Mercurial > repos > iuc > psiclass
changeset 0:1b690aa060f6 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/psiclass commit 2dc6baaeb2d595cbd8d8ffe3bf22b199a0ba23e4
| author | iuc |
|---|---|
| date | Tue, 26 Sep 2023 16:51:18 +0000 |
| parents | |
| children | |
| files | macros.xml psiclass.xml test-data/reads1.bam test-data/reads2.bam test-data/splice_sites.interval test-data/test01_annotation_sample0.gtf test-data/test01_annotation_sample1.gtf test-data/test01_meta_annotation.gtf test-data/test01_splice_sites.txt test-data/test02_annotation_sample0.gtf test-data/test02_annotation_sample1.gtf test-data/test02_meta_annotation.gtf test-data/test02_splice_sites.txt test-data/test03_annotation_sample0.gtf test-data/test03_meta_annotation.gtf test-data/test03_splice_sites.txt |
| diffstat | 16 files changed, 601 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,17 @@ +<macros> + <token name="@TOOL_VERSION@">1.0.3</token> + <token name="@VERSION_SUFFIX@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">psiclass</requirement> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41467-019-12990-0</citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>psiclass --version</version_command> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/psiclass.xml Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,151 @@ +<tool id="psiclass" name="PsiCLASS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> + <description>reference-based transcriptome assembler</description> + <macros> + <import>macros.xml</import> + </macros> + <xrefs> + <xref type="bio.tools">psiclass</xref> + </xrefs> + <expand macro="requirements" /> + <command detect_errors='exit_code'><![CDATA[ + mkdir -p "annotation_files" && + #set $bam_filenames = [] + #for $i,$file in enumerate($bam_files) + #set $name = 'bam_' + str($i) + '.bam' + ln -s '${file}' $name && + $bam_filenames.append($name) + #end for + #set $allFiles = ','.join( [ str( $file ) for $file in $bam_filenames ] ) + psiclass + -b $allFiles + -p \${GALAXY_SLOTS:-8} + #if $splice_conditional.selector == 'true' + -s '${splice_conditional.splice_file}' + #end if + -c $subexonClassifier + --sa $intronCoverage + --vd $transcriptCoverage + #if $stranded + --stranded $stranded + #end if + --maxDpConstraintSize $maxDpConstraintSize + $primaryParalog + --tssTesQuantile $tssTesQuantile + && mv *sample* "./annotation_files" + #if $splice_conditional.selector == 'false' + && cat ./splice/psiclass_bam.trusted_splice > '${splice_sites}' + #end if + ]]></command> + <inputs> + <param argument="-b" name="bam_files" type="data" format="bam" multiple="true" label="BAM file(s)" + help="PsiCLASS has been tuned to run on alignments generated with the tools HISAT and STAR" /> + <conditional name="splice_conditional"> + <param name="selector" type="select" label="Provide trusted splice sites coordinates" help="It is possible to supply + an set of trusted introns, for instance generated by RNASTAR or extracted from the GENCODE gene annotations"> + <option value="true">Enabled</option> + <option value="false" selected="true">Disabled</option> + </param> + <when value="true"> + <param argument="-s" name="splice_file" type="data" format="interval" optional="true" label="Splice junction sites file" help="High confidence collapsed splice junction file" /> + </when> + <when value="false"/> + </conditional> + <param argument="-c" type="float" name="subexonClassifier" min="0" max="1" value="0.05" label="Subexon classifier score threshold" + help="Only use the subexons with classifier score minor or equal than the given number" /> + <param argument="--sa" name="intronCoverage" type="float" min="0" value="0.5" label="Minimum retained intron converage" + help="Minimum average number of supported read for retained introns" /> + <param argument="--vd" name="transcriptCoverage" type="float" min="0" value="1" label="Minimum transcript coverage" + help="Minimum average coverage depth of a transcript to be reported" /> + <param argument="--stranded" type="select" optional="true" label="Library strand information" help="Stranded data shows advantages over + non-stranded RNA-Seq data such as higher assembly and differential expression accuracy"> + <option value="un">unstranded</option> + <option value="rf">fr-firststrand (rf): first read from the opposite strand.</option> + <option value="fr">fr-secondstrand (fr): first read from the transcript strand</option> + </param> + <param argument="--maxDpConstraintSize" type="integer" min="-1" value="7" label="Constrain cover iN median exon depth (DP)" help="-1 for infinite"/> + <param argument="--primaryParalog" type="boolean" truevalue="--primaryParalog" falsevalue="" checked="false" optional="true" + label="Use primary alignment to retain paralog genes" help="Default: use unique alignments" /> + <param argument="--tssTesQuantile" type="float" min="0" max="1" value="0.5" label="Quantile for transcription start/end sites in subexon graph"/> + </inputs> + <outputs> + <data name="meta_anotation" format="gtf" from_work_dir="psiclass_vote.gtf" label="${tool.name} on ${on_string}: meta-annotation" /> + <collection name="annotation_collection" type="list" label="${tool.name} on ${on_string}: per-sample annotations"> + <discover_datasets pattern="__designation_and_ext__" format="gtf" directory="annotation_files"/> + </collection> + <data name="splice_sites" format="interval" label="${tool.name} on ${on_string}: splice sites"> + <filter>splice_conditional["selector"] == "false"</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="2"> + <param name="bam_files" value="reads1.bam,reads2.bam"/> + <param name="subexonClassifier" value="0.05"/> + <param name="intronCoverage" value="0.5"/> + <param name="transcriptCoverage" value="1"/> + <param name="stranded" value="un"/> + <param name="maxDpConstraintSize" value="7"/> + <param name="primaryParalog" value="false"/> + <param name="tssTesQuantile" value="0.5"/> + <conditional name="splice_conditional"> + <param name="selector" value="true"/> + <param name="splice_file" value="splice_sites.interval"/> + </conditional> + <output name="meta_anotation" ftype="gtf" file="test01_meta_annotation.gtf" lines_diff="2"/> + <output_collection name="annotation_collection" type="list" count="2"> + <element name="psiclass_sample_0" ftype="gtf" file="test01_annotation_sample0.gtf" lines_diff="2"/> + <element name="psiclass_sample_1" ftype="gtf" file="test01_annotation_sample1.gtf" lines_diff="2"/> + </output_collection> + </test> + <test expect_num_outputs="3"> + <param name="bam_files" value="reads1.bam,reads2.bam"/> + <param name="subexonClassifier" value="0.05"/> + <param name="intronCoverage" value="0.3"/> + <param name="transcriptCoverage" value="0.5"/> + <param name="stranded" value="rf"/> + <param name="maxDpConstraintSize" value="6"/> + <param name="primaryParalog" value="true"/> + <param name="tssTesQuantile" value="0.4"/> + <conditional name="splice_conditional"> + <param name="selector" value="false"/> + </conditional> + <output name="meta_anotation" ftype="gtf" file="test02_meta_annotation.gtf"/> + <output_collection name="annotation_collection" type="list" count="2"> + <element name="psiclass_sample_0" ftype="gtf" file="test02_annotation_sample0.gtf" lines_diff="2"/> + <element name="psiclass_sample_1" ftype="gtf" file="test02_annotation_sample1.gtf" lines_diff="2"/> + </output_collection> + <output name="splice_sites" ftype="interval" file="test02_splice_sites.txt"/> + </test> + <test expect_num_outputs="3"> + <param name="bam_files" value="reads1.bam"/> + <output name="meta_anotation" ftype="gtf" file="test03_meta_annotation.gtf"/> + <output_collection name="annotation_collection" type="list" count="1"> + <element name="psiclass_sample_0" ftype="gtf" file="test03_annotation_sample0.gtf" lines_diff="2"/> + </output_collection> + <output name="splice_sites" file="test03_splice_sites.txt" ftype="interval"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What is PsiCLASS?** + +PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. + +Unlike conventional methods that analyze each sample separately and then merge the outcomes to create a unified set of meta-annotations, +PsiCLASS takes a multi-sample approach, simultaneously analyzing all RNA-seq data sets in an experiment. + +PsiCLASS is both a transcript assembler and a meta-assembler, producing separate transcript sets for the individual samples and a unified +set of meta-annotations. The algorithmic underpinnings of PsiCLASS include using a global subexon splice graph, statistical cross-sample +feature (intron, subexon) selection methods, and an efficient dynamic programming algorithm to select a subset of transcripts from among +those encoded in the graph, based on the read support in each sample. + +Lastly, the set of meta-annotations is selected from among the transcripts generated for individual samples by voting. While PsiCLASS is +highly accurate and efficient for medium-to-large collections of RNA-seq data, its accuracy is equally high for small RNA-seq data sets +(2-10 samples) and is competitive to reference methods for single samples. Additionally, its performance is robust with the aggregation +method used, including the built-in voting and assembly-based approaches such as StringTie-merge and TACO. Therefore, it can be effectively +used as a multi-sample and as a single-sample assembler, as well as in conventional assemble-and-merge protocols. + + ]]></help> + <expand macro="citations" /> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/splice_sites.interval Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 27 0 37 +test_chromosome 401 500 1 1 0 25 0 36
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test01_annotation_sample0.gtf Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,15 @@ +#PsiCLASS_v1.0.3 +#/home/laptop/miniconda3/envs/mulled-v1-4549fe7ad5b22a1b35ab5aa0ada6322e374f13375e517a18654c3ddd9bb8d124/bin/classes -p 1 -c 0.05 --stranded un --maxDpConstraintSize 7 -b bam_0.bam -b bam_1.bam -s ./subexon/psiclass_subexon_combined.out -o ./psiclass +#bam_0.bam +chr16 PsiCLASS transcript 784996 786471 1000 . . gene_id "chr16.1"; transcript_id "chr16.1.0"; FPKM "90057.137790"; TPM "395522.152415"; cov "33.028455"; +chr16 PsiCLASS exon 784996 786471 1000 . . gene_id "chr16.1"; transcript_id "chr16.1.0"; exon_number "1"; FPKM "90057.137790"; TPM "395522.152415"; cov "33.028455"; +chr16 PsiCLASS transcript 787203 787744 1000 . . gene_id "chr16.7"; transcript_id "chr16.7.0"; FPKM "14337.566689"; TPM "62969.192406"; cov "5.258303"; +chr16 PsiCLASS exon 787203 787744 1000 . . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "1"; FPKM "14337.566689"; TPM "62969.192406"; cov "5.258303"; +chr16 PsiCLASS transcript 790525 792347 1000 . . gene_id "chr16.17"; transcript_id "chr16.17.0"; FPKM "19967.535928"; TPM "87695.467370"; cov "7.323094"; +chr16 PsiCLASS exon 790525 792347 1000 . . gene_id "chr16.17"; transcript_id "chr16.17.0"; exon_number "1"; FPKM "19967.535928"; TPM "87695.467370"; cov "7.323094"; +chr16 PsiCLASS transcript 794054 794361 1000 . . gene_id "chr16.25"; transcript_id "chr16.25.0"; FPKM "10623.323507"; TPM "46656.599158"; cov "3.896104"; +chr16 PsiCLASS exon 794054 794361 1000 . . gene_id "chr16.25"; transcript_id "chr16.25.0"; exon_number "1"; FPKM "10623.323507"; TPM "46656.599158"; cov "3.896104"; +chr16 PsiCLASS transcript 795132 795356 1000 . . gene_id "chr16.27"; transcript_id "chr16.27.0"; FPKM "30902.067712"; TPM "135718.862884"; cov "11.333333"; +chr16 PsiCLASS exon 795132 795356 1000 . . gene_id "chr16.27"; transcript_id "chr16.27.0"; exon_number "1"; FPKM "30902.067712"; TPM "135718.862884"; cov "11.333333"; +chr16 PsiCLASS transcript 797839 798063 1000 . . gene_id "chr16.39"; transcript_id "chr16.39.0"; FPKM "61804.135424"; TPM "271437.725768"; cov "22.666667"; +chr16 PsiCLASS exon 797839 798063 1000 . . gene_id "chr16.39"; transcript_id "chr16.39.0"; exon_number "1"; FPKM "61804.135424"; TPM "271437.725768"; cov "22.666667";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test01_annotation_sample1.gtf Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,3 @@ +#PsiCLASS_v1.0.3 +#/home/laptop/miniconda3/envs/mulled-v1-4549fe7ad5b22a1b35ab5aa0ada6322e374f13375e517a18654c3ddd9bb8d124/bin/classes -p 1 -c 0.05 --stranded un --maxDpConstraintSize 7 -b bam_0.bam -b bam_1.bam -s ./subexon/psiclass_subexon_combined.out -o ./psiclass +#bam_1.bam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test01_meta_annotation.gtf Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,12 @@ +chr16 PsiCLASS transcript 784996 786471 1000 . . gene_id "chr16.1"; transcript_id "chr16.1.0"; FPKM "90057.137790"; TPM "395522.152415"; cov "33.028455"; sample_cnt "1"; +chr16 PsiCLASS exon 784996 786471 1000 . . gene_id "chr16.1"; transcript_id "chr16.1.0"; exon_number "1"; FPKM "90057.137790"; TPM "395522.152415"; cov "33.028455"; sample_cnt "1"; +chr16 PsiCLASS transcript 787203 787744 1000 . . gene_id "chr16.7"; transcript_id "chr16.7.0"; FPKM "14337.566689"; TPM "62969.192406"; cov "5.258303"; sample_cnt "1"; +chr16 PsiCLASS exon 787203 787744 1000 . . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "1"; FPKM "14337.566689"; TPM "62969.192406"; cov "5.258303"; sample_cnt "1"; +chr16 PsiCLASS transcript 790525 792347 1000 . . gene_id "chr16.17"; transcript_id "chr16.17.0"; FPKM "19967.535928"; TPM "87695.467370"; cov "7.323094"; sample_cnt "1"; +chr16 PsiCLASS exon 790525 792347 1000 . . gene_id "chr16.17"; transcript_id "chr16.17.0"; exon_number "1"; FPKM "19967.535928"; TPM "87695.467370"; cov "7.323094"; sample_cnt "1"; +chr16 PsiCLASS transcript 794054 794361 1000 . . gene_id "chr16.25"; transcript_id "chr16.25.0"; FPKM "10623.323507"; TPM "46656.599158"; cov "3.896104"; sample_cnt "1"; +chr16 PsiCLASS exon 794054 794361 1000 . . gene_id "chr16.25"; transcript_id "chr16.25.0"; exon_number "1"; FPKM "10623.323507"; TPM "46656.599158"; cov "3.896104"; sample_cnt "1"; +chr16 PsiCLASS transcript 795132 795356 1000 . . gene_id "chr16.27"; transcript_id "chr16.27.0"; FPKM "30902.067712"; TPM "135718.862884"; cov "11.333333"; sample_cnt "1"; +chr16 PsiCLASS exon 795132 795356 1000 . . gene_id "chr16.27"; transcript_id "chr16.27.0"; exon_number "1"; FPKM "30902.067712"; TPM "135718.862884"; cov "11.333333"; sample_cnt "1"; +chr16 PsiCLASS transcript 797839 798063 1000 . . gene_id "chr16.39"; transcript_id "chr16.39.0"; FPKM "61804.135424"; TPM "271437.725768"; cov "22.666667"; sample_cnt "1"; +chr16 PsiCLASS exon 797839 798063 1000 . . gene_id "chr16.39"; transcript_id "chr16.39.0"; exon_number "1"; FPKM "61804.135424"; TPM "271437.725768"; cov "22.666667"; sample_cnt "1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test01_splice_sites.txt Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,68 @@ +chr16 786377 786827 10 - 10 0 0 0 +chr16 786928 787068 10 - 10 0 0 0 +chr16 786928 787077 10 - 10 0 0 0 +chr16 787179 787354 10 - 10 0 0 0 +chr16 787477 787556 10 - 10 0 0 0 +chr16 787744 788256 10 - 10 0 0 0 +chr16 789125 789210 10 + 10 0 0 0 +chr16 789360 789547 10 + 10 0 0 0 +chr16 789715 790177 10 + 10 0 0 0 +chr16 790269 790347 10 + 10 0 0 0 +chr16 790399 790525 10 + 10 0 0 0 +chr16 790666 791161 10 + 10 0 0 0 +chr16 791370 791851 10 + 10 0 0 0 +chr16 791948 792224 10 + 10 0 0 0 +chr16 792347 792439 10 + 10 0 0 0 +chr16 792590 792718 10 + 10 0 0 0 +chr16 792811 792966 10 + 10 0 0 0 +chr16 793064 793144 10 + 10 0 0 0 +chr16 793274 794054 10 + 10 0 0 0 +chr16 794201 795132 10 + 10 0 0 0 +chr16 795356 795685 10 + 10 0 0 0 +chr16 795834 795947 10 + 10 0 0 0 +chr16 796077 796717 10 + 10 0 0 0 +chr16 796861 796961 10 + 10 0 0 0 +chr16 797092 797694 10 + 10 0 0 0 +chr16 797751 797839 10 + 10 0 0 0 +chr16 854706 868944 10 - 10 0 0 0 +chr16 869056 869883 10 - 10 0 0 0 +chr16 870066 870729 10 - 10 0 0 0 +chr16 870882 871161 10 - 10 0 0 0 +chr16 871341 879570 10 - 10 0 0 0 +chr16 893072 910931 10 - 10 0 0 0 +chr16 954666 970788 10 - 10 0 0 0 +chr19 567648 571440 10 - 10 0 0 0 +chr19 571579 580379 10 - 10 0 0 0 +chr19 572701 577774 10 - 10 0 0 0 +chr19 578121 579500 10 - 10 0 0 0 +chr19 579656 580379 10 - 10 0 0 0 +chr19 580461 580646 10 - 10 0 0 0 +chr19 580782 581315 10 - 10 0 0 0 +chr19 581610 582514 10 - 10 0 0 0 +chr19 582582 582750 10 - 10 0 0 0 +chr19 590577 603544 10 - 10 0 0 0 +chr19 603967 605061 10 - 10 0 0 0 +chr19 605222 607964 10 - 10 0 0 0 +chr19 608182 610259 10 - 10 0 0 0 +chr19 610405 613248 10 - 10 0 0 0 +chr19 613488 613852 10 - 10 0 0 0 +chr19 614016 615795 10 - 10 0 0 0 +chr19 617323 617419 10 - 10 0 0 0 +chr19 617480 617570 10 - 10 0 0 0 +chr19 617655 617777 10 - 10 0 0 0 +chr19 617849 618488 10 - 10 0 0 0 +chr19 618586 618705 10 - 10 0 0 0 +chr19 618760 618997 10 - 10 0 0 0 +chr19 619110 619210 10 - 10 0 0 0 +chr19 619765 619958 10 - 10 0 0 0 +chr19 620080 620365 10 - 10 0 0 0 +chr19 620487 621058 10 - 10 0 0 0 +chr19 621846 622149 10 - 10 0 0 0 +chr19 622373 622582 10 - 10 0 0 0 +chr19 622752 622821 10 - 10 0 0 0 +chr19 622985 623454 10 - 10 0 0 0 +chr19 623603 624719 10 - 10 0 0 0 +chr19 624905 625124 10 - 10 0 0 0 +chr19 625254 629540 10 - 10 0 0 0 +chr19 630168 632834 10 - 10 0 0 0 +chr19 632938 633425 10 - 10 0 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test02_annotation_sample0.gtf Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,44 @@ +#PsiCLASS_v1.0.3 +#/home/laptop/miniconda3/envs/mulled-v1-4549fe7ad5b22a1b35ab5aa0ada6322e374f13375e517a18654c3ddd9bb8d124/bin/classes -p 1 -c 0.05 --stranded rf --maxDpConstraintSize 6 --primaryParalog -b bam_0.bam -b bam_1.bam -s ./subexon/psiclass_subexon_combined.out -o ./psiclass +#bam_0.bam +chr16 PsiCLASS transcript 784996 788300 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; +chr16 PsiCLASS exon 784996 786377 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "1"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; +chr16 PsiCLASS exon 786827 786928 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "2"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; +chr16 PsiCLASS exon 787077 787179 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "3"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; +chr16 PsiCLASS exon 787354 787477 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "4"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; +chr16 PsiCLASS exon 787556 787744 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "5"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; +chr16 PsiCLASS exon 788256 788300 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "6"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; +chr16 PsiCLASS transcript 789075 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 789075 789125 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "1"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 789210 789360 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "2"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 789547 789715 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "3"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 790177 790269 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "4"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 790347 790399 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "5"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 790525 790666 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "6"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 791161 791370 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "7"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 791851 791948 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "8"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 792224 792347 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "9"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 792439 792590 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "10"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 792718 792811 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "11"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 792966 793064 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "12"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 793144 793274 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "13"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 794054 794201 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "14"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 795132 795356 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "15"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 795685 795834 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "16"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 795947 796077 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "17"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 796717 796861 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "18"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 796961 797092 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "19"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 797694 797751 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "20"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS exon 797839 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "21"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; +chr16 PsiCLASS transcript 806296 806764 1000 . . gene_id "chr16.5"; transcript_id "chr16.5.0"; FPKM "10464.766439"; TPM "62200.074061"; cov "3.837953"; +chr16 PsiCLASS exon 806296 806764 1000 . . gene_id "chr16.5"; transcript_id "chr16.5.0"; exon_number "1"; FPKM "10464.766439"; TPM "62200.074061"; cov "3.837953"; +chr16 PsiCLASS transcript 854556 879737 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; +chr16 PsiCLASS exon 854556 854706 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "1"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; +chr16 PsiCLASS exon 868944 869056 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "2"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; +chr16 PsiCLASS exon 869883 870066 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "3"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; +chr16 PsiCLASS exon 870729 870882 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "4"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; +chr16 PsiCLASS exon 871161 871341 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "5"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; +chr16 PsiCLASS exon 879570 879737 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "6"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; +chr16 PsiCLASS transcript 954357 970856 1000 - . gene_id "chr16.8"; transcript_id "chr16.8.0"; FPKM "8633.202217"; TPM "51313.693465"; cov "3.166227"; +chr16 PsiCLASS exon 954357 954666 1000 - . gene_id "chr16.8"; transcript_id "chr16.8.0"; exon_number "1"; FPKM "8633.202217"; TPM "51313.693465"; cov "3.166227"; +chr16 PsiCLASS exon 970788 970856 1000 - . gene_id "chr16.8"; transcript_id "chr16.8.0"; exon_number "2"; FPKM "8633.202217"; TPM "51313.693465"; cov "3.166227";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test02_annotation_sample1.gtf Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,3 @@ +#PsiCLASS_v1.0.3 +#/home/laptop/miniconda3/envs/mulled-v1-4549fe7ad5b22a1b35ab5aa0ada6322e374f13375e517a18654c3ddd9bb8d124/bin/classes -p 1 -c 0.05 --stranded rf --maxDpConstraintSize 6 --primaryParalog -b bam_0.bam -b bam_1.bam -s ./subexon/psiclass_subexon_combined.out -o ./psiclass +#bam_1.bam
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test02_meta_annotation.gtf Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,41 @@ +chr16 PsiCLASS transcript 784996 788300 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 784996 786377 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "1"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 786827 786928 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "2"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 787077 787179 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "3"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 787354 787477 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "4"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 787556 787744 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "5"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 788256 788300 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "6"; FPKM "80537.900652"; TPM "478698.059272"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS transcript 789075 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 789075 789125 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "1"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 789210 789360 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "2"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 789547 789715 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "3"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 790177 790269 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "4"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 790347 790399 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "5"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 790525 790666 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "6"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 791161 791370 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "7"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 791851 791948 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "8"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 792224 792347 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "9"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 792439 792590 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "10"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 792718 792811 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "11"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 792966 793064 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "12"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 793144 793274 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "13"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 794054 794201 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "14"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 795132 795356 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "15"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 795685 795834 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "16"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 795947 796077 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "17"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 796717 796861 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "18"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 796961 797092 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "19"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 797694 797751 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "20"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS exon 797839 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "21"; FPKM "54415.405737"; TPM "323432.184222"; cov "19.956850"; sample_cnt "1"; +chr16 PsiCLASS transcript 806296 806764 1000 . . gene_id "chr16.5"; transcript_id "chr16.5.0"; FPKM "10464.766439"; TPM "62200.074061"; cov "3.837953"; sample_cnt "1"; +chr16 PsiCLASS exon 806296 806764 1000 . . gene_id "chr16.5"; transcript_id "chr16.5.0"; exon_number "1"; FPKM "10464.766439"; TPM "62200.074061"; cov "3.837953"; sample_cnt "1"; +chr16 PsiCLASS transcript 854556 879737 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; sample_cnt "1"; +chr16 PsiCLASS exon 854556 854706 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "1"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; sample_cnt "1"; +chr16 PsiCLASS exon 868944 869056 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "2"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; sample_cnt "1"; +chr16 PsiCLASS exon 869883 870066 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "3"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; sample_cnt "1"; +chr16 PsiCLASS exon 870729 870882 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "4"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; sample_cnt "1"; +chr16 PsiCLASS exon 871161 871341 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "5"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; sample_cnt "1"; +chr16 PsiCLASS exon 879570 879737 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "6"; FPKM "14192.358060"; TPM "84355.988981"; cov "5.205047"; sample_cnt "1"; +chr16 PsiCLASS transcript 954357 970856 1000 - . gene_id "chr16.8"; transcript_id "chr16.8.0"; FPKM "8633.202217"; TPM "51313.693465"; cov "3.166227"; sample_cnt "1"; +chr16 PsiCLASS exon 954357 954666 1000 - . gene_id "chr16.8"; transcript_id "chr16.8.0"; exon_number "1"; FPKM "8633.202217"; TPM "51313.693465"; cov "3.166227"; sample_cnt "1"; +chr16 PsiCLASS exon 970788 970856 1000 - . gene_id "chr16.8"; transcript_id "chr16.8.0"; exon_number "2"; FPKM "8633.202217"; TPM "51313.693465"; cov "3.166227"; sample_cnt "1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test02_splice_sites.txt Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,68 @@ +chr16 786377 786827 10 - 10 0 0 0 +chr16 786928 787068 10 - 10 0 0 0 +chr16 786928 787077 10 - 10 0 0 0 +chr16 787179 787354 10 - 10 0 0 0 +chr16 787477 787556 10 - 10 0 0 0 +chr16 787744 788256 10 - 10 0 0 0 +chr16 789125 789210 10 + 10 0 0 0 +chr16 789360 789547 10 + 10 0 0 0 +chr16 789715 790177 10 + 10 0 0 0 +chr16 790269 790347 10 + 10 0 0 0 +chr16 790399 790525 10 + 10 0 0 0 +chr16 790666 791161 10 + 10 0 0 0 +chr16 791370 791851 10 + 10 0 0 0 +chr16 791948 792224 10 + 10 0 0 0 +chr16 792347 792439 10 + 10 0 0 0 +chr16 792590 792718 10 + 10 0 0 0 +chr16 792811 792966 10 + 10 0 0 0 +chr16 793064 793144 10 + 10 0 0 0 +chr16 793274 794054 10 + 10 0 0 0 +chr16 794201 795132 10 + 10 0 0 0 +chr16 795356 795685 10 + 10 0 0 0 +chr16 795834 795947 10 + 10 0 0 0 +chr16 796077 796717 10 + 10 0 0 0 +chr16 796861 796961 10 + 10 0 0 0 +chr16 797092 797694 10 + 10 0 0 0 +chr16 797751 797839 10 + 10 0 0 0 +chr16 854706 868944 10 - 10 0 0 0 +chr16 869056 869883 10 - 10 0 0 0 +chr16 870066 870729 10 - 10 0 0 0 +chr16 870882 871161 10 - 10 0 0 0 +chr16 871341 879570 10 - 10 0 0 0 +chr16 893072 910931 10 - 10 0 0 0 +chr16 954666 970788 10 - 10 0 0 0 +chr19 567648 571440 10 - 10 0 0 0 +chr19 571579 580379 10 - 10 0 0 0 +chr19 572701 577774 10 - 10 0 0 0 +chr19 578121 579500 10 - 10 0 0 0 +chr19 579656 580379 10 - 10 0 0 0 +chr19 580461 580646 10 - 10 0 0 0 +chr19 580782 581315 10 - 10 0 0 0 +chr19 581610 582514 10 - 10 0 0 0 +chr19 582582 582750 10 - 10 0 0 0 +chr19 590577 603544 10 - 10 0 0 0 +chr19 603967 605061 10 - 10 0 0 0 +chr19 605222 607964 10 - 10 0 0 0 +chr19 608182 610259 10 - 10 0 0 0 +chr19 610405 613248 10 - 10 0 0 0 +chr19 613488 613852 10 - 10 0 0 0 +chr19 614016 615795 10 - 10 0 0 0 +chr19 617323 617419 10 - 10 0 0 0 +chr19 617480 617570 10 - 10 0 0 0 +chr19 617655 617777 10 - 10 0 0 0 +chr19 617849 618488 10 - 10 0 0 0 +chr19 618586 618705 10 - 10 0 0 0 +chr19 618760 618997 10 - 10 0 0 0 +chr19 619110 619210 10 - 10 0 0 0 +chr19 619765 619958 10 - 10 0 0 0 +chr19 620080 620365 10 - 10 0 0 0 +chr19 620487 621058 10 - 10 0 0 0 +chr19 621846 622149 10 - 10 0 0 0 +chr19 622373 622582 10 - 10 0 0 0 +chr19 622752 622821 10 - 10 0 0 0 +chr19 622985 623454 10 - 10 0 0 0 +chr19 623603 624719 10 - 10 0 0 0 +chr19 624905 625124 10 - 10 0 0 0 +chr19 625254 629540 10 - 10 0 0 0 +chr19 630168 632834 10 - 10 0 0 0 +chr19 632938 633425 10 - 10 0 0 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test03_annotation_sample0.gtf Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,67 @@ +#PsiCLASS_v1.0.3 +#/home/laptop/miniconda3/envs/mulled-v1-4549fe7ad5b22a1b35ab5aa0ada6322e374f13375e517a18654c3ddd9bb8d124/bin/classes -p 1 -c 0.05 --maxDpConstraintSize 7 -b bam_0.bam -s ./subexon/psiclass_subexon_combined.out -o ./psiclass +#bam_0.bam +chr16 PsiCLASS transcript 784996 788300 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; +chr16 PsiCLASS exon 784996 786377 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "1"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; +chr16 PsiCLASS exon 786827 786928 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "2"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; +chr16 PsiCLASS exon 787077 787179 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "3"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; +chr16 PsiCLASS exon 787354 787477 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "4"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; +chr16 PsiCLASS exon 787556 787744 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "5"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; +chr16 PsiCLASS exon 788256 788300 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "6"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; +chr16 PsiCLASS transcript 789075 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 789075 789125 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "1"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 789210 789360 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "2"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 789547 789715 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "3"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 790177 790269 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "4"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 790347 790399 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "5"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 790525 792347 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "6"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 792439 792590 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "7"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 792718 792811 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "8"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 792966 793064 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "9"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 793144 793274 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "10"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 794054 794201 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "11"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 795132 795356 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "12"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 795685 795834 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "13"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 795947 796077 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "14"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 796717 796861 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "15"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 796961 797092 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "16"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 797694 797751 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "17"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS exon 797839 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "18"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; +chr16 PsiCLASS transcript 789075 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 789075 789125 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "1"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 789210 789360 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "2"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 789547 789715 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "3"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 790177 790269 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "4"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 790347 790399 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "5"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 790525 790666 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "6"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 791161 791370 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "7"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 791851 791948 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "8"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 792224 792347 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "9"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 792439 792590 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "10"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 792718 792811 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "11"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 792966 793064 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "12"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 793144 793274 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "13"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 794054 794201 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "14"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 795132 795356 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "15"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 795685 795834 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "16"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 795947 796077 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "17"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 796717 796861 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "18"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 796961 797092 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "19"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 797694 797751 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "20"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS exon 797839 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "21"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; +chr16 PsiCLASS transcript 806296 806764 1000 . . gene_id "chr16.5"; transcript_id "chr16.5.0"; FPKM "10464.766439"; TPM "61528.978043"; cov "3.837953"; +chr16 PsiCLASS exon 806296 806764 1000 . . gene_id "chr16.5"; transcript_id "chr16.5.0"; exon_number "1"; FPKM "10464.766439"; TPM "61528.978043"; cov "3.837953"; +chr16 PsiCLASS transcript 854556 911018 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; +chr16 PsiCLASS exon 854556 854706 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "1"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; +chr16 PsiCLASS exon 868944 869056 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "2"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; +chr16 PsiCLASS exon 869883 870066 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "3"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; +chr16 PsiCLASS exon 870729 870882 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "4"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; +chr16 PsiCLASS exon 871161 871341 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "5"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; +chr16 PsiCLASS exon 879570 879737 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "6"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; +chr16 PsiCLASS exon 893007 893072 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "7"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; +chr16 PsiCLASS exon 910931 911018 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "8"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; +chr16 PsiCLASS transcript 934126 970856 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537"; +chr16 PsiCLASS exon 934126 934145 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "1"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537"; +chr16 PsiCLASS exon 934244 934254 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "2"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537"; +chr16 PsiCLASS exon 954357 954666 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "3"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537"; +chr16 PsiCLASS exon 970788 970856 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "4"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test03_meta_annotation.gtf Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,64 @@ +chr16 PsiCLASS transcript 784996 788300 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 784996 786377 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "1"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 786827 786928 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "2"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 787077 787179 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "3"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 787354 787477 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "4"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 787556 787744 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "5"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS exon 788256 788300 1000 - . gene_id "chr16.0"; transcript_id "chr16.0.0"; exon_number "6"; FPKM "80537.900652"; TPM "473533.236461"; cov "29.537275"; sample_cnt "1"; +chr16 PsiCLASS transcript 789075 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 789075 789125 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "1"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 789210 789360 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "2"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 789547 789715 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "3"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 790177 790269 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "4"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 790347 790399 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "5"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 790525 792347 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "6"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 792439 792590 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "7"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 792718 792811 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "8"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 792966 793064 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "9"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 793144 793274 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "10"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 794054 794201 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "11"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 795132 795356 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "12"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 795685 795834 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "13"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 795947 796077 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "14"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 796717 796861 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "15"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 796961 797092 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "16"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 797694 797751 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "17"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS exon 797839 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.0"; exon_number "18"; FPKM "18742.007264"; TPM "110196.109976"; cov "6.873631"; sample_cnt "1"; +chr16 PsiCLASS transcript 789075 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 789075 789125 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "1"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 789210 789360 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "2"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 789547 789715 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "3"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 790177 790269 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "4"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 790347 790399 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "5"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 790525 790666 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "6"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 791161 791370 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "7"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 791851 791948 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "8"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 792224 792347 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "9"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 792439 792590 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "10"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 792718 792811 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "11"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 792966 793064 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "12"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 793144 793274 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "13"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 794054 794201 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "14"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 795132 795356 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "15"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 795685 795834 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "16"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 795947 796077 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "17"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 796717 796861 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "18"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 796961 797092 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "19"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 797694 797751 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "20"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS exon 797839 798063 1000 + . gene_id "chr16.3"; transcript_id "chr16.3.1"; exon_number "21"; FPKM "37403.744328"; TPM "219920.260694"; cov "13.717823"; sample_cnt "1"; +chr16 PsiCLASS transcript 806296 806764 1000 . . gene_id "chr16.5"; transcript_id "chr16.5.0"; FPKM "10464.766439"; TPM "61528.978043"; cov "3.837953"; sample_cnt "1"; +chr16 PsiCLASS exon 806296 806764 1000 . . gene_id "chr16.5"; transcript_id "chr16.5.0"; exon_number "1"; FPKM "10464.766439"; TPM "61528.978043"; cov "3.837953"; sample_cnt "1"; +chr16 PsiCLASS transcript 854556 911018 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; sample_cnt "1"; +chr16 PsiCLASS exon 854556 854706 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "1"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; sample_cnt "1"; +chr16 PsiCLASS exon 868944 869056 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "2"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; sample_cnt "1"; +chr16 PsiCLASS exon 869883 870066 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "3"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; sample_cnt "1"; +chr16 PsiCLASS exon 870729 870882 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "4"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; sample_cnt "1"; +chr16 PsiCLASS exon 871161 871341 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "5"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; sample_cnt "1"; +chr16 PsiCLASS exon 879570 879737 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "6"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; sample_cnt "1"; +chr16 PsiCLASS exon 893007 893072 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "7"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; sample_cnt "1"; +chr16 PsiCLASS exon 910931 911018 1000 - . gene_id "chr16.6"; transcript_id "chr16.6.0"; exon_number "8"; FPKM "12954.686358"; TPM "76168.791447"; cov "4.751131"; sample_cnt "1"; +chr16 PsiCLASS transcript 934126 970856 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537"; sample_cnt "1"; +chr16 PsiCLASS exon 934126 934145 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "1"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537"; sample_cnt "1"; +chr16 PsiCLASS exon 934244 934254 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "2"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537"; sample_cnt "1"; +chr16 PsiCLASS exon 954357 954666 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "3"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537"; sample_cnt "1"; +chr16 PsiCLASS exon 970788 970856 1000 - . gene_id "chr16.7"; transcript_id "chr16.7.0"; exon_number "4"; FPKM "9975.559878"; TPM "58652.623379"; cov "3.658537"; sample_cnt "1";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test03_splice_sites.txt Tue Sep 26 16:51:18 2023 +0000 @@ -0,0 +1,46 @@ +chr16 772096 843547 10 + 10 0 0 0 +chr16 786377 786825 10 - 10 0 0 0 +chr16 786377 786827 10 - 10 0 0 0 +chr16 786928 787068 10 - 10 0 0 0 +chr16 786928 787077 10 - 10 0 0 0 +chr16 787179 787354 10 - 10 0 0 0 +chr16 787241 787354 10 - 10 0 0 0 +chr16 787477 787556 10 - 10 0 0 0 +chr16 787477 788256 10 - 10 0 0 0 +chr16 787744 788256 10 - 10 0 0 0 +chr16 788775 788931 10 + 10 0 0 0 +chr16 789125 789210 10 + 10 0 0 0 +chr16 789360 789547 10 + 10 0 0 0 +chr16 789715 790177 10 + 10 0 0 0 +chr16 790269 790347 10 + 10 0 0 0 +chr16 790399 790525 10 + 10 0 0 0 +chr16 790666 791161 10 + 10 0 0 0 +chr16 791370 791851 10 + 10 0 0 0 +chr16 791948 792224 10 + 10 0 0 0 +chr16 792347 792439 10 + 10 0 0 0 +chr16 792590 792718 10 + 10 0 0 0 +chr16 792811 792966 10 + 10 0 0 0 +chr16 793001 856267 10 + 10 0 0 0 +chr16 793064 793144 10 + 10 0 0 0 +chr16 793274 794054 10 + 10 0 0 0 +chr16 794201 794648 10 + 10 0 0 0 +chr16 794201 795132 10 + 10 0 0 0 +chr16 794201 795248 10 + 10 0 0 0 +chr16 795356 795685 10 + 10 0 0 0 +chr16 795834 795889 10 + 10 0 0 0 +chr16 795834 795947 10 + 10 0 0 0 +chr16 796077 796717 10 + 10 0 0 0 +chr16 796861 796961 10 + 10 0 0 0 +chr16 797092 797694 10 + 10 0 0 0 +chr16 797751 797839 10 + 10 0 0 0 +chr16 854706 868944 10 - 10 0 0 0 +chr16 869056 869883 10 - 10 0 0 0 +chr16 870066 870729 10 - 10 0 0 0 +chr16 870882 871161 10 - 10 0 0 0 +chr16 871341 879570 10 - 10 0 0 0 +chr16 879737 893007 10 - 10 0 0 0 +chr16 893072 910931 10 - 10 0 0 0 +chr16 903832 904526 10 - 10 0 0 0 +chr16 934145 934244 10 - 10 0 0 0 +chr16 934254 954357 10 - 10 0 0 0 +chr16 954666 970788 10 - 10 0 0 0