| Previous changeset 22:ae618321f34a (2023-01-30) Next changeset 24:cbf488da3b2c (2024-05-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 252f4cccd66513c985b3df9480d73c8b9f994520 |
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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_out10.gtf test-data/stringtie_out11.gtf test-data/stringtie_out1_re.gtf test-data/stringtie_out2_re.gtf test-data/stringtie_out3_re.gtf test-data/stringtie_out4_re.gtf test-data/stringtie_out5.gtf test-data/stringtie_out6.gtf test-data/stringtie_out8.gtf test-data/stringtie_out9.gtf test-data/stringtie_out_coverage.gtf |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 macros.xml --- a/macros.xml Mon Jan 30 12:01:28 2023 +0000 +++ b/macros.xml Tue Apr 30 11:53:08 2024 +0000 |
| b |
| @@ -1,10 +1,10 @@ <macros> - <token name="@TOOL_VERSION@">2.2.1</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">2.2.2</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">stringtie</requirement> - <requirement type="package" version="1.16.1">samtools</requirement> + <requirement type="package" version="1.20">samtools</requirement> <yield/> </requirements> </xml> |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 stringtie.xml --- a/stringtie.xml Mon Jan 30 12:01:28 2023 +0000 +++ b/stringtie.xml Tue Apr 30 11:53:08 2024 +0000 |
| b |
| b'@@ -1,11 +1,11 @@\n-<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">\n+<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">\n <description>transcript assembly and quantification</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n <xrefs>\n <xref type="bio.tools">stringtie</xref>\n </xrefs>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n <expand macro="requirements" />\n <expand macro="stdio" />\n <expand macro="version_command" />\n@@ -148,12 +148,12 @@\n </when>\n <when value="long_reads">\n <param name="input_bam" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM 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+ <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,cram" label="Input short mapped reads" help="Input BAM/SAM/CRAM file containing the short reads you want to assemble into transcripts"/>\n <param name="input_bam_long" type="data" format="sam,bam,cram" label="Input long mapped reads" help="Input BAM/SAM/CRAM 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+ <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 </conditional>\n <param name="rna_strandness" type="select" label="Specify strand information"\n@@ -177,13 +177,13 @@\n <when value="cached">\n <param name="ref_builtin" type="select" label="Use a built-in GTF" help="If the GTF file for your transcriptome of interest is not listed, contact your Galaxy administrator">\n <options from_data_table="gene_sets">\n- <filter type="sort_by" column="2" />\n- <validator type="no_options" message="No GTF file is available." />\n+ <filter type="sort_by" column="2"/>\n+ <validator type="no_options" message="No GTF file is available."/>\n </options>\n </param>\n </when>\n <when value="history">\n- <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly" />\n+ <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly"/>\n </when>\n </conditional>\n <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Use Refer'..b'ingtie_in1.bam" />\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" compare="re_match" sort="true"/>\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="2"/>\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+ <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_out10.gtf" ftype="gtf" compare="re_match" sort="true"/>\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_out10.gtf" ftype="gtf" lines_diff="2"/>\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+ <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" compare="re_match" sort="true"/>\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="2"/>\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+ <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" ftype="gtf">\n <assert_contents>\n@@ -429,8 +429,8 @@\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="cram" value="stringtie_in.cram" />\n- <param name="input_bam_long" ftype="cram" value="stringtie_in.cram" />\n+ <param name="input_bam_short" ftype="cram" value="stringtie_in.cram"/>\n+ <param name="input_bam_long" ftype="cram" value="stringtie_in.cram"/>\n </conditional> \n <output name="output_gtf" ftype="gtf">\n <assert_contents>\n' |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 stringtie_merge.xml --- a/stringtie_merge.xml Mon Jan 30 12:01:28 2023 +0000 +++ b/stringtie_merge.xml Tue Apr 30 11:53:08 2024 +0000 |
| b |
| @@ -1,11 +1,11 @@ <tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>transcripts</description> + <macros> + <import>macros.xml</import> + </macros> <xrefs> <xref type="bio.tools">stringtie</xref> </xrefs> - <macros> - <import>macros.xml</import> - </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> @@ -26,35 +26,35 @@ -o '$out_gtf' '$inputs' ]]></command> <inputs> - <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" /> - <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" /> - <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge" /> - <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge" /> - <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge" /> - <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge" /> - <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" /> - <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together" /> - <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" /> + <param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format"/> + <param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging"/> + <param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge"/> + <param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge"/> + <param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge"/> + <param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge"/> + <param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction"/> + <param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together"/> + <param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them"/> </inputs> <outputs> - <data name="out_gtf" format="gtf" /> + <data name="out_gtf" format="gtf"/> </outputs> <tests> <test> - <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" /> - <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" /> - <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf"/> + <param name="guide_gff" ftype="gtf" value="stringtie_in.gtf"/> + <output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2"/> </test> <test> - <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> + <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/> <param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" /> - <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true"/> + <output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="4"/> </test> <test> - <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" /> + <param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/> <output name="out_gtf" ftype="gtf"> <assert_contents> - <has_text text="stringtie --merge" /> + <has_text text="stringtie --merge"/> </assert_contents> </output> </test> |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_merge_out1.gtf --- a/test-data/stringtie_merge_out1.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_merge_out1.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; +# stringtie --merge -p 1 -G /tmp/tmpr8yl388j/files/d/8/3/dataset_d8325888-f757-4336-9e42-1101c6ec296d.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpr8yl388j/job_working_directory/000/6/outputs/dataset_51c0f399-1d26-44c7-a4fd-e6f8897fe843.dat /tmp/tmpr8yl388j/files/5/5/b/dataset_55be25a6-c7f0-474e-a011-bb4cd427cfa2.dat /tmp/tmpr8yl388j/files/b/2/e/dataset_b2ef2a9d-3640-4858-8424-b4a29c57164d.dat /tmp/tmpr8yl388j/files/d/9/b/dataset_d9be016a-da47-4ad1-89bd-e9781f2751db.dat /tmp/tmpr8yl388j/files/b/e/f/dataset_befee6d4-95fb-4ee9-83a4-9b1302e6a21a.dat +# StringTie version 2.2.2 +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 ae618321f34a -r 8eb8750070d4 test-data/stringtie_merge_out2.gtf --- a/test-data/stringtie_merge_out2.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_merge_out2.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| b'@@ -1,100 +1,100 @@\n-# StringTie version 2\\.2\\.1\n-# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\\.dat -m 50 -c 0 -F 1\\.0 -T 1\\.0 -f 0\\.01 -g 250 -o /[-_/a-zA-Z0-9]+\\.dat /[-_/a-zA-Z0-9]+\\.dat /[-_/a-zA-Z0-9]+\\.dat\n-chr1\\tStringTie\\texon\\t3189811\\t3193042\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3200023\\t3200191\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3201078\\t3201809\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3204563\\t3207049\\t1000\\t-\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; \n-chr1\\tStringTie\\texon\\t3212214\\t3212439\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3212718\\t3212801\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3213096\\t3213242\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3242634\\t3243079\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3243348\\t3243401\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3277914\\t3278390\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3280687\\t3280741\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3282761\\t3282832\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3290489\\t3291273\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3299444\\t3299664\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3319000\\t3319051\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3351241\\t3351311\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3355908\\t3356119\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3363077\\t3363446\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3363754\\t3363849\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3377212\\t3377262\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3386740\\t3386836\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3411783\\t3411982\\t1000\\t-\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; \n-chr1\\tStringTie\\texon\\t3450907\\t3451109\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; \n-chr1\\tStringTie\\texon\\t3660633\\t3661579\\t1000\\t-\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; \n-chr1\\tStringTie\\ttranscript\\t3189811\\t3193042\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; \n-chr1\\tStringTie\\ttranscript\\t3200023\\t3200191\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; \n-chr1\\tStringTie\\ttranscript\\t3201078\\t3201809\\t1000\\t\\.\\t\\.\\tgene_id "MSTRG\\.[0-9]+"; transcript_id "MSTRG\\.[0-9]+\\.1"; \n-chr1\\tStringTie\\ttranscript\\t3204563\\t3661579\\t1000\\t-\\t\\.\\tgene_id "MSTRG\\.[0-9]+'..b'_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3";\n+chr1\tmm9_refFlat\texon\t4774032\t4774186\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4";\n+chr1\tmm9_refFlat\texon\t4775654\t4775807\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5";\n+chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15";\n+chr1\tmm9_refFlat\texon\t4763279\t4764597\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1";\n+chr1\tmm9_refFlat\texon\t4767606\t4767729\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2";\n+chr1\tmm9_refFlat\texon\t4772649\t4772814\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3";\n+chr1\tmm9_refFlat\texon\t4774032\t4774186\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4";\n+chr1\tmm9_refFlat\texon\t4775654\t4775807\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5";\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";\n+chr1\tmm9_refFlat\texon\t4767606\t4767729\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2";\n+chr1\tmm9_refFlat\texon\t4772649\t4772814\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3";\n+chr1\tmm9_refFlat\texon\t4775654\t4775807\t.\t-\t.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4";\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";\n+chr1\tmm9_refFlat\texon\t4798536\t4798567\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2";\n+chr1\tmm9_refFlat\texon\t4818665\t4818730\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3";\n+chr1\tmm9_refFlat\texon\t4820349\t4820396\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4";\n+chr1\tmm9_refFlat\texon\t4822392\t4822462\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5";\n+chr1\tmm9_refFlat\texon\t4827082\t4827155\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6";\n+chr1\tmm9_refFlat\texon\t4829468\t4829569\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7";\n+chr1\tmm9_refFlat\texon\t4831037\t4831213\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8";\n+chr1\tmm9_refFlat\texon\t4835044\t4836816\t.\t+\t.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9";\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";\n+chr1\tmm9_refFlat\texon\t4857551\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2";\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";\n+chr1\tmm9_refFlat\texon\t4857551\t4857613\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2";\n+chr1\tmm9_refFlat\texon\t4868108\t4868213\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3";\n+chr1\tmm9_refFlat\texon\t4876825\t4876912\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4";\n+chr1\tmm9_refFlat\texon\t4879538\t4879683\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5";\n+chr1\tmm9_refFlat\texon\t4880821\t4880877\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6";\n+chr1\tmm9_refFlat\texon\t4881996\t4882150\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7";\n+chr1\tmm9_refFlat\texon\t4883498\t4883644\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8";\n+chr1\tmm9_refFlat\texon\t4885015\t4885086\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9";\n+chr1\tmm9_refFlat\texon\t4886437\t4887987\t.\t+\t.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10";\n' |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out10.gtf --- a/test-data/stringtie_out10.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out10.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie /[-_/a-zA-Z0-9]+\.dat -L -E 25 -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1 -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "54\.160000"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.777779"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.795303"; FPKM "3354967\.250000"; TPM "1000000\.000000"; +# stringtie /tmp/tmpm2qmdax_/files/8/4/7/dataset_84719807-dfbb-42a2-b1db-377469c94d05.dat -L -E 25 -o /tmp/tmpm2qmdax_/job_working_directory/000/26/outputs/dataset_4dfedf5d-98a8-4b6a-8f7d-1b6c2116bbd4.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 +# StringTie version 2.2.2 +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 ae618321f34a -r 8eb8750070d4 test-data/stringtie_out11.gtf --- a/test-data/stringtie_out11.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out11.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| b'@@ -1,58 +1,58 @@\n-# StringTie version 2\\.2\\.1\n-# stringtie /[-_/a-zA-Z0-9]+\\.dat -L -E 30 -o /[-_/a-zA-Z0-9]+\\.dat -p [0-9]+ -G guide\\.gff -b \\./special_de_output/sample1/ -f 0\\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1\n-chr19\\tStringTie\\texon\\t567221\\t567648\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "5\\.815421";\n-chr19\\tStringTie\\texon\\t571310\\t571579\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "4\\.559259";\n-chr19\\tStringTie\\texon\\t571440\\t571596\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "5\\.859873";\n-chr19\\tStringTie\\texon\\t571697\\t571736\\t1000\\t-\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "2\\.550000";\n-chr19\\tStringTie\\texon\\t572567\\t572701\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "3\\.325926";\n-chr19\\tStringTie\\texon\\t577774\\t578121\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.436781";\n-chr19\\tStringTie\\texon\\t579500\\t579656\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "7\\.000000";\n-chr19\\tStringTie\\texon\\t580379\\t580461\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "5\\.556142";\n-chr19\\tStringTie\\texon\\t580379\\t580461\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "7\\.443858";\n-chr19\\tStringTie\\texon\\t580646\\t580782\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "5\\.689962";\n-chr19\\tStringTie\\texon\\t580646\\t580782\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.631207";\n-chr19\\tStringTie\\texon\\t581315\\t581610\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "5\\.556142";\n-chr19\\tStringTie\\texon\\t581315\\t581610\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.443858";\n-chr19\\tStringTie\\texon\\t582514\\t582582\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "5\\.556142";\n-chr19\\tStringTie\\texon\\t582514\\t582582\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.443858";\n-chr19\\tStringTie\\texon\\t582750\\t583493\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "5\\.592226";\n-chr19\\tStringTie\\texon\\t582750\\t583493\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.2"; exon_number "[0-9]+"; cov "6\\.040156";\n-chr19\\tStringTie\\texon\\t589891\\t590577\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "18\\.537119";\n-chr19\\tStringTie\\texon\\t603544\\t603967\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "21\\.000000";\n-chr19\\tStringTie\\texon\\t605061\\t605222\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "21\\.000000";\n-chr19\\tStringTie\\texon\\t607964\\t608182\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "21\\.000000";\n-chr19\\tStringTie\\texon\\t610259\\t610405\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "21\\.000000";\n-chr19\\tStringTie\\texon\\t613248\\t613488\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "21\\.000000";\n-chr19\\tStringTie\\texon\\t613852\\t614016\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "21\\.000000";\n-chr19\\tStringTie\\texon\\t615795\\t617159\\t1000\\t\\+\\t\\.\\tgene_id "STRG\\.[0-9]+"; transcript_id "STRG\\.[0-9]+\\.1"; exon_number "[0-9]+"; cov "19\\.587545";\n-ch'..b'1.000000";\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+chr19\tStringTie\ttranscript\t617224\t618760\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.1"; cov "29.150192"; FPKM "193141.000000"; TPM "403830.687500";\n+chr19\tStringTie\texon\t617224\t617323\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "1"; cov "20.289286";\n+chr19\tStringTie\texon\t617419\t617480\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "2"; cov "28.788761";\n+chr19\tStringTie\texon\t617570\t618586\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "3"; cov "30.891500";\n+chr19\tStringTie\texon\t618705\t618760\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.1"; exon_number "4"; cov "13.750000";\n+chr19\tStringTie\ttranscript\t617224\t633601\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; cov "5.886094"; FPKM "38999.609375"; TPM "81542.703125";\n+chr19\tStringTie\texon\t617224\t617323\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "1"; cov "1.560714";\n+chr19\tStringTie\texon\t617419\t617480\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "2"; cov "1.985432";\n+chr19\tStringTie\texon\t617570\t617655\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "3"; cov "4.996770";\n+chr19\tStringTie\texon\t617777\t617849\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "4"; cov "5.994817";\n+chr19\tStringTie\texon\t618488\t618586\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "5"; cov "5.525252";\n+chr19\tStringTie\texon\t618705\t618760\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "6"; cov "6.875000";\n+chr19\tStringTie\texon\t618997\t619110\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "7"; cov "6.000000";\n+chr19\tStringTie\texon\t619210\t619296\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "8"; cov "6.000000";\n+chr19\tStringTie\texon\t619586\t619765\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "9"; cov "6.000000";\n+chr19\tStringTie\texon\t619958\t620080\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "10"; cov "7.000000";\n+chr19\tStringTie\texon\t620365\t620487\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "11"; cov "7.000000";\n+chr19\tStringTie\texon\t621058\t621846\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "12"; cov "6.751584";\n+chr19\tStringTie\texon\t622149\t622373\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "13"; cov "6.000000";\n+chr19\tStringTie\texon\t622582\t622752\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "14"; cov "6.000000";\n+chr19\tStringTie\texon\t622821\t622985\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "15"; cov "6.000000";\n+chr19\tStringTie\texon\t623454\t623603\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "16"; cov "6.000000";\n+chr19\tStringTie\texon\t624719\t624905\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "17"; cov "6.000000";\n+chr19\tStringTie\texon\t625124\t625254\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "18"; cov "6.000000";\n+chr19\tStringTie\texon\t629540\t630168\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "19"; cov "5.941176";\n+chr19\tStringTie\texon\t632834\t632938\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "20"; cov "5.000000";\n+chr19\tStringTie\texon\t633425\t633601\t1000\t-\t.\tgene_id "STRG.4"; transcript_id "STRG.4.2"; exon_number "21"; cov "3.988701";\n' |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out1_re.gtf --- a/test-data/stringtie_out1_re.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out1_re.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1 -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; +# stringtie /tmp/tmpm2qmdax_/files/7/c/4/dataset_7c4559ac-1803-4156-86aa-a965c40579dd.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/2/outputs/dataset_628e00eb-c42b-4122-af6b-138d203e2288.dat -p 1 -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 +# StringTie version 2.2.2 +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 "53.000004"; +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 ae618321f34a -r 8eb8750070d4 test-data/stringtie_out2_re.gtf --- a/test-data/stringtie_out2_re.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out2_re.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -f 0\.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1 -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; +# stringtie /tmp/tmpm2qmdax_/files/8/7/1/dataset_871b229a-6bb9-4fea-ad17-d71634870366.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/4/outputs/dataset_3a880427-cc94-440b-974f-61adfa148f55.dat -p 1 -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 +# StringTie version 2.2.2 +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 "53.000004"; +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 ae618321f34a -r 8eb8750070d4 test-data/stringtie_out3_re.gtf --- a/test-data/stringtie_out3_re.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out3_re.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1 -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; +# stringtie /tmp/tmpm2qmdax_/files/1/9/d/dataset_19d005b0-21af-4097-ba09-dcfd47a9639d.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/7/outputs/dataset_e7ff968a-b61b-4cce-900e-04fd85518371.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 +# StringTie version 2.2.2 +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"; |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out4_re.gtf --- a/test-data/stringtie_out4_re.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out4_re.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0( -A /[-_/a-zA-Z0-9]+\.dat)? -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; +# stringtie /tmp/tmpm2qmdax_/files/4/2/5/dataset_42595174-c98e-47c3-80d3-4e7f41bf639a.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/19/outputs/dataset_89f0738d-5fec-45ea-b655-2585a71d3d18.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.17 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 -A /tmp/tmpm2qmdax_/job_working_directory/000/19/outputs/dataset_793b9d71-4869-4258-a6a5-1d50bd53361f.dat +# StringTie version 2.2.2 +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"; |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out5.gtf --- a/test-data/stringtie_out5.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out5.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -b \./special_de_output/sample1/ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1 -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; +# stringtie /tmp/tmpm2qmdax_/files/5/b/5/dataset_5b55cbd8-f515-46d6-b1d2-71201435248b.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/13/outputs/dataset_3b84d9d9-efe9-4d58-9f34-c6d3f5da763f.dat -p 1 -G guide.gff -C /tmp/tmpm2qmdax_/job_working_directory/000/13/outputs/dataset_8fb2eb9a-4a6c-4300-9639-0a39336f7dab.dat -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 +# StringTie version 2.2.2 +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"; |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out6.gtf --- a/test-data/stringtie_out6.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out6.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -C /[-_/a-zA-Z0-9]+\.dat -e -b \./special_de_output/sample1/ -f 0\.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1 -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "53\.000004"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "21\.660000"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; cov "49\.237373"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "CUFF\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; +# stringtie /tmp/tmpm2qmdax_/files/5/f/e/dataset_5fe68ff0-f093-4d09-86ec-2e1a279bb301.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/16/outputs/dataset_821eef87-9397-4b49-8860-910104445af9.dat -p 1 -G guide.gff -C /tmp/tmpm2qmdax_/job_working_directory/000/16/outputs/dataset_5a1ac870-b1e8-4437-8b57-211b71557c52.dat -e -b ./special_de_output/sample1/ -f 0.01 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 +# StringTie version 2.2.2 +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 "53.000004"; +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 ae618321f34a -r 8eb8750070d4 test-data/stringtie_out8.gtf --- a/test-data/stringtie_out8.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out8.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1 -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; +# stringtie /tmp/tmpm2qmdax_/files/1/d/b/dataset_1db0e632-3580-4045-9441-56a6e90bafea.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/22/outputs/dataset_2072a123-60b0-41ed-b4fc-9df0db87bff0.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 +# StringTie version 2.2.2 +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"; |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out9.gtf --- a/test-data/stringtie_out9.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out9.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,6 +1,6 @@ -# StringTie version 2\.2\.1 -# stringtie /[-_/a-zA-Z0-9]+\.dat -o /[-_/a-zA-Z0-9]+\.dat -p [0-9]+ -G guide\.gff -b \./special_de_output/sample1/ -f 0\.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1 -test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "53\.000004"; -test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "21\.660000"; -test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "49\.237373"; -test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; reference_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+"; cov "45\.241611"; FPKM "3314403\.750000"; TPM "1000000\.000000"; +# stringtie /tmp/tmpm2qmdax_/files/c/8/7/dataset_c8776afe-26a8-48d2-bea6-b66d6a50a5ad.dat -o /tmp/tmpm2qmdax_/job_working_directory/000/24/outputs/dataset_721fe1c9-4aea-4e2f-84d4-76e855eb610c.dat -p 1 -G guide.gff -b ./special_de_output/sample1/ -f 0.15 -m 200 -a 10 -j 1 -c 1 -g 50 -M 1.0 +# StringTie version 2.2.2 +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"; |
| b |
| diff -r ae618321f34a -r 8eb8750070d4 test-data/stringtie_out_coverage.gtf --- a/test-data/stringtie_out_coverage.gtf Mon Jan 30 12:01:28 2023 +0000 +++ b/test-data/stringtie_out_coverage.gtf Tue Apr 30 11:53:08 2024 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -test_chromosome\tCufflinks\texon\t351\t400\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1 -test_chromosome\tCufflinks\texon\t501\t550\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1 -test_chromosome\tCufflinks\texon\t53\t250\t1000\t\+\t\.\tParent=CUFF\.[0-9]+\.1 -test_chromosome\tCufflinks\ttranscript\t53\t550\t1000\t\+\t\.\tID=CUFF\.[0-9]+\.1;geneID=CUFF\.[0-9]+;coverage=60\.97 +test_chromosome Cufflinks transcript 53 550 1000 + . ID=CUFF.1.1;geneID=CUFF.1;coverage=60.97 +test_chromosome Cufflinks exon 53 250 1000 + . Parent=CUFF.1.1 +test_chromosome Cufflinks exon 351 400 1000 + . Parent=CUFF.1.1 +test_chromosome Cufflinks exon 501 550 1000 + . Parent=CUFF.1.1 |