| Next changeset 1:fdc55fd74f78 (2013-10-01) |
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Commit message:
Uploaded tool tarball. |
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added:
cuffmerge_wrapper.py cuffmerge_wrapper.xml test-data/cuffcompare_in1.gtf test-data/cuffcompare_in2.gtf test-data/cuffcompare_in3.gtf test-data/cuffmerge_out1.gtf tool_dependencies.xml |
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| diff -r 000000000000 -r dbbd37e013aa cuffmerge_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cuffmerge_wrapper.py Tue Oct 01 12:57:24 2013 -0400 |
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| @@ -0,0 +1,138 @@ +#!/usr/bin/env python + +# Supports Cuffmerge versions 1.3 and newer. + +import optparse, os, shutil, subprocess, sys, tempfile + +def stop_err( msg ): + sys.stderr.write( '%s\n' % msg ) + sys.exit() + +# Copied from sam_to_bam.py: +def check_seq_file( dbkey, cached_seqs_pointer_file ): + seq_path = '' + for line in open( cached_seqs_pointer_file ): + line = line.rstrip( '\r\n' ) + if line and not line.startswith( '#' ) and line.startswith( 'index' ): + fields = line.split( '\t' ) + if len( fields ) < 3: + continue + if fields[1] == dbkey: + seq_path = fields[2].strip() + break + return seq_path + +def __main__(): + #Parse Command Line + parser = optparse.OptionParser() + parser.add_option( '-g', dest='ref_annotation', help='An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.' ) + parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffmerge to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.') + parser.add_option( '-p', '--num-threads', dest='num_threads', help='Use this many threads to align reads. The default is 1.' ) + + + # Wrapper / Galaxy options. + parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) + parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) + parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) + + # Outputs. + parser.add_option( '', '--merged-transcripts', dest='merged_transcripts' ) + + (options, args) = parser.parse_args() + + # output version # of tool + try: + tmp = tempfile.NamedTemporaryFile().name + tmp_stdout = open( tmp, 'wb' ) + proc = subprocess.Popen( args='cuffmerge -v 2>&1', shell=True, stdout=tmp_stdout ) + tmp_stdout.close() + returncode = proc.wait() + stdout = None + for line in open( tmp_stdout.name, 'rb' ): + if line.lower().find( 'merge_cuff_asms v' ) >= 0: + stdout = line.strip() + break + if stdout: + sys.stdout.write( '%s\n' % stdout ) + else: + raise Exception + except: + sys.stdout.write( 'Could not determine Cuffmerge version\n' ) + + # Set/link to sequence file. + if options.use_seq_data: + if options.ref_file != 'None': + # Sequence data from history. + # Create symbolic link to ref_file so that index will be created in working directory. + seq_path = "ref.fa" + os.symlink( options.ref_file, seq_path ) + else: + # Sequence data from loc file. + cached_seqs_pointer_file = os.path.join( options.index_dir, 'sam_fa_indices.loc' ) + if not os.path.exists( cached_seqs_pointer_file ): + stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) + # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, + # and the equCab2.fa file will contain fasta sequences. + seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) + if seq_path == '': + stop_err( 'No sequence data found for dbkey %s, so sequence data cannot be used.' % options.dbkey ) + + # Build command. + + # Base. + cmd = "cuffmerge -o cm_output " + + # Add options. + if options.num_threads: + cmd += ( " -p %i " % int ( options.num_threads ) ) + if options.ref_annotation: + cmd += " -g %s " % options.ref_annotation + if options.use_seq_data: + cmd += " -s %s " % seq_path + + # Add input files to a file. + inputs_file_name = tempfile.NamedTemporaryFile( dir="." ).name + inputs_file = open( inputs_file_name, 'w' ) + for arg in args: + inputs_file.write( arg + "\n" ) + inputs_file.close() + cmd += inputs_file_name + + # Debugging. + print cmd + + # Run command. + try: + tmp_name = tempfile.NamedTemporaryFile( dir="." ).name + tmp_stderr = open( tmp_name, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, stderr=tmp_stderr.fileno() ) + returncode = proc.wait() + tmp_stderr.close() + + # Get stderr, allowing for case where it's very large. + tmp_stderr = open( tmp_name, 'rb' ) + stderr = '' + buffsize = 1048576 + try: + while True: + stderr += tmp_stderr.read( buffsize ) + if not stderr or len( stderr ) % buffsize != 0: + break + except OverflowError: + pass + tmp_stderr.close() + + # Error checking. + if returncode != 0: + raise Exception, stderr + + if len( open( "cm_output/merged.gtf", 'rb' ).read().strip() ) == 0: + raise Exception, 'The output file is empty, there may be an error with your input file or settings.' + + # Copy outputs. + shutil.copyfile( "cm_output/merged.gtf" , options.merged_transcripts ) + + except Exception, e: + stop_err( 'Error running cuffmerge. ' + str( e ) ) + +if __name__=="__main__": __main__() |
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| diff -r 000000000000 -r dbbd37e013aa cuffmerge_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cuffmerge_wrapper.xml Tue Oct 01 12:57:24 2013 -0400 |
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| @@ -0,0 +1,129 @@ +<tool id="cuffmerge" name="Cuffmerge" version="0.0.5"> + <!-- Wrapper supports Cuffmerge versions 1.3 and newer --> + <description>merge together several Cufflinks assemblies</description> + <requirements> + <requirement type="package" version="2.1.1">cufflinks</requirement> + </requirements> + <command interpreter="python"> + cuffmerge_wrapper.py + + --num-threads="4" + + ## Use annotation reference? + #if $annotation.use_ref_annotation == "Yes": + -g $annotation.reference_annotation + #end if + + ## Use sequence data? + #if $seq_data.use_seq_data == "Yes": + -s + #if $seq_data.seq_source.index_source == "history": + --ref_file=$seq_data.seq_source.ref_file + #else: + --ref_file="None" + #end if + --dbkey=${first_input.metadata.dbkey} + --index_dir=${GALAXY_DATA_INDEX_DIR} + #end if + + ## Outputs. + --merged-transcripts=${merged_transcripts} + + ## Inputs. + ${first_input} + #for $input_file in $input_files: + ${input_file.additional_input} + #end for + + </command> + <inputs> + <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/> + <repeat name="input_files" title="Additional GTF Input Files"> + <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/> + </repeat> + <conditional name="annotation"> + <param name="use_ref_annotation" type="select" label="Use Reference Annotation"> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="Yes"> + <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/> + </when> + <when value="No"> + </when> + </conditional> + <conditional name="seq_data"> + <param name="use_seq_data" type="select" label="Use Sequence Data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff."> + <option value="No">No</option> + <option value="Yes">Yes</option> + </param> + <when value="No"></when> + <when value="Yes"> + <conditional name="seq_source"> + <param name="index_source" type="select" label="Choose the source for the reference list"> + <option value="cached">Locally cached</option> + <option value="history">History</option> + </param> + <when value="cached"></when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + </when> + </conditional> + </when> + </conditional> + </inputs> + + <outputs> + <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/> + </outputs> + + <tests> + <!-- + cuffmerge -g cuffcompare_in3.gtf cuffcompare_in1.gtf cuffcompare_in2.gtf + --> + <test> + <param name="first_input" value="cuffcompare_in1.gtf" ftype="gtf"/> + <param name="additional_input" value="cuffcompare_in2.gtf" ftype="gtf"/> + <param name="use_ref_annotation" value="Yes"/> + <param name="reference_annotation" value="cuffcompare_in3.gtf" ftype="gtf"/> + <param name="use_seq_data" value="No"/> + <!-- oId assignment differ/are non-deterministic --> + <output name="merged_transcripts" file="cuffmerge_out1.gtf" lines_diff="50"/> + </test> + </tests> + + <help> +**Cuffmerge Overview** + +Cuffmerge is part of Cufflinks_. Please cite: Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology doi:10.1038/nbt.1621 + +.. _Cufflinks: http://cufflinks.cbcb.umd.edu/ + +------ + +**Know what you are doing** + +.. class:: warningmark + +There is no such thing (yet) as an automated gearshift in expression analysis. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy. + +.. __: http://cufflinks.cbcb.umd.edu/manual.html#cuffmerge + +------ + +**Input format** + +Cuffmerge takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl_) + +.. _Ensembl: http://www.ensembl.org + +------ + +**Outputs** + +Cuffmerge produces the following output files: + +Merged transcripts file: + +Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. </help> +</tool> |
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| diff -r 000000000000 -r dbbd37e013aa test-data/cuffcompare_in1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in1.gtf Tue Oct 01 12:57:24 2013 -0400 |
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| b'@@ -0,0 +1,100 @@\n+chr1\tCufflinks\ttranscript\t3111450\t3111490\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\texon\t3111450\t3111490\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073";\n+chr1\tCufflinks\ttranscript\t3111546\t3111576\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";\n+chr1\tCufflinks\texon\t3111546\t3111576\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "27.2556579354"; frac "1.000000"; conf_lo "0.000000"; conf_hi "65.800979"; cov "1.741935";\n+chr1\tCufflinks\ttranscript\t3200326\t3200352\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3200326\t3200352\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3200023\t3200191\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\texon\t3200023\t3200191\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "9.9991171124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "19.998234"; cov "0.639053";\n+chr1\tCufflinks\ttranscript\t3201078\t3201481\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\texon\t3201078\t3201481\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "17.7768957078"; frac "1.000000"; conf_lo "9.153835"; conf_hi "26.399957"; cov "1.136139";\n+chr1\tCufflinks\ttranscript\t3201673\t3201699\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3201673\t3201699\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3204755\t3204833\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3204755\t3204833\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3212214\t3212292\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\texon\t3212214\t3212292\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "10.6952581772"; frac "1.000000"; conf_lo "0.000000"; conf_hi "25.820637"; cov "0.683544";\n+chr1\tCufflinks\ttranscript\t3213096\t3213192\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\texon\t3213096\t3213192\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "8.7105710927"; frac "1.000000"; conf_lo "0.000000"; conf_hi "21.029179"; cov "0.556701";\n+chr1\tCufflinks\ttranscript\t3212368\t3212439\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks\texon\t3212368\t3212439\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "29.3376873610"; frac "1.000000"; conf_lo "3.097262"; conf_hi "55.578113"; cov "1.875000";\n+chr1\tCufflinks'..b'0000";\n+chr1\tCufflinks\ttranscript\t3363215\t3363278\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\texon\t3363215\t3363278\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.872349"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3363754\t3363849\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\texon\t3363754\t3363849\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "13.2019593124"; frac "1.000000"; conf_lo "0.000000"; conf_hi "28.446269"; cov "0.843750";\n+chr1\tCufflinks\ttranscript\t3367136\t3367162\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3367136\t3367162\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3367334\t3367382\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\texon\t3367334\t3367382\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "17.2433754285"; frac "1.000000"; conf_lo "0.000000"; conf_hi "41.629191"; cov "1.102041";\n+chr1\tCufflinks\ttranscript\t3377212\t3377262\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\texon\t3377212\t3377262\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "16.5671646274"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.996674"; cov "1.058824";\n+chr1\tCufflinks\ttranscript\t3391326\t3391352\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\texon\t3391326\t3391352\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "31.2935331850"; frac "1.000000"; conf_lo "0.000000"; conf_hi "75.549272"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3435842\t3435880\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\texon\t3435842\t3435880\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "21.6647537435"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.303342"; cov "1.384615";\n+chr1\tCufflinks\ttranscript\t3447762\t3447788\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\texon\t3447762\t3447788\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "46.9402997776"; frac "1.000000"; conf_lo "0.000000"; conf_hi "101.142289"; cov "3.000000";\n+chr1\tCufflinks\ttranscript\t3450907\t3450965\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\texon\t3450907\t3450965\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "21.4811541355"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.285454"; cov "1.372881";\n+chr1\tCufflinks\ttranscript\t3451052\t3451109\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n+chr1\tCufflinks\texon\t3451052\t3451109\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.169489"; cov "0.931034";\n' |
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| diff -r 000000000000 -r dbbd37e013aa test-data/cuffcompare_in2.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in2.gtf Tue Oct 01 12:57:24 2013 -0400 |
| b |
| b'@@ -0,0 +1,100 @@\n+chr1\tCufflinks\ttranscript\t3174766\t3174792\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3174766\t3174792\t1000\t.\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3187402\t3187428\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3187402\t3187428\t1000\t.\t.\tgene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3188522\t3188548\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; 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FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3192650\t3192676\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3194707\t3194733\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3194707\t3194733\t1000\t.\t.\tgene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3197426\t3197452\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3197426\t3197452\t1000\t.\t.\tgene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1'..b'760563";\n+chr1\tCufflinks\ttranscript\t3355908\t3356119\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792";\n+chr1\tCufflinks\texon\t3355908\t3356119\t1000\t.\t.\tgene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792";\n+chr1\tCufflinks\ttranscript\t3356181\t3356225\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000";\n+chr1\tCufflinks\texon\t3356181\t3356225\t1000\t.\t.\tgene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000";\n+chr1\tCufflinks\ttranscript\t3363077\t3363176\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000";\n+chr1\tCufflinks\texon\t3363077\t3363176\t1000\t.\t.\tgene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000";\n+chr1\tCufflinks\ttranscript\t3363388\t3363446\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881";\n+chr1\tCufflinks\texon\t3363388\t3363446\t1000\t.\t.\tgene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881";\n+chr1\tCufflinks\ttranscript\t3364872\t3364919\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500";\n+chr1\tCufflinks\texon\t3364872\t3364919\t1000\t.\t.\tgene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500";\n+chr1\tCufflinks\ttranscript\t3367211\t3367237\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3367211\t3367237\t1000\t.\t.\tgene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3369581\t3369607\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3369581\t3369607\t1000\t.\t.\tgene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3375002\t3375028\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3375002\t3375028\t1000\t.\t.\tgene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3379889\t3379915\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\texon\t3379889\t3379915\t1000\t.\t.\tgene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000";\n+chr1\tCufflinks\ttranscript\t3386740\t3386836\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";\n+chr1\tCufflinks\texon\t3386740\t3386836\t1000\t.\t.\tgene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402";\n' |
| b |
| diff -r 000000000000 -r dbbd37e013aa test-data/cuffcompare_in3.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in3.gtf Tue Oct 01 12:57:24 2013 -0400 |
| b |
| b'@@ -0,0 +1,100 @@\n+chr1\tmm9_refFlat\tstop_codon\t3206103\t3206105\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tCDS\t3206106\t3207049\t0.000000\t-\t2\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\texon\t3204563\t3207049\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tCDS\t3411783\t3411982\t0.000000\t-\t1\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\texon\t3411783\t3411982\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tCDS\t3660633\t3661429\t0.000000\t-\t0\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tstart_codon\t3661427\t3661429\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\texon\t3660633\t3661579\t0.000000\t-\t.\tgene_id "Xkr4"; transcript_id "Xkr4"; \n+chr1\tmm9_refFlat\tstop_codon\t4334681\t4334683\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\tCDS\t4334684\t4340172\t0.000000\t-\t2\tgene_id "Rp1"; 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transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4827082\t4827155\t0.000000\t+\t2\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4827082\t4827155\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4829468\t4829569\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4829468\t4829569\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4831037\t4831213\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4831037\t4831213\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4835044\t4835094\t0.000000\t+\t0\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tstop_codon\t4835095\t4835097\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4835044\t4836816\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tstart_codon\t4847995\t4847997\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4847995\t4848057\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4847775\t4848057\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4857551\t4857613\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4857551\t4857613\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4868108\t4868213\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4868108\t4868213\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4876825\t4876912\t0.000000\t+\t2\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4876825\t4876912\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4879538\t4879683\t0.000000\t+\t1\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4879538\t4879683\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4880821\t4880877\t0.000000\t+\t2\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4880821\t4880877\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4881996\t4882150\t0.000000\t+\t2\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4881996\t4882150\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4883498\t4883644\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4883498\t4883644\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4885015\t4885086\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4885015\t4885086\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tCDS\t4886437\t4886442\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tstop_codon\t4886443\t4886445\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\texon\t4886437\t4887987\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; \n+chr1\tmm9_refFlat\tstart_codon\t4847995\t4847997\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n+chr1\tmm9_refFlat\tCDS\t4847995\t4848057\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n+chr1\tmm9_refFlat\texon\t4847775\t4848057\t0.000000\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n+chr1\tmm9_refFlat\tCDS\t4857551\t4857613\t0.000000\t+\t0\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; \n' |
| b |
| diff -r 000000000000 -r dbbd37e013aa test-data/cuffmerge_out1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffmerge_out1.gtf Tue Oct 01 12:57:24 2013 -0400 |
| b |
| b'@@ -0,0 +1,74 @@\n+chr1\tCufflinks\texon\t4797974\t4798063\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";\n+chr1\tCufflinks\texon\t4798536\t4798567\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";\n+chr1\tCufflinks\texon\t4818665\t4818730\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "3"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";\n+chr1\tCufflinks\texon\t4820349\t4820396\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "4"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";\n+chr1\tCufflinks\texon\t4822392\t4822462\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "5"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";\n+chr1\tCufflinks\texon\t4827082\t4827155\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "6"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";\n+chr1\tCufflinks\texon\t4829468\t4829569\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "7"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";\n+chr1\tCufflinks\texon\t4831037\t4831213\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "8"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";\n+chr1\tCufflinks\texon\t4835044\t4836816\t.\t+\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "9"; gene_name "Lypla1"; oId "Lypla1"; nearest_ref "Lypla1"; class_code "="; tss_id "TSS1";\n+chr1\tCufflinks\texon\t4847775\t4848057\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4857551\t4857613\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1_dup1"; contained_in "TCONS_00000003"; nearest_ref "Tcea1_dup1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4847775\t4848057\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "1"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4857551\t4857613\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "2"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4868108\t4868213\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "3"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4876825\t4876912\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "4"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4879538\t4879683\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "5"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4880821\t4880877\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "6"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4881996\t4882150\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "7"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4883498\t4883644\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000003"; exon_number "8"; gene_name "Tcea1"; oId "Tcea1"; nearest_ref "Tcea1"; class_code "="; tss_id "TSS2";\n+chr1\tCufflinks\texon\t4885015\t4885086\t.\t+\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000'..b'12"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS9";\n+chr1\tCufflinks\texon\t3187402\t3187428\t.\t.\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.4.1"; class_code "u"; tss_id "TSS10";\n+chr1\tCufflinks\texon\t3188522\t3188548\t.\t.\t.\tgene_id "XLOC_000011"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS11";\n+chr1\tCufflinks\texon\t3189811\t3190789\t.\t.\t.\tgene_id "XLOC_000012"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.6.1"; class_code "u"; tss_id "TSS12";\n+chr1\tCufflinks\texon\t3190859\t3191434\t.\t.\t.\tgene_id "XLOC_000013"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS13";\n+chr1\tCufflinks\texon\t3191513\t3192077\t.\t.\t.\tgene_id "XLOC_000014"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.8.1"; class_code "u"; tss_id "TSS14";\n+chr1\tCufflinks\texon\t3192251\t3192336\t.\t.\t.\tgene_id "XLOC_000015"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS15";\n+chr1\tCufflinks\texon\t3192442\t3192494\t.\t.\t.\tgene_id "XLOC_000016"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.10.1"; class_code "u"; tss_id "TSS16";\n+chr1\tCufflinks\texon\t3192551\t3192676\t.\t.\t.\tgene_id "XLOC_000017"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS17";\n+chr1\tCufflinks\texon\t3192732\t3192811\t.\t.\t.\tgene_id "XLOC_000018"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.12.1"; class_code "u"; tss_id "TSS18";\n+chr1\tCufflinks\texon\t3192941\t3193042\t.\t.\t.\tgene_id "XLOC_000019"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS19";\n+chr1\tCufflinks\texon\t3194186\t3194226\t.\t.\t.\tgene_id "XLOC_000020"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.14.1"; class_code "u"; tss_id "TSS20";\n+chr1\tCufflinks\texon\t3194303\t3194329\t.\t.\t.\tgene_id "XLOC_000021"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS21";\n+chr1\tCufflinks\texon\t3194707\t3194733\t.\t.\t.\tgene_id "XLOC_000022"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.16.1"; class_code "u"; tss_id "TSS22";\n+chr1\tCufflinks\texon\t3195084\t3195110\t.\t.\t.\tgene_id "XLOC_000023"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS23";\n+chr1\tCufflinks\texon\t3195451\t3195477\t.\t.\t.\tgene_id "XLOC_000024"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.18.1"; class_code "u"; tss_id "TSS24";\n+chr1\tCufflinks\texon\t3197090\t3197116\t.\t.\t.\tgene_id "XLOC_000025"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS25";\n+chr1\tCufflinks\texon\t3197247\t3197273\t.\t.\t.\tgene_id "XLOC_000026"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.20.1"; class_code "u"; tss_id "TSS26";\n+chr1\tCufflinks\texon\t3197347\t3197373\t.\t.\t.\tgene_id "XLOC_000027"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS27";\n+chr1\tCufflinks\texon\t3197426\t3197452\t.\t.\t.\tgene_id "XLOC_000028"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.22.1"; class_code "u"; tss_id "TSS28";\n+chr1\tCufflinks\texon\t3200023\t3200191\t.\t.\t.\tgene_id "XLOC_000029"; transcript_id "TCONS_00000032"; exon_number "1"; oId "CUFF.23.1"; class_code "u"; tss_id "TSS29";\n+chr1\tCufflinks\texon\t3200326\t3200352\t.\t.\t.\tgene_id "XLOC_000030"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.24.1"; class_code "u"; tss_id "TSS30";\n+chr1\tCufflinks\texon\t3200431\t3200457\t.\t.\t.\tgene_id "XLOC_000031"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; tss_id "TSS31";\n+chr1\tCufflinks\texon\t3201008\t3201481\t.\t.\t.\tgene_id "XLOC_000032"; transcript_id "TCONS_00000035"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS32";\n+chr1\tCufflinks\texon\t3201597\t3201809\t.\t.\t.\tgene_id "XLOC_000033"; transcript_id "TCONS_00000036"; exon_number "1"; oId "CUFF.27.1"; class_code "u"; tss_id "TSS33";\n' |
| b |
| diff -r 000000000000 -r dbbd37e013aa tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 01 12:57:24 2013 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="cufflinks" version="2.1.1"> + <repository changeset_revision="394b13717223" name="package_cufflinks_2_1_1" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |