| Previous changeset 5:f504b3b7e49d (2015-10-21) Next changeset 7:e3f369973054 (2016-07-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7 |
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modified:
stringtie.xml test-data/e2t.ctab test-data/e_data.ctab test-data/i2t.ctab test-data/i_data.ctab test-data/stringtie_out1.gtf test-data/stringtie_out2.gtf test-data/stringtie_out3.gtf test-data/stringtie_out4.gtf test-data/stringtie_out5.gtf test-data/stringtie_out6.gtf test-data/stringtie_out7.gtf test-data/t_data.ctab tool_dependencies.xml |
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added:
macros.xml stringtie_merge.xml test-data/stringtie_merge_in1.gtf test-data/stringtie_merge_in2.gtf test-data/stringtie_merge_in3.gtf test-data/stringtie_merge_out1.gtf test-data/stringtie_merge_out2.gtf |
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| diff -r f504b3b7e49d -r d0bb240d7525 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Jul 13 14:48:26 2016 -0400 |
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| @@ -0,0 +1,22 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2.3">stringtie</requirement> + <yield/> + </requirements> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" /> + </stdio> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.3122</citation> + <yield /> + </citations> + </xml> + <xml name="version_command"> + <version_command>stringtie --version</version_command> + </xml> +</macros> \ No newline at end of file |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 stringtie.xml --- a/stringtie.xml Wed Oct 21 16:07:42 2015 -0400 +++ b/stringtie.xml Wed Jul 13 14:48:26 2016 -0400 |
| [ |
| b'@@ -1,38 +1,46 @@\n-<tool id="stringtie" name="StringTie" version="1.1.0">\n+<tool id="stringtie" name="StringTie" version="1.2.3">\n <description>transcript assembly and quantification</description>\n- <requirements>\n- <requirement type="package" version="1.1.0">stringtie</requirement>\n- </requirements>\n- <command><![CDATA[\n-stringtie "$input_bam"\n--o "$output_gtf"\n--p "\\${GALAXY_SLOTS:-1}"\n-#if str($guide.use_guide) == \'yes\':\n- -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation\n- #if str($guide.output_ballgown) == \'-b\':\n- $guide.output_ballgown `pwd`\n- #end if\n-#end if\n-#if str($option_set.options) == \'advanced\':\n- -l "$option_set.name_prefix"\n- -f "$option_set.fraction"\n- -m "$option_set.min_tlen"\n- -a "$option_set.min_anchor_len"\n- -j "$option_set.min_anchor_cov"\n- -c "$option_set.min_bundle_cov"\n- -g "$option_set.bdist"\n- -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming\n- #if $option_set.A:\n- -A "$gene_abundance_estimation"\n- #end if\n- #if str($option_set.x).strip() != "":\n- -x "$option_set.x"\n- #end if\n-#end if\n-]]>\n-</command>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n+ <expand macro="version_command" />\n+ <command>\n+ <![CDATA[\n+ #if $input_bam.metadata.ftype == \'sam\':\n+ samtools sort -@ \\${GALAXY_SLOTS:-1} "$input_bam" | stringtie\n+ #else\n+ stringtie "$input_bam"\n+ #end if\n+ -o "$output_gtf"\n+ -p "\\${GALAXY_SLOTS:-1}"\n+ #if str($guide.use_guide) == \'yes\':\n+ -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation\n+ #if $guide.output_ballgown:\n+ -b .\n+ #end if\n+ #end if\n+ #if str($option_set.options) == \'advanced\':\n+ -l "$option_set.name_prefix"\n+ -f "$option_set.fraction"\n+ -m "$option_set.min_tlen"\n+ -a "$option_set.min_anchor_len"\n+ -j "$option_set.min_anchor_cov"\n+ -c "$option_set.min_bundle_cov"\n+ -g "$option_set.bdist"\n+ -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming $option_set.multi_mapping\n+ #if $option_set.abundance_estimation:\n+ -A "$gene_abundance_estimation"\n+ #end if\n+ #if str($option_set.omit_sequences).strip() != "":\n+ -x "$option_set.omit_sequences"\n+ #end if\n+ #end if\n+ ]]>\n+ </command>\n <inputs>\n- <param format="bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />\n+ <param format="sam,bam" label="Mapped reads to assemble transcripts from" name="input_bam" type="data" />\n <conditional name="guide">\n <param label="Use GFF file to guide assembly" name="use_guide" type="select">\n <option value="yes">Use GFF</option>\n@@ -40,37 +48,38 @@\n </param>\n <when value="no" />\n <when value="yes">\n- <param format="gtf,gff3" help="-G" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />\n- <param falsevalue="" help="-e" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />\n- <param falsevalue="" help="-b" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />\n+ <param argument="-G" format="gtf,gff3" help="" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />\n+ <param argument="-e" falsevalue="" help="" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />\n+ <param argument='..b'_diff="2" />\n+ <output file="stringtie_out2.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n </test>\n <test>\n <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />\n <param name="use_guide" value="yes" />\n <param name="guide_gff" value="stringtie_in.gtf" />\n <param name="options" value="default" />\n- <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />\n+ <output file="stringtie_out3.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n </test>\n <test>\n <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />\n@@ -118,7 +127,7 @@\n <param name="guide_gff" value="stringtie_in.gtf" />\n <param name="options" value="advanced" />\n <param name="fraction" value="0.17" />\n- <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />\n+ <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n </test>\n <test>\n <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />\n@@ -131,7 +140,7 @@\n <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />\n <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />\n <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />\n- <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />\n+ <output file="stringtie_out5.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />\n </test>\n <test>\n@@ -140,9 +149,9 @@\n <param name="guide_gff" value="stringtie_in.gtf" />\n <param name="options" value="advanced" />\n <param name="fraction" value="0.17" />\n- <param name="A" value="True" />\n- <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />\n- <output file="stringtie_out6.gtf" ftype="tabular" name="gene_abundance_estimation" />\n+ <param name="abundance_estimation" value="True" />\n+ <output file="stringtie_out4.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n+ <output file="stringtie_out6.gtf" ftype="gtf" lines_diff="2" name="gene_abundance_estimation" />\n </test>\n <test>\n <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />\n@@ -151,7 +160,7 @@\n <param name="options" value="advanced" />\n <param name="fraction" value="0.15" />\n <param name="c" value="test_chromosome" />\n- <output file="stringtie_out7.gtf" ftype="gtf" name="output_gtf" lines_diff="2" />\n+ <output file="stringtie_out7.gtf" ftype="gtf" lines_diff="2" name="output_gtf" />\n </test>\n </tests>\n <help>\n@@ -182,18 +191,17 @@\n -C output file with reference transcripts that are covered by reads\n -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)\n -p number of threads (CPUs) to use (default: 1)\n+ -A gene abundance estimation output file\n -B enable output of Ballgown table files which will be created in the\n same directory as the output GTF (requires -G, -o recommended)\n -b enable output of Ballgown table files but these files will be \n created under the directory path given as <dir_path>\n -e only estimates the abundance of given reference transcripts (requires -G)\n- -A gene abundance estimation output file\n -x do not assemble any transcripts on these reference sequence(s)\n-\n+ -u no multi-mapping correction default: false)\n \n ]]>\n </help>\n- <citations>\n- <citation type="doi">doi:10.1038/nbt.3122</citation>\n- </citations>\n+ <expand macro="citations" />\n </tool>\n+ \n\\ No newline at end of file\n' |
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| diff -r f504b3b7e49d -r d0bb240d7525 stringtie_merge.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/stringtie_merge.xml Wed Jul 13 14:48:26 2016 -0400 |
| [ |
| @@ -0,0 +1,85 @@ +<tool id="stringtie_merge" name="StringTie" version="0.1.0"> + <description>merge transcripts</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> + <![CDATA[ + stringtie --merge + -p \${GALAXY_SLOTS:-1} + #if str($guide_gff) != "": + -G "$guide_gff" + #end if + -m $min_len + -c $min_cov + -F $min_fpkm + -T $min_tpm + -f $min_iso + -g $gap_len + $keep_introns + #set inputs = '" "'.join(str($input_gtf).split(',')) + -o $out_gtf "$inputs" + ]]> + </command> + <inputs> + <param type="data" name="input_gtf" multiple="true" format="gtf,gff3" /> + <param type="data" name="guide_gff" optional="True" format="gtf,gff3" /> + <param argument="-m" type="integer" name="min_len" value="50" help="Minimum input transcript length to include in the merge" /> + <param argument="-c" type="integer" name="min_cov" value="0" help="Minimum input transcript coverage to include in the merge" /> + <param argument="-F" type="float" name="min_fpkm" value="1.0" help="Minimum input transcript FPKM to include in the merge" /> + <param argument="-T" type="float" name="min_tpm" value="1.0" help="Minimum input transcript TPM to include in the merge" /> + <param argument="-f" type="float" name="min_iso" value="0.01" help="Minimum isoform fraction" /> + <param argument="-g" type="integer" name="gap_len" value="250" help="Gap between transcripts to merge together" /> + <param argument="-i" type="boolean" truevalue="-i" falsevalue="" name="keep_introns" help="Keep merged transcripts with retained introns" /> + </inputs> + <outputs> + <data name="out_gtf" format="gtf" /> + </outputs> + <tests> + <test> + <param ftype="gtf" name="input_gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" /> + <param ftype="gtf" name="guide_gff" value="stringtie_in.gtf" /> + <output file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> + </test> + <test> + <param ftype="gtf" name="input_gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> + <param ftype="gtf" name="guide_gff" value="stringtie_merge_in3.gtf" /> + <output file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="2" name="out_gtf" /> + </test> + </tests> + <help><![CDATA[ + +**What it does?** + +This is a special usage mode of StringTie_, distinct from the assembly usage mode. In the merge mode, StringTie takes as input a list of GTF/GFF files and merges/assembles these transcripts into a non-redundant set of transcripts. This mode is used in the new differential analysis pipeline to generate a global, unified set of transcripts (isoforms) across multiple RNA-Seq samples. + +If a reference annotation is provided, StringTie will assemble the transfrags from the input GTF files with the reference transcripts. + +.. _StringTie: http://ccb.jhu.edu/software/stringtie/ + +------ + +StringTie --merge has the following options:: + + -G <guide_gff> reference annotation to include in the merging (GTF/GFF3) + -o <out_gtf> output file name for the merged transcripts GTF + (default: stdout) + -m <min_len> minimum input transcript length to include in the merge + (default: 50) + -c <min_cov> minimum input transcript coverage to include in the merge + (default: 0) + -F <min_fpkm> minimum input transcript FPKM to include in the merge + (default: 1.0) + -T <min_tpm> minimum input transcript TPM to include in the merge + (default: 1.0) + -f <min_iso> minimum isoform fraction (default: 0.01) + -g <gap_len> gap between transcripts to merge together (default: 250) + -i keep merged transcripts with retained introns; by default + these are not kept unless there is strong evidence for them + -l <label> name prefix for output transcripts (default: MSTRG) + ]]></help> + <expand macro="citations" /> +</tool> \ No newline at end of file |
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| diff -r f504b3b7e49d -r d0bb240d7525 test-data/e2t.ctab --- a/test-data/e2t.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/e2t.ctab Wed Jul 13 14:48:26 2016 -0400 |
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| @@ -1,4 +0,0 @@ -e_id t_id -1 1 -2 1 -3 1 |
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| diff -r f504b3b7e49d -r d0bb240d7525 test-data/e_data.ctab --- a/test-data/e_data.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/e_data.ctab Wed Jul 13 14:48:26 2016 -0400 |
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| @@ -1,4 +0,0 @@ -e_id chr strand start end rcount ucount mrcount cov cov_sd mcov mcov_sd -1 test_chromosome + 53 250 158 158 158.00 49.7778 22.0747 49.7778 22.0747 -2 test_chromosome + 351 400 73 73 73.00 54.1600 6.1753 54.1600 6.1753 -3 test_chromosome + 501 550 38 38 38.00 21.6400 12.4350 21.6400 12.4350 |
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| diff -r f504b3b7e49d -r d0bb240d7525 test-data/i2t.ctab --- a/test-data/i2t.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/i2t.ctab Wed Jul 13 14:48:26 2016 -0400 |
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| @@ -1,3 +0,0 @@ -i_id t_id -1 1 -2 1 |
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| diff -r f504b3b7e49d -r d0bb240d7525 test-data/i_data.ctab --- a/test-data/i_data.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/i_data.ctab Wed Jul 13 14:48:26 2016 -0400 |
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| @@ -1,3 +0,0 @@ -i_id chr strand start end rcount ucount mrcount -1 test_chromosome + 251 350 49 49 49.00 -2 test_chromosome + 401 500 38 38 38.00 |
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| diff -r f504b3b7e49d -r d0bb240d7525 test-data/stringtie_merge_in1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_in1.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| 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 f504b3b7e49d -r d0bb240d7525 test-data/stringtie_merge_in2.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_in2.gtf Wed Jul 13 14:48:26 2016 -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 f504b3b7e49d -r d0bb240d7525 test-data/stringtie_merge_in3.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_in3.gtf Wed Jul 13 14:48:26 2016 -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 f504b3b7e49d -r d0bb240d7525 test-data/stringtie_merge_out1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_out1.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +# stringtie --merge -p 1 -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_5.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_6.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_1.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_2.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_3.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_4.dat +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; ref_gene_id "CUFF.1"; +test_chromosome StringTie exon 53 250 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "1"; ref_gene_id "CUFF.1"; +test_chromosome StringTie exon 351 400 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "2"; ref_gene_id "CUFF.1"; +test_chromosome StringTie exon 501 550 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "3"; ref_gene_id "CUFF.1"; |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 test-data/stringtie_merge_out2.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_merge_out2.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| b'@@ -0,0 +1,100 @@\n+# stringtie --merge -p 1 -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_9.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_10.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_7.dat /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpYerZ_r/files/000/dataset_8.dat\n+# StringTie version 1.2.3\n+chr1\tStringTie\ttranscript\t3189811\t3193042\t1000\t.\t.\tgene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; \n+chr1\tStringTie\texon\t3189811\t3193042\t1000\t.\t.\tgene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3200023\t3200191\t1000\t.\t.\tgene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; \n+chr1\tStringTie\texon\t3200023\t3200191\t1000\t.\t.\tgene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3201078\t3201809\t1000\t.\t.\tgene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; \n+chr1\tStringTie\texon\t3201078\t3201809\t1000\t.\t.\tgene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3204563\t3661579\t1000\t-\t.\tgene_id "MSTRG.4"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; \n+chr1\tStringTie\texon\t3204563\t3207049\t1000\t-\t.\tgene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "1"; ref_gene_id "Xkr4"; \n+chr1\tStringTie\texon\t3411783\t3411982\t1000\t-\t.\tgene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "2"; ref_gene_id "Xkr4"; \n+chr1\tStringTie\texon\t3660633\t3661579\t1000\t-\t.\tgene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "3"; ref_gene_id "Xkr4"; \n+chr1\tStringTie\ttranscript\t3212214\t3212439\t1000\t.\t.\tgene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; \n+chr1\tStringTie\texon\t3212214\t3212439\t1000\t.\t.\tgene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3212718\t3212801\t1000\t.\t.\tgene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; \n+chr1\tStringTie\texon\t3212718\t3212801\t1000\t.\t.\tgene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3213096\t3213242\t1000\t.\t.\tgene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; \n+chr1\tStringTie\texon\t3213096\t3213242\t1000\t.\t.\tgene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3242634\t3243079\t1000\t.\t.\tgene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; \n+chr1\tStringTie\texon\t3242634\t3243079\t1000\t.\t.\tgene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3243348\t3243401\t1000\t.\t.\tgene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; \n+chr1\tStringTie\texon\t3243348\t3243401\t1000\t.\t.\tgene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3277914\t3278390\t1000\t.\t.\tgene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; \n+chr1\tStringTie\texon\t3277914\t3278390\t1000\t.\t.\tgene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3280687\t3280741\t1000\t.\t.\tgene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; \n+chr1\tStringTie\texon\t3280687\t3280741\t1000\t.\t.\tgene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3282761\t3282832\t1000\t.\t.\tgene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; \n+chr1\tStringTie\texon\t3282761\t3282832\t1000\t.\t.\tgene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3290489\t3291273\t1000\t.\t.\tgene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; \n+chr1\tStringTie\texon\t3290489\t3291273\t1000\t.\t.\tgene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3299444\t3299664\t1000\t.\t.\tgene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; \n+chr1\tStringTie\texon\t3299444\t3299664\t1000\t.\t.\tgene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3319000\t3319051\t1000\t.\t.\tgene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; \n+chr1\tStringTie\texon\t3319000\t3319051\t1000\t.\t.\tgene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; exon_number "1"; \n+chr1\tStringTie\ttranscript\t3351241\t3351311\t1000\t.\t.\tgene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; \n+chr1\tStr'..b'r1\tmm9_refFlat\texon\t4772649\t4772814\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3"; ref_gene_id "Mrpl15";\n+chr1\tmm9_refFlat\texon\t4774032\t4774186\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4"; ref_gene_id "Mrpl15";\n+chr1\tmm9_refFlat\texon\t4775654\t4775807\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5"; ref_gene_id "Mrpl15";\n+chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15";\n+chr1\tmm9_refFlat\texon\t4763279\t4764597\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1"; ref_gene_id "Mrpl15";\n+chr1\tmm9_refFlat\texon\t4767606\t4767729\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2"; ref_gene_id "Mrpl15";\n+chr1\tmm9_refFlat\texon\t4772649\t4772814\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3"; ref_gene_id "Mrpl15";\n+chr1\tmm9_refFlat\texon\t4775654\t4775807\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4"; ref_gene_id "Mrpl15";\n+chr1\tmm9_refFlat\ttranscript\t4797974\t4836816\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4797974\t4798063\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4798536\t4798567\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4818665\t4818730\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4820349\t4820396\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4822392\t4822462\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4827082\t4827155\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4829468\t4829569\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4831037\t4831213\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\texon\t4835044\t4836816\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9"; ref_gene_id "Lypla1";\n+chr1\tmm9_refFlat\ttranscript\t4847775\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4847775\t4848057\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4857551\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\ttranscript\t4847775\t4887987\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4847775\t4848057\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4857551\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4868108\t4868213\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4876825\t4876912\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4879538\t4879683\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4880821\t4880877\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4881996\t4882150\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4883498\t4883644\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4885015\t4885086\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9"; ref_gene_id "Tcea1";\n+chr1\tmm9_refFlat\texon\t4886437\t4887987\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10"; ref_gene_id "Tcea1";\n' |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 test-data/stringtie_out1.gtf --- a/test-data/stringtie_out1.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out1.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_1.dat -o /tmp/tmpoOYb63/files/000/dataset_2.dat -p 1 -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "995243.375000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_1.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_2.dat -p 1 +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "975770.250000"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.948147"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000"; |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 test-data/stringtie_out2.gtf --- a/test-data/stringtie_out2.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out2.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_9.dat -o /tmp/tmpoOYb63/files/000/dataset_10.dat -p 1 -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "995243.375000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_9.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_10.dat -p 1 -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "44.682419"; FPKM "3273437.500000"; TPM "975770.250000"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "48.948147"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.090000"; |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 test-data/stringtie_out3.gtf --- a/test-data/stringtie_out3.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out3.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_16.dat -o /tmp/tmpoOYb63/files/000/dataset_18.dat -p 1 -C /tmp/tmpoOYb63/files/000/dataset_20.dat -G /tmp/tmpoOYb63/files/000/dataset_17.dat -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "996187.875000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_16.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_18.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_20.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_17.dat +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000"; |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 test-data/stringtie_out4.gtf --- a/test-data/stringtie_out4.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out4.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_35.dat -o /tmp/tmpoOYb63/files/000/dataset_37.dat -p 1 -C /tmp/tmpoOYb63/files/000/dataset_39.dat -G /tmp/tmpoOYb63/files/000/dataset_36.dat -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /tmp/tmpoOYb63/files/000/dataset_38.dat -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "996187.875000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_1.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_3.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_5.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_2.dat -l STRG -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpv7zmop/files/000/dataset_4.dat +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000"; |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 test-data/stringtie_out5.gtf --- a/test-data/stringtie_out5.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out5.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_25.dat -o /tmp/tmpoOYb63/files/000/dataset_27.dat -p 1 -C /tmp/tmpoOYb63/files/000/dataset_29.dat -G /tmp/tmpoOYb63/files/000/dataset_26.dat -b /tmp/tmpoOYb63/job_working_directory/000/13 -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "996187.875000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_25.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_27.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_29.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_26.dat -B +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000"; |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 test-data/stringtie_out6.gtf --- a/test-data/stringtie_out6.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out6.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -1,3 +1,3 @@ -Gene ID Gene Name Strand Start End Length Coverage FPKM TPM -CUFF.1 - + 53 550 298 44.895973 3289082.250000 1000000.000000 -STRG.1 - + 53 550 298 44.895973 3289082.250000 1000000.000000 +Gene ID Gene Name Reference Strand Start End Coverage FPKM TPM +CUFF.1 - test_chromosome + 53 550 45.791946 3354721.250000 1000000.062500 +STRG.1 - test_chromosome + 53 550 45.791946 3354721.250000 1000000.062500 |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 test-data/stringtie_out7.gtf --- a/test-data/stringtie_out7.gtf Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/stringtie_out7.gtf Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /tmp/tmpoOYb63/files/000/dataset_40.dat -o /tmp/tmpoOYb63/files/000/dataset_42.dat -p 1 -C /tmp/tmpoOYb63/files/000/dataset_43.dat -G /tmp/tmpoOYb63/files/000/dataset_41.dat -l STRG -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 1.1.0 -test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "996187.875000"; +# stringtie /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_39.dat -o /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_41.dat -p 1 -C /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_42.dat -G /var/folders/s0/0v_znjzj3kb3jbhlqt9kyb800000gn/T/tmpd2SP9G/files/000/dataset_40.dat -l STRG -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 1.2.3 +test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "44.724823"; FPKM "3276543.750000"; TPM "976696.312500"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "49.011967"; test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "51.382565"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; reference_id "CUFF.1.1"; ref_gene_id "CUFF.1"; cov "21.090000"; |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 test-data/t_data.ctab --- a/test-data/t_data.ctab Wed Oct 21 16:07:42 2015 -0400 +++ b/test-data/t_data.ctab Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -1,2 +0,0 @@ -t_id chr strand start end t_name num_exons length gene_id gene_name cov FPKM -1 test_chromosome + 53 550 CUFF.1.1 3 298 CUFF.1 . 44.724823 3276543.750000 |
| b |
| diff -r f504b3b7e49d -r d0bb240d7525 tool_dependencies.xml --- a/tool_dependencies.xml Wed Oct 21 16:07:42 2015 -0400 +++ b/tool_dependencies.xml Wed Jul 13 14:48:26 2016 -0400 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="stringtie" version="1.1.0"> - <repository changeset_revision="62a98ebf406f" name="package_stringtie_1_1_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <package name="stringtie" version="1.2.3"> + <repository changeset_revision="ee804c6f3b97" name="package_stringtie_1_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |