATGATCTTATCAGTCTTGAGGACTACATCACTAAGATGCCCGA\n+ACATCAAAAGAACATTTATTTCATCACTGGTGAATCTAAGCAAGCCGTTGAGAACTCTCC\n+CTTCTTGGAAATCTTCCGTGCCAAGAAGTTTGATGTTCTCTTCATGGTTGACCCCATTGA\n+TGAGTACGCTGTCACTCAACTCAAGGAATTCGAGGGCAAGAAATTGGTTAACATTACTAA\n+GGATGGTCTTGAGTTGGAAGAGACTGACGAGGAGAAGGCTGCTCGCGAGAAGCTCGAAAA\n+AGAGTATGAGGAGTTTGCTAAGCAACTTAAGACCATTTTGGGTGACAAGGTTGAAAAGGT\n+TGTTGTTTCTAACAAGATTGTTGGTTCTCCTTGCTTGTTAACTACCGGTCAATATGGTTG\n+GTCTGCTAACATGGAACGTATCATGAAGGCTCAAGCCCTTCGTGATACTTCTATGAGTGC\n+CTATATGTCTAGCCGCAAGACTTTTGAGATTAACCCCAAGTCTCCCATCATTGCTGAGCT\n+CAAGAAGAAGGTTGAGGAGAATGGTGCCGAAGACCGCTCTGTGAAGGATCTTGCTACTAT\n+TTTGTATGAGACCGCCTTGTTGTCCTCTGGTTTCACTCTTGATGACCCTAGTGCTTATGC\n+TCAACGTATCAACCGTCTTATTTCTCTTGGTCTTAGCATTGACGAAGAGGAGGAGGCTCC\n+TATTGAGGAAATTTCTACCGAATCCGTCGCTGCTGAAAACAATGCTGAGAGCAAGATGGA\n+GGAAGTCGATTAAATCAAATGCATCTAATGTGTCTTTCCAAAATTTATGCATATAATGTT\n+TTTCTTGGATTAAAGCAAGTTATCCTATACATTGTTAACGATTCTAGTGTCTGTTGTCAT\n+TCAAAAATTTCTTTCTACACGATTTTTCTTAATACACACTAGATTACAGGTTGTTTGGAA\n+GTTGTTATAATATGGAATGTTGATTAGTAATATTAAAGTTTATGGATACTTATTAGTACA\n+TCA\n+>TRINITY_DN72_c0_g1_i1 len=381 path=[551:0-380] [-1, 551, -2]\n+TTCCAGTCCTGTCTTATGAGAACCGTACTTTGAATTCTGAAGTCCATTTCTTAAAATTTG\n+TTTTACCGGTGAAGACGGTAAACTCAAATCAGGATTACTAACGACCCTTTGCTTTTTATG\n+CAGTCGTTTAGACACGGTCTGTCCTGGCGAGCGCTTTTGCTTGTTTAACTCTGAAACTGT\n+CACGTCTAAAAAGTTCCAAACTTCCGATTCCGAAGAAATTCTCTTCAAACCATTATCTTT\n+TTCCTTACATTTTCCTCTTTTCATTTCAAGGTTTCTTCAATCCGCCTGGCTTGACATCGA\n+TTCTTTACAAAAATGGAGGAACACGGTCGTACCAACTCACAATGTAGCTTG'..b'GCTTTCCAATGGATTGAACG\n+AATTGCTTGACAGTCTCCTTGGGACTCTCAGTGCTACCACTGTATACAAAAAGGTCGATA\n+ACACCACCGATCATTCGATACTGAAGATAATCTTGGCGCAAAAGAACATCCATTCCATTA\n+GCTGTAAGCATAAGAACACCATGAGAAGAAGAAGTATAAGTGGTTTCGTTCAAAGTTGAA\n+TTTATACCATCCGCCTTGTATCTTTGTTCTAAATAGTATGGATGACTTCCGTACATGTTT\n+TGGTCCACGGGGCTAGGTTCATCATTAGCCCAAAAGGTACGGGTTAAGTTATTTCCCAGA\n+CGTAAACCATGGATGGTTTCAGCGAGACCATAAAGATTATAATTTTCAACCATATTAGTA\n+GTTAACTCAATATACTGATCTTCGAAAACCAATTTCTGTCCGCGTGTATCAAATAAAACT\n+TCACCATCGCTCTTACGTGTAACCCAAAATTCGAAAGGATTGGCATTGTACGAAAAGTTG\n+TACAGAAGGTTTGTGTTATTGTAAGAAGGTGAATATAAGGGAGCATCCCAAAGATCTTTC\n+CTACTGGTAAATTGGAATTGAGTGTTATTAGCGTCTTTGATTGATATATGAACTCGGTCG\n+GCTTCCTCATATGTGACGTTGAGGAACAACAATGGGTAATCAGTACCATAGGCATAGCAA\n+GGCTCGCCGAGTAGTGCGAGATAGGCAGTAACGCCATTTTGTGACTCAGATATGTTAACA\n+GCTTGATATCCTTGACAATTTACACCGCGATATGGGTCATATACGGATAAGCGTTGAGGG\n+ATACCATTGGTAGGGATAGTGACATTGCGATCACCAATGACATTGAAAGTTTGGTAGACG\n+TTACCGACAGCAATCGAGATTGCTGAAAACAGAGCAGTTAAAAATAGAGATTGGTAGGCA\n+GTAGAAATCATCATCGTTAAAAAAAAACAAAAAAGAGATCAAAAAGTTTTAAGAAAAATC\n+AAAGTACCAACTAAAAAGAATCGTAGAGAAAAAGAATGGAAAAGATTAACCAAAAAGGCA\n+ATTTGGCAATAGAAGGGCGGTTTAAAGAGGCGAAATCGTAAAGAAAAGGAGGGTTTTAAG\n+AGACAGACAAAAAATTAAGCAAGAACTACAACAATAGAATTGTAGACTTTCTTGTCCAAG\n+TTTTTTTTTCAATATAAATAAAAAGTTATATATATATATGTGTGTGTGTATGTATATATA\n+TAGTAAGTTAGGAAAGAAAAGCTCTTTCACGAAAAGCTTGAAAGGGTTTGTTTAAACGCG\n+CGTTTTAAAAAGGAGCGAAACCCAAAAAAAGGTAAGAGGTAGGATTAACCAATCAAGTCC\n+AAAACGACGTAATTAAGAGCGGCTAAGCGAACCTTATAAAAGTGGGGGAGAAACTTTTGT\n+AGCTTGTGTTACTTAGCACTTTTTGCAAAACGAAGTGTATGTTCGCTTGAAGGTGCAAAG\n+AACGAGGAGGAAGCGAAAAGCCTTGATTAATTGATTTGATGGGTAAAGCCTTTGAAAGCC\n+AAGTCGAATCGAATCAATCTAAAAGCAAAAAAAAAGATAATCAAACCCAACGTTTAGTAA\n+CTTTTTTGTAAAAAAAGTAGGGCGATAGGTTGGAAAATGGATCGATTTTCTCGTGGGGAT\n+GGAATCAATCGACTCGTTTCTTTTGCAATGTGGGGAGACTTACTAAGGCGGATGTGGGGG\n+GAGGACAAAAAAACAAGTAGCAAAGAATCAAAACTTAACAAAATAAATTAAAGGTGTGGA\n+AGGTTTGAGAGCACTTCTGTTCTAGTGGAACAGATATTGCTTGGTTTTAATAAAGGGAGT\n+GGTGTAATCACAGGAGAAAACAGTAGGAAAACTATTGAGTTATACCCAACTGTGTTACCA\n+ATAGAGTACAGACACTGGAAGATTTCGGATCAAAAAAGTTGATGAAAACTTAGAACCAAA\n+AAGGCGCGAGGTATTCACTTGACTTATG\n+>TRINITY_DN217_c0_g1_i1 len=1840 path=[1:0-1839] [-1, 1, -2]\n+AAGAAATCTGCAGCTTAATTTGAAAACACTAAAAAAACCTGCATTCTTCTTTTTTCCACG\n+AAAGATCTGTTGCTGCTTACGCTATTATTTGTTATTATTATAAATAATAATAACATTTCT\n+ATCGATAACTTCGTTTCATATAGTTTTTAACATTTACTCCTTCCCACTTTTTTGTATAAT\n+ACTCTTCAAAAATGGCCCCTCAATTCAAACGCCCTGAGCTCTTTGGCTTTGATAAGTCTC\n+ATGCTCAATCTTTTGTTCAAGGAAAATGGATTTCTTCTCCTAACAACAAAACTTTTGAGG\n+TTGATAACCCAGCTACTGGTGAAATAATCGGTAAAGTGGCCGATGTCTCAGTAGAGGAAA\n+CAAAAAAAGCCATCAGTGCCGCTAACGAGGCCTTCAAAACTTATAAAAATTTTACTCATG\n+TCCAACGTAGTCAGTTATTGGAACGCTGGGCAGAGCTTATTATGGAGAACAAAGACGACT\n+TGGTCAAGATGCTTACCTTAGAAAACGGCAAGCCTTTGAGCCAAGCTGAGATGGAGGTCA\n+CCACATGTAGCGGATATCTTAAATGGTATGCTGCTGAAGCCGTTCGTACCTTTGGCGATG\n+TAGCTCCTTCCAGCTTACAAAGTCAAAACTTTCTCATCTCCATCAAACAGCCAGTTGGTG\n+TCAGTGCCTTGATTACTCCTTGGAACTTCCCCGCCGCCATGATTGCTCGTAAAGGTGGTG\n+CCGCTTTGGCTGCTGGTTGTACCGCTATTTTCTTGCCTGCTTTCCGCACTCCCTACGTTT\n+GCTTAGGTTTAGTCAGGTTGGCGCAAGAGGCCGGTTTCCCTGACGGTGTCTTAAATGTGA\n+TCACTTCTTCTGATGCATCTGCTCATGGTAAAGAACTGACTACCAACCCTATCGTTCGTA\n+AGGTTTCCTTCACTGGTAGTACTAATGTCGGTAAAATTCTTATGGGACAAAGTGCCAGCA\n+CAATCAAGAAGGTTTCAATGGAGTTAGGAGGTAATGCCCCTTTCATTGTATTCCCTGACT\n+TCCCCATTGATCAGGCTGTCGAATCTTTCTGCACTATCAAGTTTAACTCTTGTGGTCAAG\n+TTTGTGTCTGCCCTAACAGAGTTTACGTTCACAAGAATGTTTACGACGAATTCGTCAGCA\n+AGCTTACCGAAAAAGTCAAGACCATTAAAGTAGGAGATGGATTTGACTCTTCTTCTGCTG\n+TTGGCCCTTTGATTTCTCAAGATGGATGCAAAAAGGTCAGCAAGCACATTGAAGATGCTG\n+TTTCAAAGGGTGCCAAAATCACTGTTGGTGGAAAGGAGATTTCCTCAAGCAAAGGTTATT\n+TTTTTGAACCAACCGTGCTCTCCGGTGTAACTCAAGACATGTTGGTTGCTAGCGAGGAAA\n+CATTCGGCCCACTCGCCTCTGTCTTCAAGTTCGACGACACCGAAGAGGTGATCGAATGGG\n+CTAACGACAGTGATGTTGGCTTGGCCGGTTACGTCTTTACCAATAACTTGTCCACAATGA\n+TCCACGTTGCCAAAGAACTAGAGGTGGGTCTTGTAGGTGCCAATATCGAAATGGTTGACG\n+AACCATTTATTTCCTTTGGCGGCATCAAACAGAGCGGTTTTGGCAAGGAAGCCGGTCGTT\n+TGGGCGTTCAAGAATTTATGGTGGTTAAGGAAATCAATCTCAAGACTCTTTAAGGATTTT\n+CGCTTTAGAAAGCTGCATATTATTGAACAAGCAATGATGTCCTCTTTTGGTTAATGACTA\n+AAAAATCCTGATGTTATGACTGTTTTACATGTTTGCGATACAAATCGTATTTTAGTTTAA\n+TGATATCAAAAAAATTTAATACCTGAAAAAAAAAAAAAAA\n' 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| diff -r 000000000000 -r f36264827fb4 test-data/Sp.counts.matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Sp.counts.matrix Tue Jul 17 11:52:09 2018 -0400 |
| b |
| b'@@ -0,0 +1,353 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|