Mercurial > repos > iuc > stringtie
changeset 23:8eb8750070d4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stringtie commit 252f4cccd66513c985b3df9480d73c8b9f994520
| author | iuc |
|---|---|
| date | Tue, 30 Apr 2024 11:53:08 +0000 |
| parents | ae618321f34a |
| children | cbf488da3b2c |
| files | 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 |
| diffstat | 16 files changed, 335 insertions(+), 335 deletions(-) [+] |
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--- a/macros.xml Mon Jan 30 12:01:28 2023 +0000 +++ b/macros.xml Tue Apr 30 11:53:08 2024 +0000 @@ -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>
--- a/stringtie.xml Mon Jan 30 12:01:28 2023 +0000 +++ b/stringtie.xml Tue Apr 30 11:53:08 2024 +0000 @@ -1,11 +1,11 @@ -<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> +<tool id="stringtie" name="StringTie" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> <description>transcript assembly and quantification</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" /> @@ -148,12 +148,12 @@ </when> <when value="long_reads"> <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"/> - <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" /> + <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"/> </when> <when value="mixed_reads"> <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"/> <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"/> - <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" /> + <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"/> </when> </conditional> <param name="rna_strandness" type="select" label="Specify strand information" @@ -177,13 +177,13 @@ <when value="cached"> <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"> <options from_data_table="gene_sets"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No GTF file is available." /> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No GTF file is available."/> </options> </param> </when> <when value="history"> - <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly" /> + <param name="ref_hist" type="data" format="gtf,gff3" label="GTF/GFF3 dataset to guide assembly"/> </when> </conditional> <param name="input_estimation" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="Use Reference transcripts only?" help="Limit the processing of read alignments to only estimate and output the assembled transcripts matching the reference transcripts given with the -G option. With this option, read bundles with no reference transcripts (novel transcripts) will be entirely skipped, which may provide a considerable speed boost when the given set of reference transcripts is limited to a set of target genes, for example. Default: No"/> @@ -195,9 +195,9 @@ </param> <when value="ballgown" /> <when value="deseq2"> - <param name="read_length" argument="--length" type="integer" min="0" value="75" label="Specify the average read length" help="Default: 75" /> - <param name="clustering" argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" checked="false" label="Cluster overlapping genes" help="Choose whether to cluster genes with different gene IDs that overlap. Transcripts containing the geneID prefix will be ignored. Default: No" /> - <param argument="--string" type="text" label="Prefix used for transcripts" help="If a different prefix was used for geneIDs assigned by StringTie than the default, specify it here. Only letters and numbers will be retained in this field. Default: MSTRG" > + <param name="read_length" argument="--length" type="integer" min="0" value="75" label="Specify the average read length" help="Default: 75"/> + <param name="clustering" argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" checked="false" label="Cluster overlapping genes" help="Choose whether to cluster genes with different gene IDs that overlap. Transcripts containing the geneID prefix will be ignored. Default: No"/> + <param argument="--string" type="text" label="Prefix used for transcripts" help="If a different prefix was used for geneIDs assigned by StringTie than the default, specify it here. Only letters and numbers will be retained in this field. Default: MSTRG"> <sanitizer> <valid initial="string.letters,string.digits"></valid> </sanitizer> @@ -215,7 +215,7 @@ </conditional> <section name="adv" title="Advanced Options"> <param name="abundance_estimation" argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Output gene abundance estimation file?" help="If selected, gene abundances will be reported in a tab-delimited file, see below for more information"/> - <param name="omit_sequences" argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="Ignore all read alignments (and thus do not attempt to perform transcript assembly) on the specified reference sequences. This parameter can be a single reference sequence name (e.g. chrM) or a comma-delimited list of sequence names (e.g. chrM,chrX,chrY). This can speed up StringTie especially in the case of excluding the mitochondrial genome, whose genes may have very high coverage in some cases, even though they may be of no interest for a particular RNA-Seq analysis. The reference sequence names are case sensitive, they must match identically the names of chromosomes/contigs of the target genome against which the RNA-Seq reads were aligned in the first place." /> + <param name="omit_sequences" argument="-x" type="text" value="" label="Do not assemble any transcripts on these reference sequence(s)" help="Ignore all read alignments (and thus do not attempt to perform transcript assembly) on the specified reference sequences. This parameter can be a single reference sequence name (e.g. chrM) or a comma-delimited list of sequence names (e.g. chrM,chrX,chrY). This can speed up StringTie especially in the case of excluding the mitochondrial genome, whose genes may have very high coverage in some cases, even though they may be of no interest for a particular RNA-Seq analysis. The reference sequence names are case sensitive, they must match identically the names of chromosomes/contigs of the target genome against which the RNA-Seq reads were aligned in the first place."/> <param name="name_prefix" argument="-l" type="text" label="Name prefix for output transcripts" help="This prefix will be added to the name of the transcripts that are output. Only letters and numbers will be retained in this field. Default: STRG"> <sanitizer> <valid initial="string.letters,string.digits"></valid> @@ -223,18 +223,18 @@ </param> <param name="fraction" argument="-f" type="float" min="0.0" max="1.0" value="0.01" label="Minimum isoform fraction" help="Sets the minimum isoform abundance of the predicted transcripts as a fraction of the most abundant transcript assembled at a given locus. Lower abundance transcripts are often artifacts of incompletely spliced precursors of processed transcripts. Default: 0.05"/> <param name="min_tlen" argument="-m" type="integer" min="0" value="200" label="Minimum assembled transcript length" help="Sets the minimum length allowed for the predicted transcripts. Default: 200"/> - <param name="min_anchor_len" argument="-a" type="integer" min="0" value="10" label="Minimum anchor length for junctions" help="Junctions that don't have spliced reads that align across them with at least this amount of bases on both sides are filtered out. Default: 10" /> - <param name="min_anchor_cov" argument="-j" type="integer" min="0" value="1" label="Minimum junction coverage" help="There should be at least this many spliced reads that align across a junction (i.e. junction coverage). This number can be fractional, since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the junction coverage. Default: 1" /> + <param name="min_anchor_len" argument="-a" type="integer" min="0" value="10" label="Minimum anchor length for junctions" help="Junctions that don't have spliced reads that align across them with at least this amount of bases on both sides are filtered out. Default: 10"/> + <param name="min_anchor_cov" argument="-j" type="integer" min="0" value="1" label="Minimum junction coverage" help="There should be at least this many spliced reads that align across a junction (i.e. junction coverage). This number can be fractional, since some reads align in more than one place. A read that aligns in n places will contribute 1/n to the junction coverage. Default: 1"/> <param name="min_bundle_cov" argument="-c" type="integer" min="0" value="1" label="Minimum bundle reads per bp coverage to consider for assembly" help="Sets the minimum read coverage allowed for the predicted transcripts. A transcript with a lower coverage than this value is not shown in the output. Default: 2"/> <param name="bdist" argument="-g" type="integer" min="0" value="50" label="Gap between read mappings triggering a new bundle" help="Minimum locus gap separation value. Reads that are mapped closer than this distance are merged together in the same processing bundle. Default: 50 (bp)"/> <param name="bundle_fraction" argument="-M" type="float" min="0.0" max="1.0" value="1" label="Fraction of bundle allowed to be covered by multi-hit reads" help="Sets the maximum fraction of muliple-location-mapped reads that are allowed to be present at a given locus. Default: 0.95"/> - <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No" /> + <param name="disable_trimming" argument="-t" type="boolean" truevalue="-t" falsevalue="" checked="false" label="Disable trimming of predicted transcripts based on coverage" help="This parameter disables trimming at the ends of the assembled transcripts. By default StringTie adjusts the predicted transcript's start and/or stop coordinates based on sudden drops in coverage of the assembled transcript. Default: No"/> <param name="multi_mapping" argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="false" label="Disable multi-mapping correction" help="Default: No"/> <param name="point_features" type="data" format="tabular" optional="true" label="Input point-features dataset" help="Loads a list of point-features from a text feature file to guide the transcriptome assembly. Accepted point features are transcription start sites (TSS) and polyadenylation sites (CPAS). There are four tab-delimited columns in the feature file. The first three define the location of the point feature on the cromosome (sequence name, coordinate and strand), and the last is the type of the feature (TSS or CPAS)."/> </section> </inputs> <outputs> - <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" /> + <data name="output_gtf" format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts"/> <data name="gene_abundance_estimation" format="tabular" label="${tool.name} on ${on_string}: Gene abundance estimates"> <filter>adv['abundance_estimation']</filter> </data> @@ -276,146 +276,146 @@ <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="short_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" compare="re_match" sort="true"/> + <output name="output_gtf" file="stringtie_out1_re.gtf" ftype="gtf" lines_diff="2"/> </test> <!--Ensure fraction option works --> <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="short_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <param name="fraction" value="0.17" /> - <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="fraction" value="0.17"/> + <output name="output_gtf" file="stringtie_out2_re.gtf" ftype="gtf" lines_diff="2"/> </test> <!--Ensure guide option works --> <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="short_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <param name="use_guide" value="yes" /> - <param name="guide_gff_select" value="history" /> + <param name="use_guide" value="yes"/> + <param name="guide_gff_select" value="history"/> <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> - <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" compare="re_match" sort="true"/> + <output name="output_gtf" file="stringtie_out3_re.gtf" ftype="gtf" lines_diff="2"/> </test> <!--Ensure guide with fraction works --> <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="short_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <param name="use_guide" value="yes" /> - <param name="guide_gff_select" value="history" /> - <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> - <param name="fraction" value="0.17" /> - <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="use_guide" value="yes"/> + <param name="guide_gff_select" value="history"/> + <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/> + <param name="fraction" value="0.17"/> + <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="2"/> </test> <!--Ensure coverage and output for Ballgown works --> <test expect_num_outputs="7"> <conditional name="input_options"> <param name="input_mode" value="short_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <param name="use_guide" value="yes" /> - <param name="guide_gff_select" value="history" /> - <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> - <param name="special_outputs_select" value="ballgown" /> - <param name="coverage_file" value="true" /> - <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular" /> - <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular" /> - <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular" /> - <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular" /> - <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular" /> - <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" compare="re_match" sort="true"/> - <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="use_guide" value="yes"/> + <param name="guide_gff_select" value="history"/> + <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/> + <param name="special_outputs_select" value="ballgown"/> + <param name="coverage_file" value="true"/> + <output name="exon_expression" file="./ballgown/e_data.ctab" ftype="tabular"/> + <output name="intron_expression" file="./ballgown/i_data.ctab" ftype="tabular"/> + <output name="transcript_expression" file="./ballgown/t_data.ctab" ftype="tabular"/> + <output name="exon_transcript_mapping" file="./ballgown/e2t.ctab" ftype="tabular"/> + <output name="intron_transcript_mapping" file="./ballgown/i2t.ctab" ftype="tabular"/> + <output name="output_gtf" file="stringtie_out5.gtf" ftype="gtf" lines_diff="2"/> + <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="2"/> </test> <!--Ensure output for edgeR works --> <test expect_num_outputs="5"> <conditional name="input_options"> <param name="input_mode" value="short_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <param name="use_guide" value="yes" /> - <param name="special_outputs_select" value="deseq2" /> - <param name="input_estimation" value="true" /> + <param name="use_guide" value="yes"/> + <param name="special_outputs_select" value="deseq2"/> + <param name="input_estimation" value="true"/> <param name="guide_gff_select" value="history" /> - <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> - <param name="coverage_file" value="true" /> - <param name="clustering" value="true" /> - <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular" /> - <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular" /> - <output name="legend" file="legend.tsv" ftype="tabular" /> - <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" compare="re_match" sort="true"/> - <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/> + <param name="coverage_file" value="true"/> + <param name="clustering" value="true"/> + <output name="gene_counts" file="gene_counts_edger.tsv" ftype="tabular"/> + <output name="transcript_counts" file="transcript_counts_edger.tsv" ftype="tabular"/> + <output name="legend" file="legend.tsv" ftype="tabular"/> + <output name="output_gtf" file="stringtie_out6.gtf" ftype="gtf" lines_diff="2"/> + <output name="coverage" file="stringtie_out_coverage.gtf" ftype="gtf" lines_diff="2"/> </test> <!--Ensure gene abundances output works --> <test expect_num_outputs="2"> <conditional name="input_options"> <param name="input_mode" value="short_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <param name="use_guide" value="yes" /> - <param name="guide_gff_select" value="history" /> - <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> - <param name="fraction" value="0.17" /> - <param name="abundance_estimation" value="true" /> - <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="use_guide" value="yes"/> + <param name="guide_gff_select" value="history"/> + <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/> + <param name="fraction" value="0.17"/> + <param name="abundance_estimation" value="true"/> + <output name="output_gtf" file="stringtie_out4_re.gtf" ftype="gtf" lines_diff="2"/> <output name="gene_abundance_estimation" file="stringtie_out7.tsv" ftype="tabular" lines_diff="2" /> </test> <!--Ensure another fraction value works --> <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="short_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <param name="use_guide" value="yes" /> - <param name="guide_gff_select" value="history" /> - <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf" /> - <param name="fraction" value="0.15" /> - <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="use_guide" value="yes"/> + <param name="guide_gff_select" value="history"/> + <param name="ref_hist" ftype="gtf" value="stringtie_in.gtf"/> + <param name="fraction" value="0.15"/> + <output name="output_gtf" file="stringtie_out8.gtf" ftype="gtf" lines_diff="2"/> </test> <!--Ensure built-in GTFs work --> <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="short_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <param name="use_guide" value="yes" /> - <param name="guide_gff_select" value="cached" /> - <param name="fraction" value="0.15" /> - <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="use_guide" value="yes"/> + <param name="guide_gff_select" value="cached"/> + <param name="fraction" value="0.15"/> + <output name="output_gtf" file="stringtie_out9.gtf" ftype="gtf" lines_diff="2"/> </test> <!-- Test long reads input --> <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="long_reads"/> - <param name="input_bam" ftype="bam" value="stringtie_in1.bam" /> + <param name="input_bam" ftype="bam" value="stringtie_in1.bam"/> </conditional> - <param name="use_guide" value="yes" /> - <param name="guide_gff_select" value="cached" /> - <param name="fraction" value="0.15" /> - <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="use_guide" value="yes"/> + <param name="guide_gff_select" value="cached"/> + <param name="fraction" value="0.15"/> + <output name="output_gtf" file="stringtie_out10.gtf" ftype="gtf" lines_diff="2"/> </test> <!-- Test error splice option --> <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="long_reads"/> - <param name="input_bam" ftype="bam" value="long_reads.bam" /> - <param name="error_splice" value="30" /> + <param name="input_bam" ftype="bam" value="long_reads.bam"/> + <param name="error_splice" value="30"/> </conditional> - <param name="use_guide" value="yes" /> - <param name="guide_gff_select" value="cached" /> - <param name="fraction" value="0.15" /> - <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" compare="re_match" sort="true"/> + <param name="use_guide" value="yes"/> + <param name="guide_gff_select" value="cached"/> + <param name="fraction" value="0.15"/> + <output name="output_gtf" file="stringtie_out11.gtf" ftype="gtf" lines_diff="2"/> </test> <!-- Test mixed reads input --> <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="mixed_reads"/> - <param name="input_bam_short" ftype="bam" value="short_reads.bam" /> - <param name="input_bam_long" ftype="bam" value="long_reads.bam" /> + <param name="input_bam_short" ftype="bam" value="short_reads.bam"/> + <param name="input_bam_long" ftype="bam" value="long_reads.bam"/> </conditional> <output name="output_gtf" ftype="gtf"> <assert_contents> @@ -429,8 +429,8 @@ <test expect_num_outputs="1"> <conditional name="input_options"> <param name="input_mode" value="mixed_reads"/> - <param name="input_bam_short" ftype="cram" value="stringtie_in.cram" /> - <param name="input_bam_long" ftype="cram" value="stringtie_in.cram" /> + <param name="input_bam_short" ftype="cram" value="stringtie_in.cram"/> + <param name="input_bam_long" ftype="cram" value="stringtie_in.cram"/> </conditional> <output name="output_gtf" ftype="gtf"> <assert_contents>
--- a/stringtie_merge.xml Mon Jan 30 12:01:28 2023 +0000 +++ b/stringtie_merge.xml Tue Apr 30 11:53:08 2024 +0000 @@ -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>
--- 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";
--- 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 @@ -1,100 +1,100 @@ -# 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 -chr1\tStringTie\texon\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3204563\t3207049\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; -chr1\tStringTie\texon\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3411783\t3411982\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; -chr1\tStringTie\texon\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; exon_number "[0-9]+"; -chr1\tStringTie\texon\t3660633\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; exon_number "[0-9]+"; ref_gene_id "Xkr4"; -chr1\tStringTie\ttranscript\t3189811\t3193042\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3200023\t3200191\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3201078\t3201809\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3204563\t3661579\t1000\t-\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; -chr1\tStringTie\ttranscript\t3212214\t3212439\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3212718\t3212801\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3213096\t3213242\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3242634\t3243079\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3243348\t3243401\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3277914\t3278390\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3280687\t3280741\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3282761\t3282832\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3290489\t3291273\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3299444\t3299664\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3319000\t3319051\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3351241\t3351311\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3355908\t3356119\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3363077\t3363446\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3363754\t3363849\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3377212\t3377262\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3386740\t3386836\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tStringTie\ttranscript\t3450907\t3451109\t1000\t\.\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "MSTRG\.[0-9]+\.1"; -chr1\tmm9_refFlat\texon\t4334224\t4340172\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4341991\t4342162\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4342283\t4342918\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4350281\t4350473\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4481009\t4482749\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4483181\t4483547\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4483853\t4483944\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4485217\t4486023\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4486372\t4486494\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4763279\t4764597\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4763279\t4764597\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4763279\t4766882\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4767606\t4767729\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4772649\t4772814\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4774032\t4774186\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4774032\t4774186\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4775654\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4797974\t4798063\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4798536\t4798567\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4818665\t4818730\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4820349\t4820396\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4822392\t4822462\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4827082\t4827155\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4829468\t4829569\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4831037\t4831213\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4835044\t4836816\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4847775\t4848057\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4847775\t4848057\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4857551\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4857551\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4868108\t4868213\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4876825\t4876912\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4879538\t4879683\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4880821\t4880877\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4881996\t4882150\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4883498\t4883644\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4885015\t4885086\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\texon\t4886437\t4887987\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; exon_number "[0-9]+"; -chr1\tmm9_refFlat\ttranscript\t4334224\t4350473\t\.\t-\t\.\tgene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1"; -chr1\tmm9_refFlat\ttranscript\t4481009\t4486494\t\.\t-\t\.\tgene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17"; -chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15"; -chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15"; -chr1\tmm9_refFlat\ttranscript\t4763279\t4775807\t\.\t-\t\.\tgene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15"; -chr1\tmm9_refFlat\ttranscript\t4797974\t4836816\t\.\t\+\t\.\tgene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1"; -chr1\tmm9_refFlat\ttranscript\t4847775\t4857613\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1"; -chr1\tmm9_refFlat\ttranscript\t4847775\t4887987\t\.\t\+\t\.\tgene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1"; \ No newline at end of file +# stringtie --merge -p 1 -G /tmp/tmpr8yl388j/files/9/2/b/dataset_92bbbdee-6cfa-4cff-bab3-0d0836475341.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpr8yl388j/job_working_directory/000/10/outputs/dataset_81bd1351-3b74-4332-b789-a4f53357a8fa.dat /tmp/tmpr8yl388j/files/3/c/3/dataset_3c3b1fdc-0351-48ef-a6eb-6c226751f619.dat /tmp/tmpr8yl388j/files/2/a/4/dataset_2a44d87f-131b-4587-bf25-2527d7d89964.dat +# StringTie version 2.2.2 +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"; +chr1 StringTie exon 3200023 3200191 1000 . . gene_id "MSTRG.2"; transcript_id "MSTRG.2.1"; exon_number "1"; +chr1 StringTie transcript 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; +chr1 StringTie exon 3201078 3201809 1000 . . gene_id "MSTRG.3"; transcript_id "MSTRG.3.1"; exon_number "1"; +chr1 StringTie transcript 3204563 3661579 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; ref_gene_id "Xkr4"; +chr1 StringTie exon 3204563 3207049 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "1"; ref_gene_id "Xkr4"; +chr1 StringTie exon 3411783 3411982 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "2"; ref_gene_id "Xkr4"; +chr1 StringTie exon 3660633 3661579 1000 - . gene_id "MSTRG.4"; transcript_id "Xkr4"; exon_number "3"; ref_gene_id "Xkr4"; +chr1 StringTie transcript 3212214 3212439 1000 . . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; +chr1 StringTie exon 3212214 3212439 1000 . . gene_id "MSTRG.5"; transcript_id "MSTRG.5.1"; exon_number "1"; +chr1 StringTie transcript 3212718 3212801 1000 . . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; +chr1 StringTie exon 3212718 3212801 1000 . . gene_id "MSTRG.6"; transcript_id "MSTRG.6.1"; exon_number "1"; +chr1 StringTie transcript 3213096 3213242 1000 . . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; +chr1 StringTie exon 3213096 3213242 1000 . . gene_id "MSTRG.7"; transcript_id "MSTRG.7.1"; exon_number "1"; +chr1 StringTie transcript 3242634 3243079 1000 . . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; +chr1 StringTie exon 3242634 3243079 1000 . . gene_id "MSTRG.8"; transcript_id "MSTRG.8.1"; exon_number "1"; +chr1 StringTie transcript 3243348 3243401 1000 . . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; +chr1 StringTie exon 3243348 3243401 1000 . . gene_id "MSTRG.9"; transcript_id "MSTRG.9.1"; exon_number "1"; +chr1 StringTie transcript 3277914 3278390 1000 . . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; +chr1 StringTie exon 3277914 3278390 1000 . . gene_id "MSTRG.10"; transcript_id "MSTRG.10.1"; exon_number "1"; +chr1 StringTie transcript 3280687 3280741 1000 . . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; +chr1 StringTie exon 3280687 3280741 1000 . . gene_id "MSTRG.11"; transcript_id "MSTRG.11.1"; exon_number "1"; +chr1 StringTie transcript 3282761 3282832 1000 . . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; +chr1 StringTie exon 3282761 3282832 1000 . . gene_id "MSTRG.12"; transcript_id "MSTRG.12.1"; exon_number "1"; +chr1 StringTie transcript 3290489 3291273 1000 . . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; +chr1 StringTie exon 3290489 3291273 1000 . . gene_id "MSTRG.13"; transcript_id "MSTRG.13.1"; exon_number "1"; +chr1 StringTie transcript 3299444 3299664 1000 . . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; +chr1 StringTie exon 3299444 3299664 1000 . . gene_id "MSTRG.14"; transcript_id "MSTRG.14.1"; exon_number "1"; +chr1 StringTie transcript 3319000 3319051 1000 . . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; +chr1 StringTie exon 3319000 3319051 1000 . . gene_id "MSTRG.15"; transcript_id "MSTRG.15.1"; exon_number "1"; +chr1 StringTie transcript 3351241 3351311 1000 . . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; +chr1 StringTie exon 3351241 3351311 1000 . . gene_id "MSTRG.16"; transcript_id "MSTRG.16.1"; exon_number "1"; +chr1 StringTie transcript 3355908 3356119 1000 . . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; +chr1 StringTie exon 3355908 3356119 1000 . . gene_id "MSTRG.17"; transcript_id "MSTRG.17.1"; exon_number "1"; +chr1 StringTie transcript 3363077 3363446 1000 . . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; +chr1 StringTie exon 3363077 3363446 1000 . . gene_id "MSTRG.18"; transcript_id "MSTRG.18.1"; exon_number "1"; +chr1 StringTie transcript 3363754 3363849 1000 . . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; +chr1 StringTie exon 3363754 3363849 1000 . . gene_id "MSTRG.19"; transcript_id "MSTRG.19.1"; exon_number "1"; +chr1 StringTie transcript 3377212 3377262 1000 . . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; +chr1 StringTie exon 3377212 3377262 1000 . . gene_id "MSTRG.20"; transcript_id "MSTRG.20.1"; exon_number "1"; +chr1 StringTie transcript 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; +chr1 StringTie exon 3386740 3386836 1000 . . gene_id "MSTRG.21"; transcript_id "MSTRG.21.1"; exon_number "1"; +chr1 StringTie transcript 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; +chr1 StringTie exon 3450907 3451109 1000 . . gene_id "MSTRG.22"; transcript_id "MSTRG.22.1"; exon_number "1"; +chr1 mm9_refFlat transcript 4334224 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; ref_gene_id "Rp1"; +chr1 mm9_refFlat exon 4334224 4340172 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "1"; +chr1 mm9_refFlat exon 4341991 4342162 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "2"; +chr1 mm9_refFlat exon 4342283 4342918 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "3"; +chr1 mm9_refFlat exon 4350281 4350473 . - . gene_id "Rp1"; transcript_id "Rp1"; exon_number "4"; +chr1 mm9_refFlat transcript 4481009 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; ref_gene_id "Sox17"; +chr1 mm9_refFlat exon 4481009 4482749 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "1"; +chr1 mm9_refFlat exon 4483181 4483547 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "2"; +chr1 mm9_refFlat exon 4483853 4483944 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "3"; +chr1 mm9_refFlat exon 4485217 4486023 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "4"; +chr1 mm9_refFlat exon 4486372 4486494 . - . gene_id "Sox17"; transcript_id "Sox17"; exon_number "5"; +chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4763279 4766882 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "1"; +chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "2"; +chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "3"; +chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "4"; +chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15"; exon_number "5"; +chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "1"; +chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "2"; +chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "3"; +chr1 mm9_refFlat exon 4774032 4774186 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "4"; +chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; exon_number "5"; +chr1 mm9_refFlat transcript 4763279 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; ref_gene_id "Mrpl15"; +chr1 mm9_refFlat exon 4763279 4764597 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "1"; +chr1 mm9_refFlat exon 4767606 4767729 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "2"; +chr1 mm9_refFlat exon 4772649 4772814 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "3"; +chr1 mm9_refFlat exon 4775654 4775807 . - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; exon_number "4"; +chr1 mm9_refFlat transcript 4797974 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; ref_gene_id "Lypla1"; +chr1 mm9_refFlat exon 4797974 4798063 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "1"; +chr1 mm9_refFlat exon 4798536 4798567 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "2"; +chr1 mm9_refFlat exon 4818665 4818730 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "3"; +chr1 mm9_refFlat exon 4820349 4820396 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "4"; +chr1 mm9_refFlat exon 4822392 4822462 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "5"; +chr1 mm9_refFlat exon 4827082 4827155 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "6"; +chr1 mm9_refFlat exon 4829468 4829569 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "7"; +chr1 mm9_refFlat exon 4831037 4831213 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "8"; +chr1 mm9_refFlat exon 4835044 4836816 . + . gene_id "Lypla1"; transcript_id "Lypla1"; exon_number "9"; +chr1 mm9_refFlat transcript 4847775 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "1"; +chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; exon_number "2"; +chr1 mm9_refFlat transcript 4847775 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; ref_gene_id "Tcea1"; +chr1 mm9_refFlat exon 4847775 4848057 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "1"; +chr1 mm9_refFlat exon 4857551 4857613 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "2"; +chr1 mm9_refFlat exon 4868108 4868213 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "3"; +chr1 mm9_refFlat exon 4876825 4876912 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "4"; +chr1 mm9_refFlat exon 4879538 4879683 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "5"; +chr1 mm9_refFlat exon 4880821 4880877 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "6"; +chr1 mm9_refFlat exon 4881996 4882150 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "7"; +chr1 mm9_refFlat exon 4883498 4883644 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "8"; +chr1 mm9_refFlat exon 4885015 4885086 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "9"; +chr1 mm9_refFlat exon 4886437 4887987 . + . gene_id "Tcea1"; transcript_id "Tcea1"; exon_number "10";
--- 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";
--- 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 @@ -1,58 +1,58 @@ -# StringTie version 2\.2\.1 -# 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 -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -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"; -chr19\tStringTie\texon\t617224\t617323\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "20\.289286"; -chr19\tStringTie\texon\t617224\t617323\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "1\.560714"; -chr19\tStringTie\texon\t617419\t617480\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "28\.788761"; -chr19\tStringTie\texon\t617419\t617480\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "1\.985432"; -chr19\tStringTie\texon\t617570\t617655\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "4\.996770"; -chr19\tStringTie\texon\t617570\t618586\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "30\.891500"; -chr19\tStringTie\texon\t617777\t617849\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.994817"; -chr19\tStringTie\texon\t618488\t618586\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.525252"; -chr19\tStringTie\texon\t618705\t618760\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; exon_number "[0-9]+"; cov "13\.750000"; -chr19\tStringTie\texon\t618705\t618760\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.875000"; -chr19\tStringTie\texon\t618997\t619110\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000"; -chr19\tStringTie\texon\t619210\t619296\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000"; -chr19\tStringTie\texon\t619586\t619765\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000"; -chr19\tStringTie\texon\t619958\t620080\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.000000"; -chr19\tStringTie\texon\t620365\t620487\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "7\.000000"; -chr19\tStringTie\texon\t621058\t621846\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.751584"; -chr19\tStringTie\texon\t622149\t622373\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000"; -chr19\tStringTie\texon\t622582\t622752\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000"; -chr19\tStringTie\texon\t622821\t622985\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000"; -chr19\tStringTie\texon\t623454\t623603\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000"; -chr19\tStringTie\texon\t624719\t624905\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000"; -chr19\tStringTie\texon\t625124\t625254\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "6\.000000"; -chr19\tStringTie\texon\t629540\t630168\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.941176"; -chr19\tStringTie\texon\t632834\t632938\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "5\.000000"; -chr19\tStringTie\texon\t633425\t633601\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; exon_number "[0-9]+"; cov "3\.988701"; -chr19\tStringTie\ttranscript\t567221\t571736\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "5\.617600"; FPKM "37220\.644531"; TPM "77823\.132812"; -chr19\tStringTie\ttranscript\t571310\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "5\.416068"; FPKM "35885\.347656"; TPM "75031\.218750"; -chr19\tStringTie\ttranscript\t572567\t583493\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; cov "6\.175826"; FPKM "40919\.292969"; TPM "85556\.492188"; -chr19\tStringTie\ttranscript\t589891\t617159\t1000\t\+\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "19\.938414"; FPKM "132106\.343750"; TPM "276215\.781250"; -chr19\tStringTie\ttranscript\t617224\t618760\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.1"; cov "29\.150192"; FPKM "193141\.000000"; TPM "403830\.687500"; -chr19\tStringTie\ttranscript\t617224\t633601\t1000\t-\t\.\tgene_id "STRG\.[0-9]+"; transcript_id "STRG\.[0-9]+\.2"; cov "5\.886094"; FPKM "38999\.609375"; TPM "81542\.703125"; +# stringtie /tmp/tmpm2qmdax_/files/c/e/f/dataset_cefc5152-4ac0-4e7e-9223-1b55c7b7ac85.dat -L -E 30 -o /tmp/tmpm2qmdax_/job_working_directory/000/28/outputs/dataset_5597b8ed-94cb-4345-9b86-8ad715fbe328.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 +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";
--- 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";
--- 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";
--- 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";
--- 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";
--- 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";
--- 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";
--- 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";
--- 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";
--- 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