| Previous changeset 17:1ebd14235b92 (2020-02-25) Next changeset 19:333a6e13b622 (2021-11-30) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 999b45e8bcf810f871cda58cb66573f7d6ae37f3" |
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modified:
macros.xml stringtie.xml stringtie_merge.xml test-data/stringtie_merge_out1.gtf test-data/stringtie_merge_out2.gtf 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_out8.gtf |
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added:
test-data/long_reads.bam test-data/short_reads.bam test-data/stringtie_out10.gtf test-data/stringtie_out11.gtf test-data/stringtie_out12.gtf test-data/stringtie_out9.gtf |
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| diff -r 1ebd14235b92 -r 258d696dbd7e macros.xml --- a/macros.xml Tue Feb 25 18:07:47 2020 -0500 +++ b/macros.xml Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,9 +1,9 @@ <macros> - <token name="@TOOL_VERSION@">2.1.1</token> + <token name="@TOOL_VERSION@">2.1.7</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">stringtie</requirement> - <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="1.13">samtools</requirement> <yield/> </requirements> </xml> |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e stringtie.xml --- a/stringtie.xml Tue Feb 25 18:07:47 2020 -0500 +++ b/stringtie.xml Sat Sep 25 18:20:22 2021 +0000 |
| [ |
| b'@@ -1,5 +1,8 @@\n <tool id="stringtie" name="StringTie" version="@TOOL_VERSION@">\n <description>transcript assembly and quantification</description>\n+ <xrefs>\n+ <xref type="bio.tools">stringtie</xref>\n+ </xrefs>\n <macros>\n <import>macros.xml</import>\n </macros>\n@@ -20,14 +23,33 @@\n #end if\n #end if\n \n-#if $input_bam.metadata.ftype == \'sam\':\n- samtools sort -@ \\${GALAXY_SLOTS:-1} \'$input_bam\' -T "\\${TMPDIR:-.}" | stringtie\n+#if $input_options.input_mode in [\'short_reads\',\'long_reads\']:\n+ #if $input_options.input_bam.metadata.ftype == \'sam\':\n+ samtools sort -@ \\${GALAXY_SLOTS:-1} \'$input_options.input_bam\' -T "\\${TMPDIR:-.}" | stringtie\n+ #else\n+ stringtie \'$input_options.input_bam\'\n+ #end if\n+ #if $input_options.input_mode == \'long_reads\'\n+ -L\n+ -E $input_options.error_splice\n+ #end if\n #else\n- stringtie \'$input_bam\'\n+ #if $input_options.input_bam_short.metadata.ftype == \'bam\' and $input_options.input_bam_long.metadata.ftype == \'bam\':\n+ strigtie \'$input_options.input_bam_short\' \'$input_options.input_bam_long\'\n+ #else if $input_options.input_bam_short.metadata.ftype == \'sam\' and $input_options.input_bam_long.metadata.ftype == \'bam\':\n+ samtools sort -@ \\${GALAXY_SLOTS:-1} \'$input_options.input_bam_short\' -T "\\${TMPDIR:-.}" -o short_sorted.sam\n+ && stringtie short_sorted.sam \'$input_options.input_bam_long\'\n+ #else if $input_options.input_bam_short.metadata.ftype == \'bam\' and $input_options.input_bam_long.metadata.ftype == \'sam\':\n+ samtools sort -@ \\${GALAXY_SLOTS:-1} \'$input_options.input_bam_long\' -T "\\${TMPDIR:-.}" -o long_sorted.sam\n+ && stringtie\'$input_options.input_bam_short\' long_sorted.sam\n+ #else\n+ samtools sort -@ \\${GALAXY_SLOTS:-1} \'$input_options.input_bam_short\' -T "\\${TMPDIR:-.}" -o short_sorted.sam\n+ && samtools sort -@ \\${GALAXY_SLOTS:-1} \'$input_options.input_bam_long\' -T "\\${TMPDIR:-.}" -o long_sorted.sam\n+ && stringtie short_sorted.sam long_sorted.sam\n+ #end if\n+ -E $input_options.error_splice\n #end if\n \n-$long_reads\n-\n -o \'$output_gtf\'\n -p "\\${GALAXY_SLOTS:-1}"\n \n@@ -111,8 +133,25 @@\n #end if\n ]]></command>\n <inputs>\n- <param name="input_bam" type="data" format="sam,bam" label="Input mapped reads" help="Input BAM/SAM file containing reads you want to assemble into transcripts"/>\n- <param name="long_reads" argument="-L" type="boolean" truevalue="-L" falsevalue="" checked="false" label="Input contains long reads?" help="Select if the input contains long error-prone reads, e.g. from Oxford Nanopore or PacBio sequencing."/>\n+ <conditional name="input_options">\n+ <param name="input_mode" type="select" label="Input options">\n+ <option value="short_reads">Short reads</option>\n+ <option value="long_reads">Long reads</option>\n+ <option value="mixed_reads">Mixed mode: short and long reads</option>\n+ </param>\n+ <when value="short_reads">\n+ <param name="input_bam" type="data" format="sam,bam" label="Input short mapped reads" help="Input BAM/SAM file containing the short reads you want to assemble into transcripts"/>\n+ </when>\n+ <when value="long_reads">\n+ <param name="input_bam" type="data" format="sam,bam" label="Input long mapped reads" help="Input BAM/SAM file containing the long reads you want to assemble into transcripts"/>\n+ <param name="error_splice" argument="-E" type="integer" min="0" max="50" value="25" label="Window around possibly erroneous splice sites" help="This option allows to define window around possibly erroneous splice sites from long reads to look out for correct splice sites. Default: 25" />\n+ </when>\n+ <when value="mixed_reads">\n+ <param name="input_bam_short" type="data" format="sam,bam" label="Input short mapped reads" help="Input B'..b'.bam" />\n+ </conditional> \n <param name="use_guide" value="yes" />\n <param name="guide_gff_select" value="history" />\n <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" />\n@@ -310,11 +374,46 @@\n </test>\n <!--Ensure built-in GTFs work -->\n <test expect_num_outputs="1">\n- <param name="input_bam" ftype="bam" dbkey="hg38" value="stringtie_in1.bam" />\n+ <conditional name="input_options">\n+ <param name="input_mode" value="short_reads"/>\n+ <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />\n+ </conditional> \n+ <param name="use_guide" value="yes" />\n+ <param name="guide_gff_select" value="cached" />\n+ <param name="fraction" value="0.15" />\n+ <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="4" />\n+ </test>\n+ <!-- Test long reads input -->\n+ <test expect_num_outputs="1">\n+ <conditional name="input_options">\n+ <param name="input_mode" value="long_reads"/>\n+ <param name="input_bam" ftype="bam" value="stringtie_in1.bam" />\n+ </conditional> \n <param name="use_guide" value="yes" />\n <param name="guide_gff_select" value="cached" />\n <param name="fraction" value="0.15" />\n- <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="4" />\n+ <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="4" />\n+ </test>\n+ <!-- Test error splice option -->\n+ <test expect_num_outputs="1">\n+ <conditional name="input_options">\n+ <param name="input_mode" value="long_reads"/>\n+ <param name="input_bam" ftype="bam" value="long_reads.bam" />\n+ <param name="error_splice" value="30" />\n+ </conditional> \n+ <param name="use_guide" value="yes" />\n+ <param name="guide_gff_select" value="cached" />\n+ <param name="fraction" value="0.15" />\n+ <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="4" />\n+ </test>\n+ <!-- Test mixed reads input -->\n+ <test expect_num_outputs="1">\n+ <conditional name="input_options">\n+ <param name="input_mode" value="mixed_reads"/>\n+ <param name="input_bam_short" ftype="bam" value="short_reads.bam" />\n+ <param name="input_bam_long" ftype="bam" value="long_reads.bam" />\n+ </conditional> \n+ <output name="output_gtf" file="stringtie_out12.gtf" ftype="gtf" lines_diff="4" />\n </test>\n </tests>\n <help><![CDATA[\n@@ -476,14 +575,14 @@\n .. _Bioconductor: https://www.bioconductor.org/\n .. _SAM: http://samtools.github.io/hts-specs/SAMv1.pdf\n .. _HISAT2: http://ccb.jhu.edu/software/hisat2\n-.. _`GTF/GFF3`: https://ccb.jhu.edu/software/stringtie/gff.shtml\n+.. _`GTF/GFF3`: http://ccb.jhu.edu/software/stringtie/gff.shtml\n .. _`this link`: https://github.com/alyssafrazee/ballgown#ballgown-readable-expression-output\n .. _`Ensembl site here`: http://useast.ensembl.org/info/website/upload/gff.html\n .. _here: http://www.rna-seqblog.com/rpkm-fpkm-and-tpm-clearly-explained/\n .. _`by B. Li and C. Dewey here`: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323\n-.. _`GFF utilities page`: https://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare\n+.. _`GFF utilities page`: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffcompare\n .. _`protocol paper`: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5032908/\n-.. _`StringTie manual here`: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual\n+.. _`StringTie manual here`: http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual\n \n ]]></help>\n <expand macro="citations" />\n' |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e stringtie_merge.xml --- a/stringtie_merge.xml Tue Feb 25 18:07:47 2020 -0500 +++ b/stringtie_merge.xml Sat Sep 25 18:20:22 2021 +0000 |
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| @@ -1,5 +1,8 @@ <tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@"> <description>transcripts</description> + <xrefs> + <xref type="bio.tools">stringtie</xref> + </xrefs> <macros> <import>macros.xml</import> </macros> |
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| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/long_reads.bam |
| b |
| Binary file test-data/long_reads.bam has changed |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/short_reads.bam |
| b |
| Binary file test-data/short_reads.bam has changed |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_merge_out1.gtf --- a/test-data/stringtie_merge_out1.gtf Tue Feb 25 18:07:47 2020 -0500 +++ b/test-data/stringtie_merge_out1.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,5 +1,5 @@ -# stringtie --merge -p 1 -G /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/1/0/e/dataset_10e968ed-4fcb-4799-864f-4a845aefd7c6.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/d/4/7/dataset_d47ec42c-d204-4b1a-b863-c54d1f0f8aba.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/b/4/9/dataset_b496e60c-ee18-4c69-99eb-70f9445725f5.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/4/b/a/dataset_4bac764c-1632-4ba8-bf86-dbeda729238e.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/9/3/3/dataset_933d8dbf-024c-4bad-b90f-05f847a7406f.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/f/a/2/dataset_fa27d83d-cfd4-4910-abdb-b83cf2668486.dat -# StringTie version 2.1.1 +# stringtie --merge -p 1 -G /tmp/tmp9cgbzsli/files/f/8/0/dataset_f808ceaa-08fb-4e16-8d00-3af3bd707ede.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmp9cgbzsli/files/1/2/f/dataset_12ff3ea2-5306-479a-915b-9af32e1defa1.dat /tmp/tmp9cgbzsli/files/5/e/0/dataset_5e0ac785-035b-41ca-acb3-1276d358574d.dat /tmp/tmp9cgbzsli/files/b/3/1/dataset_b3195d2c-e25d-4c21-a9f8-14c79961b98b.dat /tmp/tmp9cgbzsli/files/a/5/f/dataset_a5f7edd6-3748-4854-bd0d-68c03c3ba68e.dat /tmp/tmp9cgbzsli/files/4/5/d/dataset_45d17dfd-c663-43fd-a2ef-e41dd94caa53.dat +# StringTie version 2.1.7 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"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_merge_out2.gtf --- a/test-data/stringtie_merge_out2.gtf Tue Feb 25 18:07:47 2020 -0500 +++ b/test-data/stringtie_merge_out2.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,5 +1,5 @@ -# stringtie --merge -p 1 -G /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/e/3/7/dataset_e372bcb2-3b02-4fa2-8e9a-e5f9fb2ddd1a.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/b/d/4/dataset_bd4ebf5e-a629-4b3e-ab7c-bba17f0e7651.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/c/4/8/dataset_c480ac0d-da44-4477-a115-43d849c4e0fb.dat /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/1/b/a/dataset_1ba088e7-52b5-4783-a7a5-b023862e36e2.dat -# StringTie version 2.1.1 +# stringtie --merge -p 1 -G /tmp/tmp9cgbzsli/files/d/3/d/dataset_d3debef6-0cc0-44aa-898c-086d4fa8adb0.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmp9cgbzsli/files/b/4/d/dataset_b4dd908f-5f52-428f-bc2c-ba62cd00a83e.dat /tmp/tmp9cgbzsli/files/8/1/a/dataset_81a6719e-2f36-40ca-9d63-325d6eadd1d3.dat /tmp/tmp9cgbzsli/files/2/2/f/dataset_22f857ec-0df8-40d8-ba00-28b709b98b03.dat +# StringTie version 2.1.7 chr1 StringTie transcript 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; chr1 StringTie exon 3189811 3193042 1000 . . gene_id "MSTRG.1"; transcript_id "MSTRG.1.1"; exon_number "1"; chr1 StringTie transcript 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out1.gtf --- a/test-data/stringtie_out1.gtf Tue Feb 25 18:07:47 2020 -0500 +++ b/test-data/stringtie_out1.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/c/7/a/dataset_c7af8b5d-2e42-4fea-b8d6-7fad0726e917.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/3/5/7/dataset_357301ba-858d-44ea-9ead-8160748e75fc.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.1 +# stringtie /tmp/tmpgqe071sy/files/8/a/5/dataset_8a57065f-d332-4a26-8aa0-9d511312d8a6.dat -o /tmp/tmpgqe071sy/files/b/4/6/dataset_b46e6244-1199-4c7b-946c-111d2b3c98c7.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 2.1.7 test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.237373"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "53.000000"; +test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "53.000004"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.660000"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out10.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out10.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +# stringtie /tmp/tmpgqe071sy/files/8/8/6/dataset_886a7110-225b-4286-8de0-3e630fa369da.dat -L -E 25 -o /tmp/tmpgqe071sy/files/d/5/4/dataset_d54d1211-a9e6-4f03-b0b6-58182b101e8b.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 2.1.7 +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 "45.795303"; FPKM "3354967.250000"; TPM "1000000.000000"; +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 "49.777779"; +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 "54.160000"; +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 "21.660000"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out11.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out11.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -0,0 +1,58 @@ +# stringtie /tmp/tmpgqe071sy/files/5/f/e/dataset_5feb7af0-84a3-4590-975e-97b02b89c256.dat -L -E 30 -o /tmp/tmpgqe071sy/files/d/9/c/dataset_d9c60f6e-5062-4d09-a7e3-05b74adcebca.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 2.1.7 +chr19 StringTie transcript 567221 571736 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.617600"; FPKM "37220.644531"; TPM "77823.132812"; +chr19 StringTie exon 567221 567648 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.815421"; +chr19 StringTie exon 571440 571596 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "5.859873"; +chr19 StringTie exon 571697 571736 1000 - . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "2.550000"; +chr19 StringTie transcript 571310 583493 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; cov "5.416068"; FPKM "35885.347656"; TPM "75031.218750"; +chr19 StringTie exon 571310 571579 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "4.559259"; +chr19 StringTie exon 580379 580461 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "5.556142"; +chr19 StringTie exon 580646 580782 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "5.689962"; +chr19 StringTie exon 581315 581610 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "5.556142"; +chr19 StringTie exon 582514 582582 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "5.556142"; +chr19 StringTie exon 582750 583493 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "5.592226"; +chr19 StringTie transcript 572567 583493 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; cov "6.175826"; FPKM "40919.292969"; TPM "85556.492188"; +chr19 StringTie exon 572567 572701 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "3.325926"; +chr19 StringTie exon 577774 578121 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "6.436781"; +chr19 StringTie exon 579500 579656 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "7.000000"; +chr19 StringTie exon 580379 580461 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "7.443858"; +chr19 StringTie exon 580646 580782 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "6.631207"; +chr19 StringTie exon 581315 581610 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "6.443858"; +chr19 StringTie exon 582514 582582 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "6.443858"; +chr19 StringTie exon 582750 583493 1000 + . gene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "8"; cov "6.040156"; +chr19 StringTie transcript 589891 617159 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; cov "19.938414"; FPKM "132106.343750"; TPM "276215.781250"; +chr19 StringTie exon 589891 590577 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "18.537119"; +chr19 StringTie exon 603544 603967 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "21.000000"; +chr19 StringTie exon 605061 605222 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "21.000000"; +chr19 StringTie exon 607964 608182 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "21.000000"; +chr19 StringTie exon 610259 610405 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "21.000000"; +chr19 StringTie exon 613248 613488 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "6"; cov "21.000000"; +chr19 StringTie exon 613852 614016 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "7"; cov "21.000000"; +chr19 StringTie exon 615795 617159 1000 + . gene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "8"; cov "19.587545"; +chr19 StringTie transcript 617224 618760 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; cov "29.150192"; FPKM "193141.000000"; TPM "403830.687500"; +chr19 StringTie exon 617224 617323 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "20.289286"; +chr19 StringTie exon 617419 617480 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "28.788761"; +chr19 StringTie exon 617570 618586 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "3"; cov "30.891500"; +chr19 StringTie exon 618705 618760 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "4"; cov "13.750000"; +chr19 StringTie transcript 617224 633601 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; cov "5.886094"; FPKM "38999.609375"; TPM "81542.703125"; +chr19 StringTie exon 617224 617323 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "1"; cov "1.560714"; +chr19 StringTie exon 617419 617480 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "2"; cov "1.985432"; +chr19 StringTie exon 617570 617655 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "3"; cov "4.996770"; +chr19 StringTie exon 617777 617849 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "4"; cov "5.994817"; +chr19 StringTie exon 618488 618586 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "5"; cov "5.525252"; +chr19 StringTie exon 618705 618760 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "6"; cov "6.875000"; +chr19 StringTie exon 618997 619110 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "7"; cov "6.000000"; +chr19 StringTie exon 619210 619296 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "8"; cov "6.000000"; +chr19 StringTie exon 619586 619765 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "9"; cov "6.000000"; +chr19 StringTie exon 619958 620080 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "10"; cov "7.000000"; +chr19 StringTie exon 620365 620487 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "11"; cov "7.000000"; +chr19 StringTie exon 621058 621846 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "12"; cov "6.751584"; +chr19 StringTie exon 622149 622373 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "13"; cov "6.000000"; +chr19 StringTie exon 622582 622752 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "14"; cov "6.000000"; +chr19 StringTie exon 622821 622985 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "15"; cov "6.000000"; +chr19 StringTie exon 623454 623603 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "16"; cov "6.000000"; +chr19 StringTie exon 624719 624905 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "17"; cov "6.000000"; +chr19 StringTie exon 625124 625254 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "18"; cov "6.000000"; +chr19 StringTie exon 629540 630168 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "19"; cov "5.941176"; +chr19 StringTie exon 632834 632938 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "20"; cov "5.000000"; +chr19 StringTie exon 633425 633601 1000 - . gene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "21"; cov "3.988701"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out12.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out12.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| b'@@ -0,0 +1,73 @@\n+# stringtie short_sorted.sam long_sorted.sam -E 25 -o /tmp/tmpgqe071sy/files/9/5/b/dataset_95b1ec38-2151-43e7-8584-aa4aff72e957.dat -p 1 -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95\n+# StringTie version 2.1.7\n+chr19\tStringTie\ttranscript\t567221\t571736\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; cov "5.043160"; FPKM "15396.282227"; TPM "50141.804688";\n+chr19\tStringTie\texon\t567221\t567648\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "5.815421";\n+chr19\tStringTie\texon\t571440\t571596\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "3.573089";\n+chr19\tStringTie\texon\t571697\t571736\t1000\t-\t.\tgene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "2.550000";\n+chr19\tStringTie\ttranscript\t571310\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; cov "4.701019"; FPKM "14351.757812"; TPM "46740.058594";\n+chr19\tStringTie\texon\t571310\t571579\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "1"; cov "5.888981";\n+chr19\tStringTie\texon\t580379\t580461\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "2"; cov "4.879346";\n+chr19\tStringTie\texon\t580646\t580782\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "3"; cov "4.616338";\n+chr19\tStringTie\texon\t581315\t581610\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "4"; cov "4.479919";\n+chr19\tStringTie\texon\t582514\t582582\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "5"; cov "4.504012";\n+chr19\tStringTie\texon\t582750\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.1"; exon_number "6"; cov "4.371838";\n+chr19\tStringTie\ttranscript\t572567\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; cov "6.933517"; FPKM "21167.359375"; TPM "68936.750000";\n+chr19\tStringTie\texon\t572567\t572701\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "1"; cov "3.325926";\n+chr19\tStringTie\texon\t577774\t578121\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "2"; cov "6.436781";\n+chr19\tStringTie\texon\t579500\t579656\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "3"; cov "7.000000";\n+chr19\tStringTie\texon\t580379\t580461\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "4"; cov "8.120653";\n+chr19\tStringTie\texon\t580646\t580782\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "5"; cov "7.682931";\n+chr19\tStringTie\texon\t581315\t581610\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "6"; cov "7.455892";\n+chr19\tStringTie\texon\t582514\t582582\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "7"; cov "7.495987";\n+chr19\tStringTie\texon\t582750\t583493\t1000\t+\t.\tgene_id "STRG.2"; transcript_id "STRG.2.2"; exon_number "8"; cov "7.276011";\n+chr19\tStringTie\ttranscript\t589891\t617159\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; cov "19.937536"; FPKM "60867.378906"; TPM "198229.687500";\n+chr19\tStringTie\texon\t589891\t590577\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "1"; cov "18.537117";\n+chr19\tStringTie\texon\t603544\t603967\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "2"; cov "21.000000";\n+chr19\tStringTie\texon\t605061\t605222\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "3"; cov "20.981482";\n+chr19\tStringTie\texon\t607964\t608182\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "4"; cov "21.000000";\n+chr19\tStringTie\texon\t610259\t610405\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "5"; cov "21.000000";\n+chr19\tStringTie\texon\t613248\t613488\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "6"; cov "21.000000";\n+chr19\tStringTie\texon\t613852\t614016\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "7"; cov "21.000000";\n+chr19\tStringTie\texon\t615795\t617159\t1000\t+\t.\tgene_id "STRG.3"; transcript_id "STRG.3.1"; exon_number "8"; cov "19.587545";\n+chr16\tStringTie\ttranscript\t784986\t788300\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.1"; cov "30.3'..b'7";\n+chr16\tStringTie\texon\t789547\t789715\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "3"; cov "20.360947";\n+chr16\tStringTie\texon\t790177\t790269\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "4"; cov "18.048386";\n+chr16\tStringTie\texon\t790347\t790399\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "5"; cov "21.396227";\n+chr16\tStringTie\texon\t790525\t790666\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "6"; cov "19.359156";\n+chr16\tStringTie\texon\t791161\t791370\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "7"; cov "22.309525";\n+chr16\tStringTie\texon\t791851\t791948\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "8"; cov "16.336735";\n+chr16\tStringTie\texon\t792224\t792347\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "9"; cov "19.322580";\n+chr16\tStringTie\texon\t792439\t792590\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "10"; cov "8.835526";\n+chr16\tStringTie\texon\t792718\t792811\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "11"; cov "21.244680";\n+chr16\tStringTie\texon\t792966\t793064\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "12"; cov "19.494951";\n+chr16\tStringTie\texon\t793144\t793274\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "13"; cov "16.229008";\n+chr16\tStringTie\texon\t794054\t794201\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "14"; cov "22.121622";\n+chr16\tStringTie\texon\t795132\t795356\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "15"; cov "30.586666";\n+chr16\tStringTie\texon\t795685\t795834\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "16"; cov "14.393333";\n+chr16\tStringTie\texon\t795947\t796077\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "17"; cov "27.061069";\n+chr16\tStringTie\texon\t796717\t796861\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "18"; cov "39.082760";\n+chr16\tStringTie\texon\t796961\t797092\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "19"; cov "43.295456";\n+chr16\tStringTie\texon\t797694\t797751\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "20"; cov "53.689655";\n+chr16\tStringTie\texon\t797839\t798048\t1000\t+\t.\tgene_id "STRG.5"; transcript_id "STRG.5.1"; exon_number "21"; cov "44.473808";\n+chr16\tStringTie\ttranscript\t854482\t911074\t1000\t-\t.\tgene_id "STRG.6"; transcript_id "STRG.6.1"; cov "5.773279"; FPKM "17625.265625"; TPM "57401.042969";\n+chr16\tStringTie\texon\t854482\t854706\t1000\t-\t.\tgene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "1"; cov "3.262222";\n+chr16\tStringTie\texon\t868944\t869056\t1000\t-\t.\tgene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "2"; cov "9.176991";\n+chr16\tStringTie\texon\t869883\t870066\t1000\t-\t.\tgene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "3"; cov "11.130435";\n+chr16\tStringTie\texon\t870729\t870882\t1000\t-\t.\tgene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "4"; cov "10.467532";\n+chr16\tStringTie\texon\t871161\t871341\t1000\t-\t.\tgene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "5"; cov "3.563536";\n+chr16\tStringTie\texon\t879570\t879737\t1000\t-\t.\tgene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "6"; cov "2.625000";\n+chr16\tStringTie\texon\t893007\t893072\t1000\t-\t.\tgene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "7"; cov "3.242424";\n+chr16\tStringTie\texon\t910931\t911074\t1000\t-\t.\tgene_id "STRG.6"; transcript_id "STRG.6.1"; exon_number "8"; cov "2.770833";\n+chr16\tStringTie\ttranscript\t934126\t970901\t1000\t-\t.\tgene_id "STRG.7"; transcript_id "STRG.7.1"; cov "3.068716"; FPKM "9368.495117"; TPM "30510.824219";\n+chr16\tStringTie\texon\t934126\t934254\t1000\t-\t.\tgene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "1"; cov "1.131783";\n+chr16\tStringTie\texon\t954357\t954666\t1000\t-\t.\tgene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "2"; cov "4.341936";\n+chr16\tStringTie\texon\t970788\t970901\t1000\t-\t.\tgene_id "STRG.7"; transcript_id "STRG.7.1"; exon_number "3"; cov "1.798246";\n' |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out2.gtf --- a/test-data/stringtie_out2.gtf Tue Feb 25 18:07:47 2020 -0500 +++ b/test-data/stringtie_out2.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/0/b/d/dataset_0bdef9bb-4df2-495e-96e5-172272d8d091.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/e/a/2/dataset_ea28bbaf-b541-4047-a923-87fad9958466.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.1 +# stringtie /tmp/tmpgqe071sy/files/c/e/6/dataset_ce6d871e-dc50-4710-8c21-385b1a4fcd2e.dat -o /tmp/tmpgqe071sy/files/e/8/2/dataset_e82c3d81-e413-4566-a538-1ef066ef2348.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 2.1.7 test_chromosome StringTie transcript 53 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; test_chromosome StringTie exon 53 250 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "1"; cov "49.237373"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "53.000000"; +test_chromosome StringTie exon 351 400 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "2"; cov "53.000004"; test_chromosome StringTie exon 501 550 1000 + . gene_id "STRG.1"; transcript_id "STRG.1.1"; exon_number "3"; cov "21.660000"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out3.gtf --- a/test-data/stringtie_out3.gtf Tue Feb 25 18:07:47 2020 -0500 +++ b/test-data/stringtie_out3.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/3/8/4/dataset_384eded7-d60c-439d-be66-1b9963159f17.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/b/4/8/dataset_b482f931-c707-4535-b3e0-500c8d8e871b.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.1 +# stringtie /tmp/tmpgqe071sy/files/8/6/e/dataset_86e4ed94-6458-4fd6-b8ae-dc5f7acd75ac.dat -o /tmp/tmpgqe071sy/files/5/7/7/dataset_57773891-c25a-4102-a817-04fa6e876cf3.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 2.1.7 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 "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; 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 "49.237373"; -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 "53.000000"; +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 "53.000004"; 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 "21.660000"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out4.gtf --- a/test-data/stringtie_out4.gtf Tue Feb 25 18:07:47 2020 -0500 +++ b/test-data/stringtie_out4.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/0/6/f/dataset_06f2148a-c2bc-4d89-a2d7-e3e1a8afa1c6.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/1/1/c/dataset_11c0064f-b50b-4810-b856-1b16030c6a6b.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.1 +# stringtie /tmp/tmpgqe071sy/files/5/8/5/dataset_5851f244-d011-47e4-b6ac-bb6119b6497b.dat -o /tmp/tmpgqe071sy/files/d/a/6/dataset_da695139-3493-41cc-9409-8085cad59f40.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.17 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -A /tmp/tmpgqe071sy/files/8/7/d/dataset_87d1ffdf-8041-4fc6-b9d7-7cd794f69cd8.dat +# StringTie version 2.1.7 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 "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; 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 "49.237373"; -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 "53.000000"; +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 "53.000004"; 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 "21.660000"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out5.gtf --- a/test-data/stringtie_out5.gtf Tue Feb 25 18:07:47 2020 -0500 +++ b/test-data/stringtie_out5.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/7/d/b/dataset_7db84341-79f0-4976-93ae-077d5bc204fe.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/9/c/0/dataset_9c0876b6-2850-4467-9983-65e7e1e60147.dat -p 1 -G guide.gff -C /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/7/0/f/dataset_70fc75f5-d3a9-4f0e-b3e5-ae748f5ea145.dat -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.1 +# stringtie /tmp/tmpgqe071sy/files/0/e/1/dataset_0e10eba1-035e-4481-9311-22277f50cd38.dat -o /tmp/tmpgqe071sy/files/d/a/a/dataset_daa0c96d-9176-476d-82fc-e2b7ef2dcd8e.dat -p 1 -G guide.gff -C /tmp/tmpgqe071sy/files/9/6/1/dataset_9614085c-99c8-4957-9b89-2391d231ddb8.dat -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 2.1.7 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 "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; 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 "49.237373"; -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 "53.000000"; +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 "53.000004"; 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 "21.660000"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out6.gtf --- a/test-data/stringtie_out6.gtf Tue Feb 25 18:07:47 2020 -0500 +++ b/test-data/stringtie_out6.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/9/7/9/dataset_979811c5-c516-4209-bd38-3677704d573f.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/2/5/6/dataset_256d374e-00c0-40ba-979b-0a65edd889e2.dat -p 1 -G guide.gff -C /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmplvw3jqqu/files/e/4/f/dataset_e4fa5924-6856-4ba9-97d7-99aa2b3cff62.dat -e -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.1 +# stringtie /tmp/tmpgqe071sy/files/a/7/3/dataset_a739b50f-5870-4fab-becb-e667dfdfd00e.dat -o /tmp/tmpgqe071sy/files/8/3/6/dataset_8365f524-36d5-4bce-89dd-0c362b90be45.dat -p 1 -G guide.gff -C /tmp/tmpgqe071sy/files/3/9/6/dataset_39649d2b-5fe0-4cbe-8d5a-cd4c8b2663c9.dat -e -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 2.1.7 test_chromosome StringTie transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; cov "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; test_chromosome StringTie exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; cov "49.237373"; -test_chromosome StringTie exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; cov "53.000000"; +test_chromosome StringTie exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; cov "53.000004"; test_chromosome StringTie exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; cov "21.660000"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out8.gtf --- a/test-data/stringtie_out8.gtf Tue Feb 25 18:07:47 2020 -0500 +++ b/test-data/stringtie_out8.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ -# stringtie /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmp6o9_xiyd/files/4/4/4/dataset_444ed4bd-2499-449b-b9d9-22d1704cea80.dat -o /private/var/folders/68/qbzdmjy16z56csxjly83cgy00000gn/T/tmp6o9_xiyd/files/d/5/e/dataset_d5e42756-7a1f-4cdc-8cc7-7b9cb62ffb3a.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 -# StringTie version 2.1.1 +# stringtie /tmp/tmpgqe071sy/files/d/e/8/dataset_de884427-d510-47bf-acb3-4375c0ce2337.dat -o /tmp/tmpgqe071sy/files/2/7/e/dataset_27e677d1-ed55-49db-bfb2-a38c2c6bf911.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 2.1.7 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 "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; 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 "49.237373"; -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 "53.000000"; +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 "53.000004"; 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 "21.660000"; |
| b |
| diff -r 1ebd14235b92 -r 258d696dbd7e test-data/stringtie_out9.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stringtie_out9.gtf Sat Sep 25 18:20:22 2021 +0000 |
| b |
| @@ -0,0 +1,6 @@ +# stringtie /tmp/tmpgqe071sy/files/a/3/b/dataset_a3ba39e7-c812-41eb-a15c-e039ad42a33a.dat -o /tmp/tmpgqe071sy/files/7/4/7/dataset_74713e40-e879-4efa-b57e-f3d95a82284f.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 2 -g 50 -M 0.95 +# StringTie version 2.1.7 +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 "45.241611"; FPKM "3314403.750000"; TPM "1000000.000000"; +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 "49.237373"; +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 "53.000004"; +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 "21.660000"; |