| Next changeset 1:9a3f7a890da6 (2013-10-01) |
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Commit message:
Uploaded tool tarball. |
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added:
cuffcompare_wrapper.py cuffcompare_wrapper.xml test-data/cuffcompare_in1.gtf test-data/cuffcompare_in1_liftover_mapped.bed test-data/cuffcompare_in1_liftover_unmapped.bed test-data/cuffcompare_in1_mult_liftover_mapped.bed test-data/cuffcompare_in1_mult_liftover_unmapped.bed test-data/cuffcompare_in2.gtf test-data/cuffcompare_in3.gtf test-data/cuffcompare_out1.tmap test-data/cuffcompare_out2.refmap test-data/cuffcompare_out3.tmap test-data/cuffcompare_out4.refmap test-data/cuffcompare_out5.gtf test-data/cuffcompare_out6.tracking test-data/cuffcompare_out7.txt test-data/cuffmerge_out1.gtf tool_dependencies.xml |
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| diff -r 000000000000 -r 9d35cf35634e cuffcompare_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cuffcompare_wrapper.py Tue Oct 01 12:49:41 2013 -0400 |
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| @@ -0,0 +1,138 @@ +#!/usr/bin/env python + +# Supports Cuffcompare versions v1.3.0 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( '-r', 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( '-R', action="store_true", dest='ignore_nonoverlap', help='If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts accuracy file' ) + parser.add_option( '-s', dest='use_seq_data', action="store_true", help='Causes cuffcompare 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.') + + # 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( '', '--combined-transcripts', dest='combined_transcripts' ) + + (options, args) = parser.parse_args() + + # output version # of tool + try: + tmp = tempfile.NamedTemporaryFile().name + tmp_stdout = open( tmp, 'wb' ) + proc = subprocess.Popen( args='cuffcompare 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( 'cuffcompare v' ) >= 0: + stdout = line.strip() + break + if stdout: + sys.stdout.write( '%s\n' % stdout ) + else: + raise Exception + except: + sys.stdout.write( 'Could not determine Cuffcompare 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 = "cuffcompare -o cc_output " + + # Add options. + if options.ref_annotation: + cmd += " -r %s " % options.ref_annotation + if options.ignore_nonoverlap: + cmd += " -R " + if options.use_seq_data: + cmd += " -s %s " % seq_path + + # Add input files. + + # Need to symlink inputs so that output files are written to temp directory. + for i, arg in enumerate( args ): + input_file_name = "./input%i" % ( i+1 ) + os.symlink( arg, input_file_name ) + cmd += "%s " % input_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 + + # Copy outputs. + shutil.copyfile( "cc_output.combined.gtf" , options.combined_transcripts ) + + # check that there are results in the output file + cc_output_fname = "cc_output.stats" + if len( open( cc_output_fname, 'rb' ).read().strip() ) == 0: + raise Exception, 'The main output file is empty, there may be an error with your input file or settings.' + except Exception, e: + stop_err( 'Error running cuffcompare. ' + str( e ) ) + +if __name__=="__main__": __main__() |
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| diff -r 000000000000 -r 9d35cf35634e cuffcompare_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cuffcompare_wrapper.xml Tue Oct 01 12:49:41 2013 -0400 |
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| b'@@ -0,0 +1,223 @@\n+<tool id="cuffcompare" name="Cuffcompare" version="0.0.5">\n+ <!-- Wrapper supports Cuffcompare versions v1.3.0 and newer -->\n+ <description>compare assembled transcripts to a reference annotation and track Cufflinks transcripts across multiple experiments</description>\n+ <requirements>\n+ <requirement type="package" version="2.1.1">cufflinks</requirement>\n+ </requirements>\n+ <version_command>cuffcompare 2>&1 | head -n 1</version_command>\n+ <command interpreter="python">\n+ cuffcompare_wrapper.py \n+ \n+ ## Use annotation reference?\n+ #if $annotation.use_ref_annotation == "Yes":\n+ -r $annotation.reference_annotation\n+ #if $annotation.ignore_nonoverlapping_reference:\n+ -R\n+ #end if\n+ #end if\n+ \n+ ## Use sequence data?\n+ #if $seq_data.use_seq_data == "Yes":\n+\t -s\n+ #if $seq_data.seq_source.index_source == "history":\n+ --ref_file=$seq_data.seq_source.ref_file\n+ #else:\n+ --ref_file="None"\n+ #end if\n+ --dbkey=${first_input.metadata.dbkey} \n+ --index_dir=${GALAXY_DATA_INDEX_DIR}\n+ #end if\n+ \n+ ## Outputs.\n+ --combined-transcripts=${transcripts_combined}\n+ \n+ ## Inputs.\n+ ${first_input}\n+ #for $input_file in $input_files:\n+ ${input_file.additional_input}\n+ #end for\n+ \n+ </command>\n+ <inputs>\n+ <param format="gtf" name="first_input" type="data" label="GTF file produced by Cufflinks" help=""/>\n+ <repeat name="input_files" title="Additional GTF Input Files">\n+ <param format="gtf" name="additional_input" type="data" label="GTF file produced by Cufflinks" help=""/>\n+ </repeat>\n+ <conditional name="annotation">\n+ <param name="use_ref_annotation" type="select" label="Use Reference Annotation">\n+ <option value="No">No</option>\n+ <option value="Yes">Yes</option>\n+ </param>\n+ <when value="Yes">\n+ <param format="gff3,gtf" name="reference_annotation" type="data" label="Reference Annotation" help="Requires an annotation file in GFF3 or GTF format."/> \n+ <param name="ignore_nonoverlapping_reference" type="boolean" label="Ignore reference transcripts that are not overlapped by any transcript in input files"/>\n+ </when>\n+ <when value="No">\n+ </when>\n+ </conditional>\n+ <conditional name="seq_data">\n+ <param name="use_seq_data" type="select" label="Use Sequence Data" help="Use sequence data for some optional classification functions, including the addition of the p_id attribute required by Cuffdiff.">\n+ <option value="Yes">Yes</option>\n+ <option value="No">No</option>\n+ </param>\n+ <when value="No"></when>\n+ <when value="Yes">\n+ <conditional name="seq_source">\n+ <param name="index_source" type="select" label="Choose the source for the reference list">\n+ <option value="cached">Locally cached</option>\n+ <option value="history">History</option>\n+ </param>\n+ <when value="cached"></when>\n+ <when value="history">\n+ <param name="ref_file" type="data" format="fasta" label="Using reference file" />\n+ </when>\n+ </conditional>\n+ </when>\n+ </conditional>\n+ </inputs>\n+\n+ <outputs>\n+ <data format="txt" name="transcripts_accuracy" label="${tool.name} on ${on_string}: transcript accuracy" \n+ from_work_dir="cc_output.stats" />\n+ <data format="tabular" name="input1_tm'..b'th of the first and last exons, since these lengths will naturally vary from sample to sample due to the random nature of sequencing.\n+If you ran cuffcompare with the -r option, the first and second columns contain the closest matching reference transcript to the one described by each row.\n+\n+Here\'s an example of a line from the tracking file::\n+\n+ TCONS_00000045 XLOC_000023 Tcea|uc007afj.1\tj\t\\\n+ q1:exp.115|exp.115.0|100|3.061355|0.350242|0.350207 \\\n+ q2:60hr.292|60hr.292.0|100|4.094084|0.000000|0.000000\n+\n+In this example, a transcript present in the two input files, called exp.115.0 in the first and 60hr.292.0 in the second, doesn\'t match any reference transcript exactly, but shares exons with uc007afj.1, an isoform of the gene Tcea, as indicated by the class code j. The first three columns are as follows::\n+\n+ Column number Column name Example Description\n+ -----------------------------------------------------------------------\n+ 1 Cufflinks transfrag id TCONS_00000045 A unique internal id for the transfrag\n+ 2 Cufflinks locus id XLOC_000023 A unique internal id for the locus\n+ 3 Reference gene id Tcea The gene_name attribute of the reference GTF record for this transcript, or \'-\' if no reference transcript overlaps this Cufflinks transcript\n+ 4 Reference transcript id uc007afj.1 The transcript_id attribute of the reference GTF record for this transcript, or \'-\' if no reference transcript overlaps this Cufflinks transcript\n+ 5 Class code c The type of match between the Cufflinks transcripts in column 6 and the reference transcript. See class codes\n+ \n+Each of the columns after the fifth have the following format:\n+ qJ:gene_id|transcript_id|FMI|FPKM|conf_lo|conf_hi\n+\n+A transcript need be present in all samples to be reported in the tracking file. A sample not containing a transcript will have a "-" in its entry in the row for that transcript.\n+\n+Class Codes\n+\n+If you ran cuffcompare with the -r option, tracking rows will contain the following values. If you did not use -r, the rows will all contain "-" in their class code column::\n+\n+ Priority\t Code\t Description\n+ ---------------------------------\n+ 1\t =\t Match\n+ 2\t c\t Contained\t\n+ 3\t j\t New isoform\t\n+ 4\t e\t A single exon transcript overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.\t\n+ 5\t i\t A single exon transcript falling entirely with a reference intron\t\n+ 6\t r\t Repeat. Currently determined by looking at the reference sequence and applied to transcripts where at least 50% of the bases are lower case\t\n+ 7\t p\t Possible polymerase run-on fragment\t\n+ 8\t u\t Unknown, intergenic transcript\t\n+ 9\t o\t Unknown, generic overlap with reference\t\n+ 10 .\t (.tracking file only, indicates multiple classifications)\n+ \n+-------\n+\n+**Settings**\n+\n+All of the options have a default value. You can change any of them. Most of the options in Cuffcompare have been implemented here.\n+\n+------\n+\n+**Cuffcompare parameter list**\n+\n+This is a list of implemented Cuffcompare options::\n+\n+ -r 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.\n+ -R If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the transcripts_accuracy file\n+ </help>\n+</tool>\n' |
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| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_in1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in1.gtf Tue Oct 01 12:49:41 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' |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_in1_liftover_mapped.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in1_liftover_mapped.bed Tue Oct 01 12:49:41 2013 -0400 |
| b |
| b'@@ -0,0 +1,86 @@\n+chr1\tCufflinks\ttranscript\t3022555\t3022596\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\t3022555\t3022596\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\t3117334\t3117360\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\t3117334\t3117360\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\t3117031\t3117199\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\t3117031\t3117199\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\t3118118\t3118521\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\t3118118\t3118521\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\t3118713\t3118739\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\t3118713\t3118739\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\t3121789\t3121867\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\t3121789\t3121867\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\t3128503\t3128581\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\t3128503\t3128581\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\t3129386\t3129482\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\t3129386\t3129482\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\t3128657\t3128728\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\t3128657\t3128728\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\ttranscript\t3162445\t3162500\t1000\t.\t.\tgene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";\n+chr1\tCufflinks\texon\t3162445\t3162500\t1000\t.\t.\tgene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "23.4701498888"; frac "1.000000"; conf_lo "0.000000"; conf_hi "50.571145"; cov "1.500000";\n+chr1\tCuffli'..b'0000";\n+chr1\tCufflinks\ttranscript\t3285318\t3285381\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\t3285318\t3285381\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\t3285858\t3285953\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\t3285858\t3285953\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\t3289268\t3289294\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\t3289268\t3289294\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\t3289466\t3289514\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\t3289466\t3289514\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\t3300382\t3300432\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\t3300382\t3300432\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\t3317446\t3317472\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\t3317446\t3317472\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\t3365246\t3365284\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\t3365246\t3365284\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\t3377607\t3377633\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\t3377607\t3377633\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\t3381259\t3381317\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\t3381259\t3381317\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\t3381404\t3381474\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\t3381404\t3381474\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' |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_in1_liftover_unmapped.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in1_liftover_unmapped.bed Tue Oct 01 12:49:41 2013 -0400 |
| b |
| @@ -0,0 +1,28 @@ +# Deleted in new +chr1 Cufflinks transcript 3111546 3111576 1000 . . gene_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"; +# Deleted in new +chr1 Cufflinks exon 3111546 3111576 1000 . . gene_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"; +# Partially deleted in new +chr1 Cufflinks transcript 3243019 3243079 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246"; +# Partially deleted in new +chr1 Cufflinks exon 3243019 3243079 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246"; +# Partially deleted in new +chr1 Cufflinks transcript 3242634 3242923 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034"; +# Partially deleted in new +chr1 Cufflinks exon 3242634 3242923 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "14.5676792413"; frac "1.000000"; conf_lo "5.354270"; conf_hi "23.781089"; cov "0.931034"; +# Partially deleted in new +chr1 Cufflinks transcript 3191877 3191945 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174"; +# Partially deleted in new +chr1 Cufflinks exon 3191877 3191945 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "104.0850125502"; frac "1.000000"; conf_lo "53.596365"; conf_hi "154.573660"; cov "6.652174"; +# Partially deleted in new +chr1 Cufflinks transcript 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +# Partially deleted in new +chr1 Cufflinks exon 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +# Deleted in new +chr1 Cufflinks transcript 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857"; +# Deleted in new +chr1 Cufflinks exon 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857"; +# Deleted in new +chr1 Cufflinks transcript 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +# Deleted in new +chr1 Cufflinks exon 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_in1_mult_liftover_mapped.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in1_mult_liftover_mapped.bed Tue Oct 01 12:49:41 2013 -0400 |
| b |
| b'@@ -0,0 +1,92 @@\n+chr1\tCufflinks\ttranscript\t3022555\t3022596\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\t3022555\t3022596\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\t3117334\t3117360\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\t3117334\t3117360\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\t3117031\t3117199\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\t3117031\t3117199\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\t3118118\t3118521\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\t3118118\t3118521\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\t3118713\t3118739\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\t3118713\t3118739\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\t3121789\t3121867\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\t3121789\t3121867\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\t3128503\t3128581\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\t3128503\t3128581\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\t3129386\t3129482\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\t3129386\t3129482\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\t3128657\t3128728\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\t3128657\t3128728\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\ttranscript\t3162123\t3162179\t1000\t.\t.\tgene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";\n+chr1\tCufflinks\texon\t3162123\t3162179\t1000\t.\t.\tgene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "13.8512359999"; frac "1.000000"; conf_lo "0.000000"; conf_hi "33.439842"; cov "0.885246";\n+chr1\tCuffli'..b'0000";\n+chr1\tCufflinks\ttranscript\t3285318\t3285381\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\t3285318\t3285381\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\t3285858\t3285953\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\t3285858\t3285953\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\t3289268\t3289294\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\t3289268\t3289294\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\t3289466\t3289514\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\t3289466\t3289514\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\t3300382\t3300432\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\t3300382\t3300432\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\t3317446\t3317472\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\t3317446\t3317472\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\t3365246\t3365284\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\t3365246\t3365284\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\t3377607\t3377633\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\t3377607\t3377633\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\t3381259\t3381317\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\t3381259\t3381317\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\t3381404\t3381474\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\t3381404\t3381474\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' |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_in1_mult_liftover_unmapped.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in1_mult_liftover_unmapped.bed Tue Oct 01 12:49:41 2013 -0400 |
| b |
| @@ -0,0 +1,16 @@ +# Deleted in new +chr1 Cufflinks transcript 3111546 3111576 1000 . . gene_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"; +# Deleted in new +chr1 Cufflinks exon 3111546 3111576 1000 . . gene_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"; +# Partially deleted in new +chr1 Cufflinks transcript 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +# Partially deleted in new +chr1 Cufflinks exon 3194186 3194226 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "20.6079364877"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.751960"; cov "1.317073"; +# Deleted in new +chr1 Cufflinks transcript 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857"; +# Deleted in new +chr1 Cufflinks exon 3277191 3277218 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "45.2638604998"; frac "1.000000"; conf_lo "0.000000"; conf_hi "97.530065"; cov "2.892857"; +# Deleted in new +chr1 Cufflinks transcript 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; +# Deleted in new +chr1 Cufflinks exon 3278237 3278263 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "15.6467665925"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.940300"; cov "1.000000"; |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_in2.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in2.gtf Tue Oct 01 12:49:41 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"; conf_hi "59.889707"; cov "1.205672";\n+chr1\tCufflinks\texon\t3188522\t3188548\t1000\t.\t.\tgene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672";\n+chr1\tCufflinks\ttranscript\t3190859\t3191434\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500";\n+chr1\tCufflinks\texon\t3190859\t3191434\t1000\t.\t.\tgene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500";\n+chr1\tCufflinks\ttranscript\t3191513\t3192077\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341";\n+chr1\tCufflinks\texon\t3191513\t3192077\t1000\t.\t.\tgene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341";\n+chr1\tCufflinks\ttranscript\t3189811\t3190789\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804";\n+chr1\tCufflinks\texon\t3189811\t3190789\t1000\t.\t.\tgene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804";\n+chr1\tCufflinks\ttranscript\t3192251\t3192336\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860";\n+chr1\tCufflinks\texon\t3192251\t3192336\t1000\t.\t.\tgene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860";\n+chr1\tCufflinks\ttranscript\t3192650\t3192676\t1000\t.\t.\tgene_id "CUFF.15"; transcript_id "CUFF.15.1"; 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 9d35cf35634e test-data/cuffcompare_in3.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_in3.gtf Tue Oct 01 12:49:41 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"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\texon\t4334224\t4340172\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\tCDS\t4341991\t4342162\t0.000000\t-\t0\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\texon\t4341991\t4342162\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\tCDS\t4342283\t4342906\t0.000000\t-\t0\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\tstart_codon\t4342904\t4342906\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\texon\t4342283\t4342918\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\texon\t4350281\t4350473\t0.000000\t-\t.\tgene_id "Rp1"; transcript_id "Rp1"; \n+chr1\tmm9_refFlat\tstop_codon\t4481797\t4481799\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\tCDS\t4481800\t4482749\t0.000000\t-\t2\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\texon\t4481009\t4482749\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\tCDS\t4483181\t4483487\t0.000000\t-\t0\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\tstart_codon\t4483485\t4483487\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\texon\t4483181\t4483547\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\texon\t4483853\t4483944\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\texon\t4485217\t4486023\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\texon\t4486372\t4486494\t0.000000\t-\t.\tgene_id "Sox17"; transcript_id "Sox17"; \n+chr1\tmm9_refFlat\tstop_codon\t4766545\t4766547\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\tCDS\t4766548\t4766882\t0.000000\t-\t2\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\texon\t4763279\t4766882\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\tCDS\t4767606\t4767729\t0.000000\t-\t0\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\texon\t4767606\t4767729\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\tCDS\t4772649\t4772814\t0.000000\t-\t1\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\texon\t4772649\t4772814\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\tCDS\t4774032\t4774186\t0.000000\t-\t0\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\texon\t4774032\t4774186\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\tCDS\t4775654\t4775758\t0.000000\t-\t0\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\tstart_codon\t4775756\t4775758\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\texon\t4775654\t4775807\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; \n+chr1\tmm9_refFlat\tstop_codon\t4764533\t4764535\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; \n+chr1\tmm9_refFlat\tCDS\t4764536\t4764597\t0.000000\t-\t2\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; \n+chr1\tmm9_refFlat\texon\t4763279\t4764597\t0.000000\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; \n+chr1\tmm9_refFlat\tCDS\t4767606\t4767729\t0.000000\t-\t0\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; \n+chr1\tmm9_refFlat\texon\t4767606\t4'..b'Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4798536\t4798567\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4818665\t4818730\t0.000000\t+\t1\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4818665\t4818730\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4820349\t4820396\t0.000000\t+\t1\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4820349\t4820396\t0.000000\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\tCDS\t4822392\t4822462\t0.000000\t+\t1\tgene_id "Lypla1"; transcript_id "Lypla1"; \n+chr1\tmm9_refFlat\texon\t4822392\t4822462\t0.000000\t+\t.\tgene_id "Lypla1"; 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 9d35cf35634e test-data/cuffcompare_out1.tmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_out1.tmap Tue Oct 01 12:49:41 2013 -0400 |
| b |
| @@ -0,0 +1,51 @@ +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len +- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 - +Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 3634 +Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 3634 +Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 3634 +Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 3634 +Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 3634 +Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 3634 +Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 3634 +Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 3634 +- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 - +- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 - +- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 - +- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 - +- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 - +- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 - +- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 - +- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 - +- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 - +- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 - +- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 - +- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 - +- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 - +- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 - +- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 - +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 3634 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 3634 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 3634 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 3634 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 3634 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 3634 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 3634 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 3634 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 3634 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 3634 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 3634 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 3634 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 3634 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 3634 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 3634 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 3634 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 3634 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 3634 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 3634 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 3634 |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_out2.refmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_out2.refmap Tue Oct 01 12:49:41 2013 -0400 |
| b |
| @@ -0,0 +1,2 @@ +ref_gene_id ref_id class_code cuff_id_list +Xkr4 Xkr4 c CUFF.13|CUFF.13.1 |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_out3.tmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_out3.tmap Tue Oct 01 12:49:41 2013 -0400 |
| b |
| @@ -0,0 +1,51 @@ +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len +- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 - +- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 - +- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 - +- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 - +- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 - +- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 - +- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 - +- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 - +- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 - +- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 - +Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 3634 +Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 3634 +Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 3634 +Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 3634 +Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 3634 +Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 3634 +Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 3634 +Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 3634 +Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 3634 +Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 3634 +Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 3634 +Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 3634 +Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 3634 +Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 3634 +Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 3634 +Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 3634 +Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 3634 +Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 3634 +Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 3634 +Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 3634 +Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 3634 +Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 3634 +Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 3634 +Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 3634 +Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 3634 +Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 3634 +Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 3634 +Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 3634 +Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 3634 +Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 3634 +Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 3634 +Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 3634 +Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 3634 +Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 3634 |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_out4.refmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_out4.refmap Tue Oct 01 12:49:41 2013 -0400 |
| b |
| @@ -0,0 +1,1 @@ +ref_gene_id ref_id class_code cuff_id_list |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_out5.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_out5.gtf Tue Oct 01 12:49:41 2013 -0400 |
| b |
| b'@@ -0,0 +1,90 @@\n+chr1\tCufflinks\texon\t3204755\t3204833\t.\t-\t.\tgene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; tss_id "TSS1";\n+chr1\tCufflinks\texon\t3111450\t3111490\t.\t.\t.\tgene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2";\n+chr1\tCufflinks\texon\t3111546\t3111576\t.\t.\t.\tgene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3";\n+chr1\tCufflinks\texon\t3174766\t3174792\t.\t.\t.\tgene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4";\n+chr1\tCufflinks\texon\t3187402\t3187428\t.\t.\t.\tgene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5";\n+chr1\tCufflinks\texon\t3188522\t3188548\t.\t.\t.\tgene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6";\n+chr1\tCufflinks\texon\t3189811\t3190789\t.\t.\t.\tgene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7";\n+chr1\tCufflinks\texon\t3190859\t3191434\t.\t.\t.\tgene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10";\n+chr1\tCufflinks\texon\t3191513\t3192077\t.\t.\t.\tgene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11";\n+chr1\tCufflinks\texon\t3192251\t3192336\t.\t.\t.\tgene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS13";\n+chr1\tCufflinks\texon\t3192442\t3192494\t.\t.\t.\tgene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS14";\n+chr1\tCufflinks\texon\t3192551\t3192629\t.\t.\t.\tgene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS15";\n+chr1\tCufflinks\texon\t3192650\t3192676\t.\t.\t.\tgene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS16";\n+chr1\tCufflinks\texon\t3192732\t3192811\t.\t.\t.\tgene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS17";\n+chr1\tCufflinks\texon\t3192941\t3193042\t.\t.\t.\tgene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS18";\n+chr1\tCufflinks\texon\t3194186\t3194226\t.\t.\t.\tgene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS19";\n+chr1\tCufflinks\texon\t3194303\t3194329\t.\t.\t.\tgene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS20";\n+chr1\tCufflinks\texon\t3194707\t3194733\t.\t.\t.\tgene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS21";\n+chr1\tCufflinks\texon\t3195084\t3195110\t.\t.\t.\tgene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS22";\n+chr1\tCufflinks\texon\t3195451\t3195477\t.\t.\t.\tgene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS23";\n+chr1\tCufflinks\texon\t3197090\t3197116\t.\t.\t.\tgene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS24";\n+chr1\tCufflinks\texon\t3197247\t3197273\t.\t.\t.\tgene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25";\n+chr1\tCufflinks\texon\t3197347\t3197373\t.\t.\t.\tgene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26";\n+chr1\tCufflinks\texon\t3197426\t3197452\t.\t.\t.\tgene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27";\n+chr1\tCufflinks\texon\t3'..b'.\tgene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74";\n+chr1\tCufflinks\texon\t3356181\t3356225\t.\t.\t.\tgene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75";\n+chr1\tCufflinks\texon\t3363077\t3363176\t.\t.\t.\tgene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76";\n+chr1\tCufflinks\texon\t3363215\t3363278\t.\t.\t.\tgene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77";\n+chr1\tCufflinks\texon\t3363388\t3363446\t.\t.\t.\tgene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78";\n+chr1\tCufflinks\texon\t3363754\t3363849\t.\t.\t.\tgene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79";\n+chr1\tCufflinks\texon\t3364872\t3364919\t.\t.\t.\tgene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80";\n+chr1\tCufflinks\texon\t3367136\t3367162\t.\t.\t.\tgene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81";\n+chr1\tCufflinks\texon\t3367211\t3367237\t.\t.\t.\tgene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82";\n+chr1\tCufflinks\texon\t3367334\t3367382\t.\t.\t.\tgene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83";\n+chr1\tCufflinks\texon\t3369581\t3369607\t.\t.\t.\tgene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84";\n+chr1\tCufflinks\texon\t3375002\t3375028\t.\t.\t.\tgene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85";\n+chr1\tCufflinks\texon\t3377212\t3377262\t.\t.\t.\tgene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86";\n+chr1\tCufflinks\texon\t3379889\t3379915\t.\t.\t.\tgene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87";\n+chr1\tCufflinks\texon\t3386740\t3386836\t.\t.\t.\tgene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88";\n+chr1\tCufflinks\texon\t3391326\t3391352\t.\t.\t.\tgene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89";\n+chr1\tCufflinks\texon\t3435842\t3435880\t.\t.\t.\tgene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90";\n+chr1\tCufflinks\texon\t3447762\t3447788\t.\t.\t.\tgene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91";\n+chr1\tCufflinks\texon\t3450907\t3450965\t.\t.\t.\tgene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS92";\n+chr1\tCufflinks\texon\t3451052\t3451109\t.\t.\t.\tgene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS93";\n' |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_out6.tracking --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_out6.tracking Tue Oct 01 12:49:41 2013 -0400 |
| b |
| b'@@ -0,0 +1,100 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.39.1|100|52.816931|0.000000|113.804669|3.000000|-\n+TCONS_00000071\tXLOC_000039\tXkr4|Xkr4\ti\t-\tq2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|-\n+TCONS_00000072\tXLOC_000041\tXkr4|Xkr4\ti\t-\tq2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|-\n+TCONS_00000073\tXLOC_000043\tXkr4|Xkr4\ti\t-\tq2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|-\n+TCONS_00000074\tXLOC_000045\tXkr4|Xkr4\ti\t-\tq2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000075\tXLOC_000047\tXkr4|Xkr4\ti\t-\tq2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000076\tXLOC_000049\tXkr4|Xkr4\ti\t-\tq2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|-\n+TCONS_00000077\tXLOC_000050\tXkr4|Xkr4\ti\t-\tq2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|-\n+TCONS_00000078\tXLOC_000051\tXkr4|Xkr4\ti\t-\tq2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000079\tXLOC_000053\tXkr4|Xkr4\ti\t-\tq2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000080\tXLOC_000054\tXkr4|Xkr4\ti\t-\tq2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000081\tXLOC_000055\tXkr4|Xkr4\ti\t-\tq2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|-\n+TCONS_00000082\tXLOC_000056\tXkr4|Xkr4\ti\t-\tq2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000083\tXLOC_000058\tXkr4|Xkr4\ti\t-\tq2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|-\n+TCONS_00000084\tXLOC_000059\tXkr4|Xkr4\ti\t-\tq2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|-\n+TCONS_00000085\tXLOC_000060\tXkr4|Xkr4\ti\t-\tq2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|-\n+TCONS_00000086\tXLOC_000061\tXkr4|Xkr4\ti\t-\tq2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|-\n+TCONS_00000087\tXLOC_000063\tXkr4|Xkr4\ti\t-\tq2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000088\tXLOC_000064\tXkr4|Xkr4\ti\t-\tq2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|-\n+TCONS_00000089\tXLOC_000066\tXkr4|Xkr4\ti\t-\tq2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|-\n+TCONS_00000090\tXLOC_000067\tXkr4|Xkr4\ti\t-\tq2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|-\n+TCONS_00000091\tXLOC_000068\tXkr4|Xkr4\ti\t-\tq2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|-\n+TCONS_00000092\tXLOC_000069\tXkr4|Xkr4\ti\t-\tq2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|-\n+TCONS_00000093\tXLOC_000070\tXkr4|Xkr4\ti\t-\tq2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|-\n+TCONS_00000094\tXLOC_000072\tXkr4|Xkr4\ti\t-\tq2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|-\n+TCONS_00000095\tXLOC_000074\tXkr4|Xkr4\ti\t-\tq2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|-\n+TCONS_00000096\tXLOC_000076\tXkr4|Xkr4\ti\t-\tq2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000097\tXLOC_000078\tXkr4|Xkr4\ti\t-\tq2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000098\tXLOC_000079\tXkr4|Xkr4\ti\t-\tq2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000099\tXLOC_000081\tXkr4|Xkr4\ti\t-\tq2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|-\n+TCONS_00000100\tXLOC_000082\tXkr4|Xkr4\ti\t-\tq2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|-\n' |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffcompare_out7.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffcompare_out7.txt Tue Oct 01 12:49:41 2013 -0400 |
| b |
| @@ -0,0 +1,33 @@ +# Cuffcompare v2.0.2 | Command line was: +#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2 +# + +#= Summary for dataset: ./input1 : +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 1 in 1 loci (1 multi-exon) +# Corresponding super-loci: 1 +#--------------------| Sn | Sp | fSn | fSp + Base level: 2.2 2.3 - - + Exon level: 0.0 0.0 0.0 0.0 + Intron level: 0.0 nan 0.0 nan +Intron chain level: 0.0 nan 0.0 nan + Transcript level: 0.0 0.0 0.0 0.0 + Locus level: 0.0 0.0 0.0 0.0 + +Matching intron chains: 0 + Matching loci: 0 + + Missed exons: 2/3 ( 66.7%) + Novel exons: 49/50 ( 98.0%) + Missed introns: 2/2 (100.0%) + Missed loci: 0/1 ( 0.0%) + Novel loci: 49/50 ( 98.0%) + +#= Summary for dataset: ./input2 : +# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) +# (0 multi-transcript loci, ~1.0 transcripts per locus) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) + + Total union super-loci across all input datasets: 87 + (0 multi-transcript, ~1.1 transcripts per locus) |
| b |
| diff -r 000000000000 -r 9d35cf35634e test-data/cuffmerge_out1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cuffmerge_out1.gtf Tue Oct 01 12:49:41 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 9d35cf35634e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Oct 01 12:49:41 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> |