| Previous changeset 28:916cb26bd9d3 (2020-01-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/htseq_count commit 86a6c88d482d19bb7105fb17b933e19cd1e86ece |
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modified:
README.rst htseq-count.xml test-data/htseq-test.gff test-data/htseq-test_samout.bam |
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added:
test-data/htseq-test-paired_allcounts.tsv test-data/htseq-test.gtf test-data/htseq-test_allcounts.tsv test-data/htseq-test_nosq.sam |
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removed:
test-data/htseq-test-paired_othercounts.tsv test-data/htseq-test_othercounts.tsv |
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| diff -r 916cb26bd9d3 -r 4418229c501e README.rst --- a/README.rst Sun Jan 26 23:43:52 2020 -0500 +++ b/README.rst Wed Jan 31 12:51:03 2024 +0000 |
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| @@ -1,7 +1,7 @@ htseq-count wrapper for Galaxy ============================== -Galaxy wrapper for `htseq-count <https://htseq.readthedocs.io/en/release_0.9.1/count.html>`_ +Galaxy wrapper for `htseq-count <https://htseq.readthedocs.io/en/latest/history.html#version-2-0-5>`_ script from the `HTSEQ <https://readthedocs.org/projects/htseq/>`_ python package. Installation |
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| diff -r 916cb26bd9d3 -r 4418229c501e htseq-count.xml --- a/htseq-count.xml Sun Jan 26 23:43:52 2020 -0500 +++ b/htseq-count.xml Wed Jan 31 12:51:03 2024 +0000 |
| [ |
| b'@@ -1,40 +1,57 @@\n-<tool id="htseq_count" name="htseq-count" version="0.9.1+galaxy1" profile="16.04">\n+<tool id="htseq_count" name="htseq-count" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">\n <description> - Count aligned reads in a BAM file that overlap features in a GFF file</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">2.0.5</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">23.0</token>\n+ </macros>\n+ <xrefs>\n+ <xref type="bio.tools">htseq</xref>\n+ </xrefs>\n <requirements>\n- <requirement type="package" version="0.9.1">htseq</requirement>\n- <requirement type="package" version="1.7">samtools</requirement>\n+ <requirement type="package" version="@TOOL_VERSION@">htseq</requirement>\n+ <requirement type="package" version="1.19.2">samtools</requirement>\n+ <requirement type="package" version="5.3.0">gawk</requirement>\n+ <requirement type="package" version="9.4">coreutils</requirement>\n </requirements>\n \n <stdio>\n- <exit_code range="1:" level="fatal" description="Unknown error occurred" />\n+ <exit_code range="1:" level="fatal" />\n <regex match="htseq-count: (command ){0,1}not found" source="stderr" level="fatal" description="The HTSeq python package is not properly installed, contact Galaxy administrators" />\n <regex match="samtools: (command ){0,1}not found" source="stderr" level="fatal" description="The samtools package is not properly installed, contact Galaxy administrators" />\n <regex match="Error: Feature (.+) does not contain a \'(.+)\' attribute" source="both" level="fatal" description="Error parsing the GFF file, at least one feature of the specified \'Feature type\' does not have a value for the specified \'ID Attribute\'" />\n <regex match="Error occured in line (\\d+) of file" source="stderr" level="fatal" description="Unknown error parsing the GFF file" />\n+ <regex match="no SQ lines present" source="stderr" level="fatal" description="Input SAM dataset is missing header or SQ header lines. Please provide a FASTA reference sequence as additional input." />\n <regex match="Error" source="stderr" level="fatal" description="Unknown error occured" />\n </stdio>\n \n- <version_command>htseq-count -h | grep version | sed \'s/^\\(.*\\)*\\(version .*\\)\\./\\2/\'</version_command>\n+ <version_command>htseq-count --version</version_command>\n \n <command><![CDATA[\n ##set up input files\n- #set $reference_fasta_filename = "localref.fa"\n- #set $name_sorted_alignment_filename = "name_sorted_alignment.sam"\n- #if str( $advanced_options.advanced_options_selector ) == "advanced":\n- #if str( $advanced_options.samout_conditional.samout ) == "Yes":\n- #if str( $advanced_options.samout_conditional.reference_source.reference_source_selector ) == "history":\n- ln -s "${advanced_options.samout_conditional.reference_source.ref_file}" "${reference_fasta_filename}" &&\n- samtools faidx \'${reference_fasta_filename}\' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&\n- #else:\n- #set $reference_fasta_filename = str( $advanced_options.samout_conditional.reference_source.ref_file.fields.path )\n- #end if\n+ #set $name_sorted_alignment_filename = "name_sorted.bam"\n+ #set $ref_index = "ref.fai"\n+ #if $samfile.extension == \'sam\':\n+ #if str($reference_source.reference_source_selector) == "history":\n+ samtools faidx --fai-idx $ref_index \'${reference_source.ref_file}\' 2>&1 || echo "Error running samtools faidx for htseq-count" >&2 &&\n+ #elif str($reference_source.reference_source_selector) == "cached":\n+ ln -s \'${reference_source.ref_file.fields.path}.fai\' $ref_index\n #end if\n #end if\n \n- #if $samfile.extension == \'bam\':\n- samtools sort -n -T "\\${TMPDIR:-.}" --output-fmt=SAM -o \'$'..b'e="htseq-test_counts.tsv" />\n+ <output name="allcounts" file="htseq-test_allcounts.tsv" />\n </test>\n <test expect_num_outputs="2">\n <param name="samfile" value="htseq-test.bam" />\n <param name="gfffile" value="htseq-test.gff" />\n <output name="counts" file="htseq-test_counts.tsv" />\n- <output name="othercounts" file="htseq-test_othercounts.tsv" />\n+ <output name="allcounts" file="htseq-test_allcounts.tsv" />\n </test>\n <test expect_num_outputs="2">\n <param name="samfile" value="htseq-test-paired.bam" />\n <param name="gfffile" value="htseq-test.gff" />\n <output name="counts" file="htseq-test-paired_counts.tsv" />\n- <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />\n+ <output name="allcounts" file="htseq-test-paired_allcounts.tsv" />\n </test>\n <test expect_num_outputs="2">\n <param name="samfile" value="htseq-test-paired.bam" />\n <param name="gfffile" value="htseq-test.gff" />\n- <param name="samout" value="No" />\n+ <param name="samout" value="true" />\n <output name="counts" file="htseq-test-paired_counts.tsv" />\n- <output name="othercounts" file="htseq-test-paired_othercounts.tsv" />\n+ <output name="allcounts" file="htseq-test-paired_allcounts.tsv" />\n </test>\n <test expect_num_outputs="3">\n <param name="samfile" value="htseq-test.sam" />\n <param name="gfffile" value="htseq-test.gff" />\n <param name="advanced_options_selector" value="advanced" />\n- <param name="samout" value="Yes" />\n- <param name="reference_source_selector" value="history" />\n- <param name="ref_file" value="htseq-test_reference.fasta" />\n+ <param name="samout" value="true" />\n <output name="counts" file="htseq-test_counts.tsv" />\n- <output name="othercounts" file="htseq-test_othercounts.tsv" />\n- <output name="samoutfile" file="htseq-test_samout.bam" />\n+ <output name="allcounts" file="htseq-test_allcounts.tsv" />\n+ <output name="samoutfile" file="htseq-test_samout.bam" ftype="bam" compare="diff" lines_diff="4" />\n </test>\n <test expect_num_outputs="2">\n <param name="samfile" value="htseq-test.sam" />\n@@ -213,7 +227,7 @@\n <param name="secondary_alignments" value="ignore" />\n <param name="supplementary_alignments" value="ignore" />\n <output name="counts" file="htseq-test_counts_nonunique.tsv" />\n- <output name="othercounts" file="htseq-test_othercounts.tsv" />\n+ <output name="allcounts" file="htseq-test_allcounts.tsv" />\n </test>\n </tests>\n \n@@ -225,7 +239,7 @@\n This tool takes an alignment file in SAM or BAM format and feature file in GFF format\n and calculates the number of reads mapping to each feature. It uses the *htseq-count*\n script that is part of the HTSeq python module. See\n-http://www-huber.embl.de/users/anders/HTSeq/doc/count.html for details.\n+https://htseq.readthedocs.io/en/latest/ for details.\n \n A feature is an interval (i.e., a range of positions) on a chromosome or a union of\n such intervals. In the case of RNA-Seq, the features are typically genes, where\n@@ -310,7 +324,7 @@\n \n This script takes an alignment file in SAM format and a feature file in GFF\n format and calculates for each feature the number of reads mapping to it. See\n-https://htseq.readthedocs.io/en/release_0.9.1/count.html for details.\n+https://htseq.readthedocs.io/en/latest/ for details.\n \n Options:\n -f <format>, --format=<format>\n@@ -377,7 +391,7 @@\n \n Show a usage summary and exit\n \n-.. _FAQ: https://htseq.readthedocs.io/en/release_0.9.1/count.html#frequenctly-asked-questions\n+.. _FAQ: https://htseq.readthedocs.io/en/master/index.html\n \n ]]>\n </help>\n' |
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| diff -r 916cb26bd9d3 -r 4418229c501e test-data/htseq-test-paired_allcounts.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq-test-paired_allcounts.tsv Wed Jan 31 12:51:03 2024 +0000 |
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| @@ -0,0 +1,6 @@ +__no_feature 480 +__ambiguous 1 +__too_low_aQual 68 +__not_aligned 0 +__alignment_not_unique 0 +__aligned 317 |
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| diff -r 916cb26bd9d3 -r 4418229c501e test-data/htseq-test-paired_othercounts.tsv --- a/test-data/htseq-test-paired_othercounts.tsv Sun Jan 26 23:43:52 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -__no_feature 480 -__ambiguous 1 -__too_low_aQual 68 -__not_aligned 0 -__alignment_not_unique 0 |
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| diff -r 916cb26bd9d3 -r 4418229c501e test-data/htseq-test.gff --- a/test-data/htseq-test.gff Sun Jan 26 23:43:52 2020 -0500 +++ b/test-data/htseq-test.gff Wed Jan 31 12:51:03 2024 +0000 |
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| b'@@ -1,492 +1,493 @@\n-I\tprotein_coding\texon\t335\t649\t.\t+\t.\t gene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; transcript_name "YAL069W";\n-I\tprotein_coding\tCDS\t335\t646\t.\t+\t0\t gene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; transcript_name "YAL069W"; protein_id "YAL069W";\n-I\tprotein_coding\tstart_codon\t335\t337\t.\t+\t0\t gene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; transcript_name "YAL069W";\n-I\tprotein_coding\tstop_codon\t647\t649\t.\t+\t0\t gene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; transcript_name "YAL069W";\n-I\tprotein_coding\texon\t538\t792\t.\t+\t.\t gene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; transcript_name "YAL068W-A";\n-I\tprotein_coding\tCDS\t538\t789\t.\t+\t0\t gene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; transcript_name "YAL068W-A"; protein_id "YAL068W-A";\n-I\tprotein_coding\tstart_codon\t538\t540\t.\t+\t0\t gene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; transcript_name "YAL068W-A";\n-I\tprotein_coding\tstop_codon\t790\t792\t.\t+\t0\t gene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; transcript_name "YAL068W-A";\n-I\tprotein_coding\texon\t1807\t2169\t.\t-\t.\t gene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; transcript_name "PAU8";\n-I\tprotein_coding\tCDS\t1810\t2169\t.\t-\t0\t gene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; transcript_name "PAU8"; protein_id "YAL068C";\n-I\tprotein_coding\tstart_codon\t2167\t2169\t.\t-\t0\t gene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; transcript_name "PAU8";\n-I\tprotein_coding\tstop_codon\t1807\t1809\t.\t-\t0\t gene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; transcript_name "PAU8";\n-I\tprotein_coding\texon\t2480\t2707\t.\t+\t.\t gene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; transcript_name "YAL067W-A";\n-I\tprotein_coding\tCDS\t2480\t2704\t.\t+\t0\t gene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; transcript_name "YAL067W-A"; protein_id "YAL067W-A";\n-I\tprotein_coding\tstart_codon\t2480\t2482\t.\t+\t0\t gene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; transcript_name "YAL067W-A";\n-I\tprotein_coding\tstop_codon\t2705\t2707\t.\t+\t0\t gene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; transcript_name "YAL067W-A";\n-I\tprotein_coding\texon\t7236\t9017\t.\t-\t.\t gene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; transcript_name "SEO1";\n-I\tprotein_coding\tCDS\t7239\t9017\t.\t-\t0\t gene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; transcript_name "SEO1"; protein_id "YAL067C";\n-I\tprotein_coding\tstart_codon\t9015\t9017\t.\t-\t0\t gene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; transcript_name "SEO1";\n-I\tprotein_coding\tstop_codon\t7236\t7238\t.\t-\t0\t gene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; transcript_name "SEO1";\n-I\tprotein_coding\texon\t10092\t10400\t.\t+\t.\t gene_id "YAL066W"; transcript_id "YAL066W"; exon_number "1"; gene_name "YAL066W"; transcript_name "YAL066W";\n-I\tprotein_coding\tCDS\t10092\t10397\t.\t+\t0\t gene_id "YAL066W"; transcript_id "YAL066W"; exon_number "1"; gene_name "YAL066W"; transcript_name "YAL066W"; protein_id "YAL066W";\n-I\tprotein_coding\tstart_codon\t10092\t10094\t.\t+\t0\t gene_id "YAL066W"; transcript_id "YAL066W"; exon_number "1"; gene_name "YAL066W"; transcript_name "YAL066W";\n-I\tprotein_coding\tstop_codon\t10398\t10400\t.\t+\t0\t gene_id "YAL066W"; transcript_id "YAL066W"; exon_number "1"; gene_name "YAL066W"; transcript_name "YAL066W";\n-I\tprotein_coding\texon\t11566\t11952\t.\t-\t.\t gene_id "YAL065C"; transcript_id "YAL065C"; exon_number "1"; gene_name "YAL065C"; transcript_name "YAL065C";\n-I\tprotein_coding\tCDS\t11569\t11952\t.\t'..b'e_id=YAR066W; transcript_id=YAR066W; exon_number=1; gene_name=YAR066W; transcript_name=YAR066W; protein_id=YAR066W;\n+I\tprotein_coding\tstart_codon\t221040\t221042\t.\t+\t0\t gene_id=YAR066W; transcript_id=YAR066W; exon_number=1; gene_name=YAR066W; transcript_name=YAR066W;\n+I\tprotein_coding\tstop_codon\t221649\t221651\t.\t+\t0\t gene_id=YAR066W; transcript_id=YAR066W; exon_number=1; gene_name=YAR066W; transcript_name=YAR066W;\n+I\tprotein_coding\texon\t222397\t222882\t.\t+\t.\t gene_id=YAR068W; transcript_id=YAR068W; exon_number=1; gene_name=YAR068W; transcript_name=YAR068W;\n+I\tprotein_coding\tCDS\t222397\t222879\t.\t+\t0\t gene_id=YAR068W; transcript_id=YAR068W; exon_number=1; gene_name=YAR068W; transcript_name=YAR068W; protein_id=YAR068W;\n+I\tprotein_coding\tstart_codon\t222397\t222399\t.\t+\t0\t gene_id=YAR068W; transcript_id=YAR068W; exon_number=1; gene_name=YAR068W; transcript_name=YAR068W;\n+I\tprotein_coding\tstop_codon\t222880\t222882\t.\t+\t0\t gene_id=YAR068W; transcript_id=YAR068W; exon_number=1; gene_name=YAR068W; transcript_name=YAR068W;\n+I\tprotein_coding\texon\t224002\t224295\t.\t-\t.\t gene_id=YAR069C; transcript_id=YAR069C; exon_number=1; gene_name=YAR069C; transcript_name=YAR069C;\n+I\tprotein_coding\tCDS\t224005\t224295\t.\t-\t0\t gene_id=YAR069C; transcript_id=YAR069C; exon_number=1; gene_name=YAR069C; transcript_name=YAR069C; protein_id=YAR069C;\n+I\tprotein_coding\tstart_codon\t224293\t224295\t.\t-\t0\t gene_id=YAR069C; transcript_id=YAR069C; exon_number=1; gene_name=YAR069C; transcript_name=YAR069C;\n+I\tprotein_coding\tstop_codon\t224002\t224004\t.\t-\t0\t gene_id=YAR069C; transcript_id=YAR069C; exon_number=1; gene_name=YAR069C; transcript_name=YAR069C;\n+I\tprotein_coding\texon\t224554\t224853\t.\t-\t.\t gene_id=YAR070C; transcript_id=YAR070C; exon_number=1; gene_name=YAR070C; transcript_name=YAR070C;\n+I\tprotein_coding\tCDS\t224557\t224853\t.\t-\t0\t gene_id=YAR070C; transcript_id=YAR070C; exon_number=1; gene_name=YAR070C; transcript_name=YAR070C; protein_id=YAR070C;\n+I\tprotein_coding\tstart_codon\t224851\t224853\t.\t-\t0\t gene_id=YAR070C; transcript_id=YAR070C; exon_number=1; gene_name=YAR070C; transcript_name=YAR070C;\n+I\tprotein_coding\tstop_codon\t224554\t224556\t.\t-\t0\t gene_id=YAR070C; transcript_id=YAR070C; exon_number=1; gene_name=YAR070C; transcript_name=YAR070C;\n+I\tprotein_coding\texon\t225451\t226854\t.\t+\t.\t gene_id=YAR071W; transcript_id=YAR071W; exon_number=1; gene_name=PHO11; transcript_name=PHO11;\n+I\tprotein_coding\tCDS\t225451\t226851\t.\t+\t0\t gene_id=YAR071W; transcript_id=YAR071W; exon_number=1; gene_name=PHO11; transcript_name=PHO11; protein_id=YAR071W;\n+I\tprotein_coding\tstart_codon\t225451\t225453\t.\t+\t0\t gene_id=YAR071W; transcript_id=YAR071W; exon_number=1; gene_name=PHO11; transcript_name=PHO11;\n+I\tprotein_coding\tstop_codon\t226852\t226854\t.\t+\t0\t gene_id=YAR071W; transcript_id=YAR071W; exon_number=1; gene_name=PHO11; transcript_name=PHO11;\n+I\tprotein_coding\texon\t227733\t228944\t.\t+\t.\t gene_id=YAR073W; transcript_id=YAR073W; exon_number=1; gene_name=IMD1; transcript_name=IMD1;\n+I\tprotein_coding\tCDS\t227733\t228941\t.\t+\t0\t gene_id=YAR073W; transcript_id=YAR073W; exon_number=1; gene_name=IMD1; transcript_name=IMD1; protein_id=YAR073W;\n+I\tprotein_coding\tstart_codon\t227733\t227735\t.\t+\t0\t gene_id=YAR073W; transcript_id=YAR073W; exon_number=1; gene_name=IMD1; transcript_name=IMD1;\n+I\tprotein_coding\tstop_codon\t228942\t228944\t.\t+\t0\t gene_id=YAR073W; transcript_id=YAR073W; exon_number=1; gene_name=IMD1; transcript_name=IMD1;\n+I\tprotein_coding\texon\t228835\t229308\t.\t+\t.\t gene_id=YAR075W; transcript_id=YAR075W; exon_number=1; gene_name=YAR075W; transcript_name=YAR075W;\n+I\tprotein_coding\tCDS\t228835\t229305\t.\t+\t0\t gene_id=YAR075W; transcript_id=YAR075W; exon_number=1; gene_name=YAR075W; transcript_name=YAR075W; protein_id=YAR075W;\n+I\tprotein_coding\tstart_codon\t228835\t228837\t.\t+\t0\t gene_id=YAR075W; transcript_id=YAR075W; exon_number=1; gene_name=YAR075W; transcript_name=YAR075W;\n+I\tprotein_coding\tstop_codon\t229306\t229308\t.\t+\t0\t gene_id=YAR075W; transcript_id=YAR075W; exon_number=1; gene_name=YAR075W; transcript_name=YAR075W;\n' |
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| diff -r 916cb26bd9d3 -r 4418229c501e test-data/htseq-test.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq-test.gtf Wed Jan 31 12:51:03 2024 +0000 |
| b |
| b'@@ -0,0 +1,492 @@\n+I\tprotein_coding\texon\t335\t649\t.\t+\t.\t gene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; transcript_name "YAL069W";\n+I\tprotein_coding\tCDS\t335\t646\t.\t+\t0\t gene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; transcript_name "YAL069W"; protein_id "YAL069W";\n+I\tprotein_coding\tstart_codon\t335\t337\t.\t+\t0\t gene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; transcript_name "YAL069W";\n+I\tprotein_coding\tstop_codon\t647\t649\t.\t+\t0\t gene_id "YAL069W"; transcript_id "YAL069W"; exon_number "1"; gene_name "YAL069W"; transcript_name "YAL069W";\n+I\tprotein_coding\texon\t538\t792\t.\t+\t.\t gene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; transcript_name "YAL068W-A";\n+I\tprotein_coding\tCDS\t538\t789\t.\t+\t0\t gene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; transcript_name "YAL068W-A"; protein_id "YAL068W-A";\n+I\tprotein_coding\tstart_codon\t538\t540\t.\t+\t0\t gene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; transcript_name "YAL068W-A";\n+I\tprotein_coding\tstop_codon\t790\t792\t.\t+\t0\t gene_id "YAL068W-A"; transcript_id "YAL068W-A"; exon_number "1"; gene_name "YAL068W-A"; transcript_name "YAL068W-A";\n+I\tprotein_coding\texon\t1807\t2169\t.\t-\t.\t gene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; transcript_name "PAU8";\n+I\tprotein_coding\tCDS\t1810\t2169\t.\t-\t0\t gene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; transcript_name "PAU8"; protein_id "YAL068C";\n+I\tprotein_coding\tstart_codon\t2167\t2169\t.\t-\t0\t gene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; transcript_name "PAU8";\n+I\tprotein_coding\tstop_codon\t1807\t1809\t.\t-\t0\t gene_id "YAL068C"; transcript_id "YAL068C"; exon_number "1"; gene_name "PAU8"; transcript_name "PAU8";\n+I\tprotein_coding\texon\t2480\t2707\t.\t+\t.\t gene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; transcript_name "YAL067W-A";\n+I\tprotein_coding\tCDS\t2480\t2704\t.\t+\t0\t gene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; transcript_name "YAL067W-A"; protein_id "YAL067W-A";\n+I\tprotein_coding\tstart_codon\t2480\t2482\t.\t+\t0\t gene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; transcript_name "YAL067W-A";\n+I\tprotein_coding\tstop_codon\t2705\t2707\t.\t+\t0\t gene_id "YAL067W-A"; transcript_id "YAL067W-A"; exon_number "1"; gene_name "YAL067W-A"; transcript_name "YAL067W-A";\n+I\tprotein_coding\texon\t7236\t9017\t.\t-\t.\t gene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; transcript_name "SEO1";\n+I\tprotein_coding\tCDS\t7239\t9017\t.\t-\t0\t gene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; transcript_name "SEO1"; protein_id "YAL067C";\n+I\tprotein_coding\tstart_codon\t9015\t9017\t.\t-\t0\t gene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; transcript_name "SEO1";\n+I\tprotein_coding\tstop_codon\t7236\t7238\t.\t-\t0\t gene_id "YAL067C"; transcript_id "YAL067C"; exon_number "1"; gene_name "SEO1"; transcript_name "SEO1";\n+I\tprotein_coding\texon\t10092\t10400\t.\t+\t.\t gene_id "YAL066W"; transcript_id "YAL066W"; exon_number "1"; gene_name "YAL066W"; transcript_name "YAL066W";\n+I\tprotein_coding\tCDS\t10092\t10397\t.\t+\t0\t gene_id "YAL066W"; transcript_id "YAL066W"; exon_number "1"; gene_name "YAL066W"; transcript_name "YAL066W"; protein_id "YAL066W";\n+I\tprotein_coding\tstart_codon\t10092\t10094\t.\t+\t0\t gene_id "YAL066W"; transcript_id "YAL066W"; exon_number "1"; gene_name "YAL066W"; transcript_name "YAL066W";\n+I\tprotein_coding\tstop_codon\t10398\t10400\t.\t+\t0\t gene_id "YAL066W"; transcript_id "YAL066W"; exon_number "1"; gene_name "YAL066W"; transcript_name "YAL066W";\n+I\tprotein_coding\texon\t11566\t11952\t.\t-\t.\t gene_id "YAL065C"; transcript_id "YAL065C"; exon_number "1"; gene_name "YAL065C"; transcript_name "YAL065C";\n+I\tprotein_coding\tCDS\t11569\t11952\t.\t-\t'..b'W";\n+I\tprotein_coding\tstop_codon\t221649\t221651\t.\t+\t0\t gene_id "YAR066W"; transcript_id "YAR066W"; exon_number "1"; gene_name "YAR066W"; transcript_name "YAR066W";\n+I\tprotein_coding\texon\t222397\t222882\t.\t+\t.\t gene_id "YAR068W"; transcript_id "YAR068W"; exon_number "1"; gene_name "YAR068W"; transcript_name "YAR068W";\n+I\tprotein_coding\tCDS\t222397\t222879\t.\t+\t0\t gene_id "YAR068W"; transcript_id "YAR068W"; exon_number "1"; gene_name "YAR068W"; transcript_name "YAR068W"; protein_id "YAR068W";\n+I\tprotein_coding\tstart_codon\t222397\t222399\t.\t+\t0\t gene_id "YAR068W"; transcript_id "YAR068W"; exon_number "1"; gene_name "YAR068W"; transcript_name "YAR068W";\n+I\tprotein_coding\tstop_codon\t222880\t222882\t.\t+\t0\t gene_id "YAR068W"; transcript_id "YAR068W"; exon_number "1"; gene_name "YAR068W"; transcript_name "YAR068W";\n+I\tprotein_coding\texon\t224002\t224295\t.\t-\t.\t gene_id "YAR069C"; transcript_id "YAR069C"; exon_number "1"; gene_name "YAR069C"; transcript_name "YAR069C";\n+I\tprotein_coding\tCDS\t224005\t224295\t.\t-\t0\t gene_id "YAR069C"; transcript_id "YAR069C"; exon_number "1"; gene_name "YAR069C"; transcript_name "YAR069C"; protein_id "YAR069C";\n+I\tprotein_coding\tstart_codon\t224293\t224295\t.\t-\t0\t gene_id "YAR069C"; transcript_id "YAR069C"; exon_number "1"; gene_name "YAR069C"; transcript_name "YAR069C";\n+I\tprotein_coding\tstop_codon\t224002\t224004\t.\t-\t0\t gene_id "YAR069C"; transcript_id "YAR069C"; exon_number "1"; gene_name "YAR069C"; transcript_name "YAR069C";\n+I\tprotein_coding\texon\t224554\t224853\t.\t-\t.\t gene_id "YAR070C"; transcript_id "YAR070C"; exon_number "1"; gene_name "YAR070C"; transcript_name "YAR070C";\n+I\tprotein_coding\tCDS\t224557\t224853\t.\t-\t0\t gene_id "YAR070C"; transcript_id "YAR070C"; exon_number "1"; gene_name "YAR070C"; transcript_name "YAR070C"; protein_id "YAR070C";\n+I\tprotein_coding\tstart_codon\t224851\t224853\t.\t-\t0\t gene_id "YAR070C"; transcript_id "YAR070C"; exon_number "1"; gene_name "YAR070C"; transcript_name "YAR070C";\n+I\tprotein_coding\tstop_codon\t224554\t224556\t.\t-\t0\t gene_id "YAR070C"; transcript_id "YAR070C"; exon_number "1"; gene_name "YAR070C"; transcript_name "YAR070C";\n+I\tprotein_coding\texon\t225451\t226854\t.\t+\t.\t gene_id "YAR071W"; transcript_id "YAR071W"; exon_number "1"; gene_name "PHO11"; transcript_name "PHO11";\n+I\tprotein_coding\tCDS\t225451\t226851\t.\t+\t0\t gene_id "YAR071W"; transcript_id "YAR071W"; exon_number "1"; gene_name "PHO11"; transcript_name "PHO11"; protein_id "YAR071W";\n+I\tprotein_coding\tstart_codon\t225451\t225453\t.\t+\t0\t gene_id "YAR071W"; transcript_id "YAR071W"; exon_number "1"; gene_name "PHO11"; transcript_name "PHO11";\n+I\tprotein_coding\tstop_codon\t226852\t226854\t.\t+\t0\t gene_id "YAR071W"; transcript_id "YAR071W"; exon_number "1"; gene_name "PHO11"; transcript_name "PHO11";\n+I\tprotein_coding\texon\t227733\t228944\t.\t+\t.\t gene_id "YAR073W"; transcript_id "YAR073W"; exon_number "1"; gene_name "IMD1"; transcript_name "IMD1";\n+I\tprotein_coding\tCDS\t227733\t228941\t.\t+\t0\t gene_id "YAR073W"; transcript_id "YAR073W"; exon_number "1"; gene_name "IMD1"; transcript_name "IMD1"; protein_id "YAR073W";\n+I\tprotein_coding\tstart_codon\t227733\t227735\t.\t+\t0\t gene_id "YAR073W"; transcript_id "YAR073W"; exon_number "1"; gene_name "IMD1"; transcript_name "IMD1";\n+I\tprotein_coding\tstop_codon\t228942\t228944\t.\t+\t0\t gene_id "YAR073W"; transcript_id "YAR073W"; exon_number "1"; gene_name "IMD1"; transcript_name "IMD1";\n+I\tprotein_coding\texon\t228835\t229308\t.\t+\t.\t gene_id "YAR075W"; transcript_id "YAR075W"; exon_number "1"; gene_name "YAR075W"; transcript_name "YAR075W";\n+I\tprotein_coding\tCDS\t228835\t229305\t.\t+\t0\t gene_id "YAR075W"; transcript_id "YAR075W"; exon_number "1"; gene_name "YAR075W"; transcript_name "YAR075W"; protein_id "YAR075W";\n+I\tprotein_coding\tstart_codon\t228835\t228837\t.\t+\t0\t gene_id "YAR075W"; transcript_id "YAR075W"; exon_number "1"; gene_name "YAR075W"; transcript_name "YAR075W";\n+I\tprotein_coding\tstop_codon\t229306\t229308\t.\t+\t0\t gene_id "YAR075W"; transcript_id "YAR075W"; exon_number "1"; gene_name "YAR075W"; transcript_name "YAR075W";\n' |
| b |
| diff -r 916cb26bd9d3 -r 4418229c501e test-data/htseq-test_allcounts.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq-test_allcounts.tsv Wed Jan 31 12:51:03 2024 +0000 |
| b |
| @@ -0,0 +1,6 @@ +__no_feature 19 +__ambiguous 0 +__too_low_aQual 0 +__not_aligned 1336 +__alignment_not_unique 0 +__aligned 343 |
| b |
| diff -r 916cb26bd9d3 -r 4418229c501e test-data/htseq-test_nosq.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq-test_nosq.sam Wed Jan 31 12:51:03 2024 +0000 |
| b |
| b"@@ -0,0 +1,1699 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798998768884/4\tXM:i:0\n+HWI-EAS225:1:11:66:1289#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAAAGCTGTTTAGTGAGGATGAAGGACAATGGGAGAC\t7@;?9@A?@?(<:A7<<117:>=68:8;<88;3687\tXM:i:0\n+HWI-EAS225:1:11:66:1547#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAAGGGATATACTGGCAAACATATGATAAAAACAACA\tBCB@@?ABBB?A>@>@@?<?@?A@>@>;><:<:<::\tXM:i:0\n+HWI-EAS225:1:11:66:2018#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTGAATACACCATTAACTTGCACAAAAGATTGCACGG\t>>A@>@=:=;>;;;?91(-6;>>;;;;;8:99;;96\tXM:i:0\n+HWI-EAS225:1:11:67:1064#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATTAAATGAACATGGTATTAGTATACTCCCAGCTAA\tBCB@@;=::<<<::9;<;;:::<<<87999334:8:\tXM:i:0\n+HWI-EAS225:1:11:67:1411#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAGGGATCCTGTACTTCAACTTCCATACTTGAAAGAT\tB@@:=??;@?=??A???@;?=<<@><78;579688;\tXM:i:0\n+HWI-EAS225:1:11:67:742#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAGATTCGCTGTCAAACTTTCAACAACGGATCTCTTG\tBB@A?>:?>84>=68:::>9857718747::98:##\tXM:i:0\n+HWI-EAS225:1:11:68:1280#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAAAGTCCAGAGAGACGGATACGGAAGAGACTGTGTA\tBB?7899>98:887C579:9988988899:888989\tXM:i:0\n+HWI-EAS225:1:11:68:656#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAAAATATGGTAGACTTGACAATTAAGGGTGATGATG\tBCB@B>@=<6>>:>?<;.889??7886949:<>399\tXM:i:0\n+HWI-EAS225:1:11:68:969#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCACATGATTTAACTCCCCCTTGACAATTGTCATATG\tB99;9;##############################\tXM:i:0\n+HWI-EAS225:1:11:69:1005#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGGTAAATTCCATCCACAGCTAAATAGTGGCGAGAGC\tB98:96/667634#######################\tXM:i:0\n+HWI-EAS225:1:11:69:1560#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAGCGTTATGTTTATCCTATGTGCGAGCATGGTATCA\tBBAA?A@<?@@AAA>>A?@?:???>>:>>999:::;\tXM:i:0\n+HWI-EAS225:1:11:70:1046#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCATAGATGACGGAATGACTGGAAAAAAAAAAAAAAA\tBCCCBBBAAABBAABAB?BAA@AAAA?@@@=@>>?@\tXM:i:0\n+HWI-EAS225:1:11:70:1197#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATAAATTAGAGGAAAATGGCTAACTTGCGTACTCAA\tBC@@@A@>><=:9998:7:<<<;;9::9949<9979\tXM:i:0\n+HWI-EAS225:1:11:70:1268#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCAGATAAGACTCCTGATATTTAAAAAAAAAAAAAAA\tBCBBBBBB?ABBAB@BBBBBBB@B@@@??>:??;99\tXM:i:0\n+HWI-EAS225:1:11:70:441#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAACGTGAAAAGGCTTTGAACGAAGAAGCAAGCTAGA\tBB=?876;::::;>:>>:::>::::626:635:756\tXM:i:0\n+HWI-EAS225:1:11:71:612#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAGGAGGAGGAGGACTCTGATGTGAGGAGGACTGGTG\tBB????7<766<68=8=55<7677776555652457\tXM:i:0\n+HWI-EAS225:1:11:72:947#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAA\tBBBB@A>?A>>AA@?B@>@=9AA@8?<<<?:::4:2\tXM:i:0\n+HWI-EAS225:1:11:73:1341#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATAGATAATCAAACAAAAAAATGGCTAAGGGAACAA\tBCBA@;?9<=?<3'4:=>:=6/5.670/434.3,59\tXM:i:0\n+HWI-EAS225:1:11:74:1238#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAA\tBBBA:8:?@@?=:<;?B?@A9@AA>:<:>;7:<8##\tXM:i:0\n+HWI-EAS225:1:11:74:1895#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAC\t;@B@@;4@>A@?;39??:@=8B??9>3;########\tXM:i:0\n+HWI-EAS225:1:11:74:646#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAC\tBCBCA=?BBBAB@A@BB@BA=BBB?@=>@?>95###\tXM:i:0\n+HWI-EAS225:1:11:75:1484#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGCGCATTGCCAAGATCAGCTCAGCAAAGTTAAGACC\t:A=9==<;89==887988:::<888:9989788886\tXM:i:0\n+HWI-EAS225:1:11:75:1494#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATGGACGATGGACGGAAAAAAGAATTGCATGACTTG\t>B??ABB>B>BA<?;AB@BBB@5??;2:@A>>C;9=\tXM:i:0\n+HWI-EAS225:1:11:75:58#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAATAGGACTAAAAATGGCTGGCGTTAAAGCTTACGA\tBBA@@>2;@?@@==><389505758;;788877755\tXM:i:0\n+HWI-EAS225:1:11:76:1414#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAA\t?BACCBBCCCBBC?BCCBCBBBBA9B@@BA=@@###\tXM:i:0\n+HWI-EAS225:1:11:76:762#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCAGTATATTCGAAATGGCCGGTGTTAAAGCTTACGA\tBBB?@A?AA?@???@?==>?=9?=?=:9=9999888\tXM:i:0\n+HWI-EAS225:1:11:7:1482#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAAGGTAGCCAAATGCCTCGTCATCTAATTAGAGGGT\tBA9<;@;??8??9>8?8<68::9698:<7888:684\tXM:i:0\n" |
| b |
| diff -r 916cb26bd9d3 -r 4418229c501e test-data/htseq-test_othercounts.tsv --- a/test-data/htseq-test_othercounts.tsv Sun Jan 26 23:43:52 2020 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -__no_feature 19 -__ambiguous 0 -__too_low_aQual 0 -__not_aligned 1336 -__alignment_not_unique 0 |
| b |
| diff -r 916cb26bd9d3 -r 4418229c501e test-data/htseq-test_samout.bam |
| b |
| Binary file test-data/htseq-test_samout.bam has changed |