| Next changeset 1:e989670c7fc7 (2021-02-18) |
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Commit message:
"planemo upload for repository https://git.ufz.de/lehmanju/rnaquast commit 89fd73a81e54e9f5722b0a83ee00dc47ab0cb1e3" |
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added:
rna_quast.xml test-data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa test-data/Saccharomyces_cerevisiae.R64-1-1.75.gtf test-data/Trinity.fasta test-data/idba.fasta |
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| diff -r 000000000000 -r 33c060ec0ac9 rna_quast.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rna_quast.xml Mon Oct 19 08:04:52 2020 +0000 |
| [ |
| b'@@ -0,0 +1,332 @@\n+<tool id="rna_quast" name="rnaQUAST" version="@TOOL_VERSION@">\n+ <description>A Quality Assessment Tool for De Novo Transcriptome Assemblies</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">2.1.0</token>\n+ <xml name="element_matching_line" token_name="" token_expression="">\n+ <element name="@NAME@">\n+ <assert_contents><has_line_matching expression="@EXPRESSION@"/></assert_contents>\n+ </element>\n+ </xml>\n+ <xml name="element_has_text" token_name="" token_text="">\n+ <element name="@NAME@">\n+ <assert_contents><has_text text="@TEXT@"/></assert_contents>\n+ </element>\n+ </xml>\n+\n+ <xml name="details_output_test" token_assembler="">\n+ <element name="@ASSEMBLER@">\n+ <element name="5000%-assembled.list"><assert_contents><has_n_lines n="0"/></assert_contents></element>\n+ <element name="9500%-assembled.list"><assert_contents><has_n_lines n="0"/></assert_contents></element>\n+ <expand macro="element_matching_line" name="alignment_metrics" expression="\\s*== ALIGNMENT METRICS \\(calculated with reference genome but without gene database\\) ==\\s*"/>\n+ <expand macro="element_matching_line" name="alignment_multiplicity" expression="unaligned=\\d+ aligned=\\d+ alignments=\\d+\\s*"/>\n+ <expand macro="element_matching_line" name="alignments_per_isoform" expression="avg=[\\d.]+\\s*"/>\n+ <expand macro="element_matching_line" name="basic_metrics" expression="\\s*== BASIC TRANSCRIPTS METRICS \\(calculated without reference genome and gene database\\) ==\\s*"/>\n+ <expand macro="element_matching_line" name="block_length" expression="avg=[\\d.]+\\s*"/>\n+ <expand macro="element_matching_line" name="blocks_per_alignment" expression="avg=[\\d.]+\\s+tot=\\d+\\s*"/>\n+ <expand macro="element_matching_line" name="database_metrics" expression="\\s*== GENE DATABASE METRICS ==\\s*"/>\n+ <expand macro="element_matching_line" name="misassemblies" expression="\\s*== ALIGNMENT METRICS FOR MISASSEMBLED \\(CHIMERIC\\) TRANSCRIPTS \\(calculated with reference genome or with gene database\\) ==\\s*"/>\n+ <expand macro="element_matching_line" name="mismatch_rate" expression="avg=[\\d.]+\\s+tot=\\d+\\s*"/>\n+ <expand macro="element_matching_line" name="sensitivity" expression="\\s*== ASSEMBLY COMPLETENESS \\(SENSITIVITY\\) ==\\s*"/>\n+ <expand macro="element_matching_line" name="specificity" expression="\\s*== ASSEMBLY SPECIFICITY ==\\s*"/>\n+ <expand macro="element_matching_line" name="transcript_length" expression="avg=[\\d.]+\\s*"/>\n+ <expand macro="element_matching_line" name="x-aligned" expression="avg=[\\d.]+\\s*"/>\n+ <expand macro="element_matching_line" name="x-assembled" expression="avg=[\\d.]+\\s*"/>\n+ <expand macro="element_matching_line" name="x-assembled_exons" expression="avg=[\\d.]+\\s*"/>\n+ <expand macro="element_matching_line" name="x-covered" expression="avg=[\\d.]+\\s*"/>\n+ <expand macro="element_matching_line" name="x-covered_exons" expression="avg=[\\d.]+\\s*"/>\n+ <expand macro="element_matching_line" name="x-matched" expression="avg=[\\d.]+\\s*"/>\n+ <expand macro="element_matching_line" name="x-matched_blocks" expression="avg=[\\d.]+\\s*"/>\n+ </element>\n+ </xml>\n+\n+ <xml name="txt_output_test" token_assembler="">\n+ <output name="short_report_txt">\n+ <assert_contents>\n+ <has_text text="SHORT SUMMARY REPORT"/>\n+ </assert_contents>\n+ </output>\n+ </xml>\n+ <xml name="tex_output_test" token_assembler="">\n+ <output name="short_report_tex">\n+ <assert_contents>\n+ <has_text text="Short summary report'..b' <param name="gtf" value="Saccharomyces_cerevisiae.R64-1-1.75.gtf" ftype="gtf" />\n+ <param name="disable_infer_genes" value="true"/>\n+ <param name="disable_infer_transcripts" value="true"/>\n+ </conditional>\n+ <param name="out_sr" value="txt,tex,tsv" />\n+ <param name="out_add" value="logs,comparison,plots,details" />\n+ <expand macro="txt_output_test"/>\n+ <expand macro="tex_output_test"/>\n+ <expand macro="tsv_output_test"/>\n+ <output_collection name="comparison_png" type="list" count="15"/>\n+ <output_collection name="comparison" type="list" count="19"/>\n+ <output_collection name="list_logs" type="list" count="8"/>\n+ <output_collection name="details" type="list:list" count="2">\n+ <expand macro="details_output_test" assembler="Trinity"/>\n+ <expand macro="details_output_test" assembler="idba"/>\n+ </output_collection>\n+ </test>\n+ <test expect_num_outputs="6">\n+ <param name="in_fasta" value="Trinity.fasta" ftype="fasta" />\n+ <conditional name="gene_coordinates">\n+ <param name="use_gtf" value="false" />\n+ </conditional>\n+ <param name="min_alignment" value="30" />\n+ <param name="lower_threshold" value="45" />\n+ <param name="upper_threshold" value="95"/>\n+ <param name="out_sr" value="txt,tex,tsv,pdf" />\n+ <param name="out_add" value="logs,details_plots" />\n+\n+ <expand macro="pdf_output_test"/>\n+ <expand macro="tex_output_test"/>\n+ <expand macro="tsv_output_test"/>\n+ <expand macro="txt_output_test"/>\n+ <output_collection name="list_logs" type="list">\n+ <expand macro="element_has_text" name="Trinity.GeneMarkS_T.err" text=""/>\n+ <expand macro="element_matching_line" name="rnaQUAST" expression="Thank you for using rnaQUAST!"/>\n+ </output_collection>\n+ <output_collection name="details_png" type="list:list" count="1">\n+ <element name="Trinity">\n+ <expand macro="element_has_text" name="Nx" text="PNG"/>\n+ <expand macro="element_has_text" name="transcript_length" text="PNG"/>\n+ </element>\n+ </output_collection>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What is rnaQUAST**\n+- a quality assessment tool for de novo transcriptome assemblies\n+- evaluating RNA-Seq assembly quality and benchmarking transcriptome assemblers using reference genome and gene database\n+- calculates various metrics that demonstrate completeness and correctness levels of the assembled transcripts\n+\n+**Using rnaQuast without reference** you wont get:\n+\n+- x-assembled (Exons)\n+- Alignments per Isoform\n+- x-covered (Exons)\n+- x-matched (Blocks)\n+- gmap build logs\n+\n+**Using rnaQuast with reference** you will get:\n+- Reports\n+- Logs\n+- Alignement/Basic Metrics\n+- Misassemblies/ Specificity/ Sensitivity\n+- Alignment multiplicity\n+- Block/ Transcript Lentgh\n+- Blocks per alignment\n+- Mismatch rate\n+- x-aligned\n+- Nx\n+- Blocks per alignment\n+- gmap build logs\n+\n+**Using rnaQuast without gene coordinates** you wont get:\n+- x-assembled (Exons)\n+- Alignments per Isoform\n+- x-covered (Exons)\n+- x-matched (Blocks)\n+- gmap build logs\n+- Database Metrics\n+- Alignment multiplicity\n+- Mismatch rate\n+- NAx\n+- x-aligned\n+**Using rnaQuast with gene coordinates** you will get:\n+- Reports\n+- Logs\n+- Alignement/Basic Metrics\n+- Misassemblies/Specificity/Sensitivity\n+- Alignment multiplicity\n+- Block/Transcript length\n+- Blocks per alignment\n+- Mismatch rate\n+- x-aligned\n+- Nx/NAx\n+- gmap build logs\n+- Database Metrics\n+- Alignment multiplicity\n+More informations, see citations.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btw218 </citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 33c060ec0ac9 test-data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa Mon Oct 19 08:04:52 2020 +0000 |
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| b'@@ -0,0 +1,10000 @@\n+>IV dna:chromosome chromosome:R64-1-1:IV:1:1531933:1 REF\r\n+ACACCACACCCACACCACACCCACACACACCACACCCACACACCACACCCACACCCACAC\r\n+ACCCACACCCACACACCACACACCACACCACACCACACCCACACCCACACCACACCCACA\r\n+CCCACACACCACACCCACACCCACACACCACACACTACCCCTAACACTACCCTATTCTAA\r\n+CCCTGATTTTACCTGTCTCCAAACCTACCCTCACATTACCCTACCTCCCCACTCGTTACC\r\n+CTGCCCCACTCAACCATCCACTCCCAACCACCATCCATCTCTCTACTTACCACTAACCAC\r\n+CGTCCACCATAACCGTTACCCTCCAATTACCCATATCCAACTCCACTACCACTTACCCTA\r\n+CTATTACCCTACCATCCACCATGTCCTACTCACTGTACTGTTGTTCTACCCTCCATATTG\r\n+AAACGTTAACAAATGATCGTAAATAATACATACATACTTACCCTACCACTCTATACCACC\r\n+ACTACCACCACCGCCACTTGCCACACTCACCTTCACTTCTACTGATATGTCATACGCACA\r\n+CGGATGCTACAGTATATACCATCTCAAACTTACCCTACTTTCATATTCCACACCATGGCC\r\n+CCATTCTCACTAAATCAGTACCAAATGCACTCACATCATTATTCACGGCACTTGCCTCAG\r\n+CGGTCTATACCCTGTGCCATTTACGCATAACTCCCACGATTATCCACATTTTATTACCTA\r\n+TATCTCATTCGGCGGCCCCAAATATTGTATAACTGCTCTTAATACATACGTTATACCACT\r\n+TTTACACCGTATACTAACCACTCAATTTATATACACTTATGCCAATATTACAAAAAAATC\r\n+ACCACTAAAATCACCTAAACATAAAAATATTCTATTCTTCAACCATAATACATAAACACA\r\n+CTTAATTGCGTCTTAATACTATCATGGTATCATTAACTTAAAGTTCCTTAATATCGTCAT\r\n+ACCACTATGCTCTATTCCATATATTGTAATATAACTGTACTCTATAGTCATACAGACGCT\r\n+TTTACTTCACCCCATCTTCTCATACTATTGTCATAGAATCTCACACTGACGCATGATTAA\r\n+AACGAATAATTTTTACTGTAAGGGCTGCCATCCGCGCTCTATCCTTTTGTTTGCAATATT\r\n+TATATACAGAATCTCAAAACAAGCGGGAGAAGTGCTAATTACCCAGAGGTCATGCATGAT\r\n+CTGAGTACCACCGTACCTCTAGGTTTTGCTTTGATCCGTTTTACAGTGACACCGAACATA\r\n+AGGGGAAGCTATTGACATGGTATCGAAAGGTTGTCCACATTGGGAAGTAACTTGGTTCTA\r\n+TGAATCTTCATGTCAGATACGTAGGACAGACTCTTTCCTGTGTAAATATTTGTGACAGCT\r\n+ACGTCTATTTTCTACTAGATGTTTACACAGTTTTGTCACAGGAAATCTACGCTTAAAATA\r\n+TGTATTTCATTCAAGCGGTAACCGCTGTACGAGCAGTGACATTGCTGGTCGCACCTTAAA\r\n+TGTAAACCAACGTTACGGCACACCGTGATGTACCCGCATTAAAGTTTTGTAAATTCGTTA\r\n+TTACGATTATTGAATTGGCTAGATAGAAAACAGGAAATGAAATGGATACCCTTTTCGAAT\r\n+AGCTGAGTTTCTTTGCCTAAAATAGCCCAACATTGTTGCCCTTTTTCTATCACGAGGTTA\r\n+CTGAGCCATTGCATGAACGCGCGCGCCTCGGCGGCTTTTTTTTCCTGCTGTATAAAAGCG\r\n+AAAAGCCAGAAGTTACTATCTCGAATAAAAAACCCCTCGAACTGCCATCTCACTACCGAA\r\n+AATGAAAGAGAATGAAGTCAAAGATGAGAAAAGCGTAGATGTGTTATCCTTCAAACAGCT\r\n+CGAATCCCAAAAGATTGTTCTACCTCAAGATCTTTTCAGAAGCAGCTTTACCTGGTTTTG\r\n+TTATGAAATTTACAAGTCCTTAGCGTTTCGCATCTGGATGCTATTATGGCTACCACTTAG\r\n+CGTCTGGTGGAAACTTTCCAACAATTGTATTTACCCACTTATAGTTTCACTTCTGGTCCT\r\n+GTTTCTGGGACCAATATTTGTCCTTGTTATTTGTGGACTTTCTCGTAAGCGTTCCTTATC\r\n+GAAACAACTCATTCAGTTTTGCAAAGAGATTACTGAAAACACACCAAGTTCTGATCCTCA\r\n+TGATTGGGAAGTCGTTGTAGCAAATCTAAATTCGTACTTATATGAAAATAAGGCTTGGAA\r\n+TACTAAGAATTTCTTTTTCAATGCTACGGATTGTGAGAAAATGTTCAGAACAACTGTTCT\r\n+TGAACCATTTTCTTTGAAAAAAGATAAAGCTGCCAAGGTTAAGTCATTTAAGGATTCTGT\r\n+CCCTTATATCGAAGAGGCTTTGCAAGTGTATGCTACAGGATTTGACAAACAGTGGAAGTT\r\n+GTTTATTACTGAAAAATCATGGAGCCCTGTTGGCCTGGAAGACGTTCAGCTTCCCAAGGA\r\n+TATTCATCGGTCCAAGCTTACTTGGTTTTTAAAGCGGATTTTCACTATTTACTCTCTACC\r\n+ATTATGGCTTGCTTTTTTGAACTGTATCTGCGTGTCACAGCATTTTTGCCTTGCATTTCG\r\n+TATCTTGTGTCCTGGATTGTTTTTCCTCATGATGGTGTGGCTTTTCCAAAATATGAGGAC\r\n+GACTGCTTTACTCGTGAAAATGGAACACAAGATGCAATTCTTGTTGACTATTATAAATGA\r\n+GCAAGAAAGTGGTGCGAATGGATGGGACGAAATTGCAAGGAAAATGAATAGGTACTTGTT\r\n+TGAGAAAAAAGCCTGGAAGAATGAAGAGTTTTTCTTCGACGGGATTGACTGTGAATGGTT\r\n+TTTTAGCCACTTCTTCTACCGCCTTCTATCTGCAAAGAAATCTATGTGGCTTTTACCATT\r\n+GAATGTGGAACTATGGCCATATATTAAAGAAGCGCAATTGTCCCGCAATGAAGAGTCTTT\r\n+AATGAAGAAATGAGAACGCCCTTCTGGACTTAAAAATTCATACTTTTGCATTCTGTTAGA\r\n+TATGAATACTACACTCTATTGAGTGACTTTAAAAGGCGAGTGGACACTTTTATCAAGCGA\r\n+TTTATCATGCAGTAATACTAATATTACTAATTAATCACTACTACCTCTCTTAAACAGGAA\r\n+ATATGCTATTCATCAGTAAGAAGCTGCACAAATGTTATATATCATACCAGGAATACACAT\r\n+AAGAGCAAAAATGCTATTCTACAATATCCTCATCTTACCAGCTCACTCACAAAATATTCT\r\n+TACTCCGAGTACGACCATAAAGCAATGCTAACGAATAGTCATACTAAAGTACTATAAAAT\r\n+CTTTCCGTGCGCTCAAACGGAGGCCATGCCATAAAGTTAAATGTGATAACTTAAAAGCAT\r\n+CATAAGAGTGATTTTCCAGTATTGTTTCAGTAATGTAAGGCCTAAAGAAGAACGCATATT\r\n+GGTAAACCTCCAACCTACTAGTAATTAAAAAGCTTTAGTTTAACCCGTAGTTCGGGATAC\r\n+ACTTCGGGCATAACGTACGTTTATTATAAATTTTTATATCTCTTGCGTACCATGTATATT\r\n+CCAGAACAGTGAATACACTTTTCTAGTTCATTTATGCTACTTTCATATCCTCCATTAAAG\r\n+CGGGAGCTACCGTTGAAAAGGCATAATAATTGAAGTTTCGAGTGGGTTAGTTACACTAGG\r\n+TGAAGGATCGTTTGCCTCCATATGGTCAAGCCATTCACGGACATTGATAATAGCTGGGAC\r\n+AATTCTGGTTTCA'..b'ACTAGTCTGGCATCAACATGGCAAACCA\r\n+CAGGACATGTTGAAGGGAATCAGTGAAAAACTACCTAAGGATGAAATGCCTGATTTTGTA\r\n+TTATGTTTGGGTGATGACTTCACTGACGAAGACATGTTTAGACAGTTGAATACCATTGAA\r\n+ACTTGTTGGAAAGAAAAATATCCTGACCAAAAAAATCAATGGGGCAACTACGGATTCTAT\r\n+CCTGTCACTGTGGGATCTGCATCCAAGAAAACTGTCGCAAAGGCTCATTTAACCGATCCT\r\n+CAGCAAGTCCTGGAGACTTTAGGTTTACTTGTTGGTGATGTCTCTCTCTTCCAAAGTGCT\r\n+GGTACGGTCGACCTGGATTCCAGAGGTCATGTCAAGAATAGTGAGAGCAGTTTGAAATCA\r\n+AAGCTAGCATCTAAAGCTTATGTTATGAAAAGATCGGCTTCTTACACCGGCGCAAAGGTT\r\n+TGAAACACCCTTTTTAACGAAATGGTTATGACTAGACAGACATCTTACGTCTTACTCCTT\r\n+CATGCTTTATTTTTTTCTTTGTATTGTATTTGAACAGTCAATATGTGGTGTTGCGACGAA\r\n+GGCATATATATAATAGTCTCAACCCACCATTTTCGAAGATTTACATACACATTATATTTT\r\n+TATAAACTTCCAATATGTAATAACTTTATATGATATGTAACTTCTCACTATTATCCTTAC\r\n+TATTAAACGGTTTTTAATAAATATCATTGTTCTTTGTTTTATTAATGAGAAAAAGAAATT\r\n+TAATACAATGTCCGGCGGGAAGAAAAAAAATCGATGAATTAATTGAAAAAAAGTATCTTT\r\n+ATCATGTGAACTGAGGAGAAGAACGGCATCTCGAAAAGAGCACGTCGAAACAGCGGTAGG\r\n+TAAAAGAGGGTACTACCAGAGGTCTTTTCTCTTTATACGTTAACCTCTCAGCTTTTTCTT\r\n+TTGCAATTCAGGACACTTTAACTTGTAGTCACACGCTAGTCCACGTAGCAAAGTAAAACA\r\n+GCACGAAAAAAGTGATTACAAATTTCAAGGGAGATATGATGGACTTAGATAAGATTATAG\r\n+CATCACTGAGAGACGGAAAACATATTCCTGAAGAAACCGTTTTTAGGCTATGTTTAAATT\r\n+CACAGGAACTATTAATGAATGAAGGCAATGTAACACAAGTCGATACACCGGTTACAATAT\r\n+GCGGTGATATACATGGCCAATTACACGATCTACTAACGCTCTTCGAAAAGAGTGGTGGTG\r\n+TAGAGAAAACAAGGTATATTTTCTTGGGCGATTTTGTGGATAGGGGATTTTACTCATTGG\r\n+AGAGTTTTTTACTTTTACTATGTTACAAATTAAGATATCCTGATAGGATTACTTTAATTA\r\n+GAGGCAATCACGAAACCCGGCAAATTACTAAAGTATACGGATTTTACGATGAAGTAGTAA\r\n+GAAAATATGGTAATAGTAACGTATGGAGGTACTGCTGTGAAGTTTTTGATTATTTATCAT\r\n+TGGGGGCAATAATAAACAATAGCATATTCTGTGTTCATGGTGGATTATCTCCGGATATGA\r\n+CCACGGTTGATGAAATACGAACAATAGACAGGAAACAAGAAGTTCCACATGAAGGTGCTA\r\n+TGTGTGACTTATTATGGAGCGACCCCGAAGACGTTGACACATGGTCATTATCACCAAGAG\r\n+GTGCTGGATTTCTTTTCGGTAAAAGAGAAGTTGATCAATTCTTAGAGAAAAACAACGTTG\r\n+AGTTAATTGCTAGAGCTCATCAGTTAGTGATGGAAGGTTACAAAGAAATGTTCGACGGTG\r\n+GATTAGTGACAGTCTGGTCGGCACCGAATTACTGTTATCGTTGTGGTAATGTAGCAGCTG\r\n+TATTGAAGATAGACGACGATTTGAATCGTGAATATACAATTTTTGAAGCTGTTCAGGCAC\r\n+AAAATGAAGTCGGAAATGCTATAATTCCAACCAAAAAATCTCAAATGGACTATTTCTTAT\r\n+AAATTTTTAACAGGCACTCTAATTGTCAAGTGCATTTTTCTTTTTTTCTTCATAATGCAA\r\n+TAAAGGAAAAAAAATTGTAATATTACATACTTCTTTTCACATCTTAGCTAATTAACAATA\r\n+TGGCTTTTGAATACTAATATATACCCAGCTACCGTTTCTTCTTTTATTTTTTATTCCTTT\r\n+TTTTCTTCAGTAGAATATGTTATAGATGCGGAGGTCCCCTAAGTTCTTCACGTGTTCTCT\r\n+TCTCATCGCGTTTGATATGAAAAATAGAAAAAAATACATAGTAGCATGACTAACTAATAA\r\n+TAAGCTCCGCTATCAAAGATGTCAAGTACATTAAGGAAAGCTTTTAGATAAGGAAAAGAA\r\n+CTTATTAATAATATATAATATGAAAATATGTCGCTTGGTATACCACTTTCCCAATTAATA\r\n+GTAGAAAGTCCAAAGCCATTAAGTAGCGGCATCACAGGATTAGATGAGATATTAAACCTG\r\n+GGATTCCAGGCAAGGTCGATCTACGAAATATTTGGGCCTCCGGGCATTGGCAAGACTAAT\r\n+TTTGGCATTCAATTGGTGTGTAATTCGTTAGAAGGCATACAACAATCGGAAATAAACGAC\r\n+GATAAAATTCTATGGATAGAAACATTTCAAGAAATGCCCATAAACATACTAAGAGAACGC\r\n+TTTCAAAAATTTAAAATCGTGGAAGAAAATGTGAAGCGGGTCCGAATAACGAAATTTGGA\r\n+CAGCTATTATATTTCTTCCAGAATTTGTTCAAATTATCTCAAAGTGTGCGATATAAACTA\r\n+GTTATAATTGATGGATTTTCTCAATTAGTCTGCGATCATCTGTGTACACTAAGTAAAAGA\r\n+GGCGGCGGAATGATAGATAAAACTATACACGAGTTAAAATGTCGACATTTGATATTAATT\r\n+TTTACGGTAATGACCAAATACACACATTCCACGGGTTCGACAATAATAGTTTTAAATGAC\r\n+TGTATGAACACCGCCTTCCAATCAAACGAATTCGAATCCTTGGAAGAATACTACGAAATT\r\n+TTAGACGACGGATCTAACTTCTTTGTCAACTCTAACAACGAAAGGCGTAAGAACAATGTA\r\n+CATATATTGAAAAGCGCGCTCGTTGCCAATATCGCTATGGGAAGCAAGGATTCCACTTGG\r\n+GAAGTATTTCTAAGAGACAGGATCGGCCTTTTTAGGGATTGGAATGAACAAGTGGACGAA\r\n+ACCGTTTTCGTGAAAAGCAAAAGAGTGAAGGCGTCATCCTCGCAGAGTAACGAGGGATGT\r\n+ACTACCATCAAAGAAATGAGAATAAACAAACGAAACTTTGAAAACTTGAGAATAGCTATT\r\n+GTTTTTAATTTACACGGCGAAGATAGAAAAAGAGAAGGACGAAATTTAAAGCGGTCAAGA\r\n+AGCAGCGACGATCGTAACTATATTGTCAAATTTGATTTTGATAAAGCAACAGGTCAACTC\r\n+CGCGATATAATTGATCTGAAACCTGATACTGCTAATATTGCCTCATTTCCAACATTATCA\r\n+ACAAGCAGCAGCAGTTGCTCACAAGTGTTTAACAATATTGACTCCAATGATAATCCATTA\r\n+CCAAATGCGGAGGGAAAGGAGGAGATAATTTATGATAGTGAAGGTTAATAGTAAAATAAA\r\n+AAAACCGAAAACCGAAAACAATAAAAAATGGAAAAACGACAACATTCCACCCAACAACTA\r\n+CAAAGAAAAGTTAAGGGTAATTTTACCTATTTAGGATTTTAATCTGTTGGAGTTAAGGTG\r\n+AATACGTTTTTCCATATTGGGGTATGCAGCTCGAACCTAAAGTGGTATGTACACATCCCC\r\n+TCAAGCACACCCATTACCCTTATAGGATTAATGTAAGCAACAGCTTACACGGAATTGGAA\r\n' |
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| diff -r 000000000000 -r 33c060ec0ac9 test-data/Saccharomyces_cerevisiae.R64-1-1.75.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Saccharomyces_cerevisiae.R64-1-1.75.gtf Mon Oct 19 08:04:52 2020 +0000 |
| b |
| b'@@ -0,0 +1,1000 @@\n+#!genome-build R64-1-1\r\n+#!genome-version R64-1-1\r\n+#!genome-date 2011-09\r\n+#!genome-build-accession :GCA_000146045.2\r\n+#!genebuild-last-updated 2011-12\r\n+IV\tprotein_coding\tgene\t1802\t2953\t.\t+\t.\tgene_id "YDL248W"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n+IV\tprotein_coding\ttranscript\t1802\t2953\t.\t+\t.\tgene_id "YDL248W"; transcript_id "YDL248W"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl";\r\n+IV\tprotein_coding\texon\t1802\t2953\t.\t+\t.\tgene_id "YDL248W"; transcript_id "YDL248W"; exon_number "1"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl"; exon_id "YDL248W.1";\r\n+IV\tprotein_coding\tCDS\t1802\t2950\t.\t+\t0\tgene_id "YDL248W"; transcript_id "YDL248W"; exon_number "1"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl"; protein_id "YDL248W";\r\n+IV\tprotein_coding\tstart_codon\t1802\t1804\t.\t+\t0\tgene_id "YDL248W"; transcript_id "YDL248W"; exon_number "1"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tstop_codon\t2951\t2953\t.\t+\t0\tgene_id "YDL248W"; transcript_id "YDL248W"; exon_number "1"; gene_name "COS7"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "COS7"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tgene\t3762\t3836\t.\t+\t.\tgene_id "YDL247W-A"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n+IV\tprotein_coding\ttranscript\t3762\t3836\t.\t+\t.\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl";\r\n+IV\tprotein_coding\texon\t3762\t3836\t.\t+\t.\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl"; exon_id "YDL247W-A.1";\r\n+IV\tprotein_coding\tCDS\t3762\t3833\t.\t+\t0\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl"; protein_id "YDL247W-A";\r\n+IV\tprotein_coding\tstart_codon\t3762\t3764\t.\t+\t0\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tstop_codon\t3834\t3836\t.\t+\t0\tgene_id "YDL247W-A"; transcript_id "YDL247W-A"; exon_number "1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "YDL247W-A"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tgene\t5985\t7814\t.\t+\t.\tgene_id "YDL247W"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n+IV\tprotein_coding\ttranscript\t5985\t7814\t.\t+\t.\tgene_id "YDL247W"; transcript_id "YDL247W"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "MPH2"; transcript_source "ensembl";\r\n+IV\tprotein_coding\texon\t5985\t7814\t.\t+\t.\tgene_id "YDL247W"; transcript_id "YDL247W"; exon_number "1"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "MPH2"; transcript_source "ensembl"; exon_id "YDL247W.1";\r\n+IV\tprotein_coding\tCDS\t5985\t7811\t.\t+\t0\tgene_id "YDL247W"; transcript_id "YDL247W"; exon_number "1"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "MPH2"; transcript_source "ensembl"; protein_id "YDL247W";\r\n+IV\tprotein_coding\tstart_codon\t5985\t5987\t.\t+\t0\tgene_id "YDL247W"; transcript_id "YDL247W"; exon_number "1"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "MPH2"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tstop_codon\t7812\t7814\t.\t+\t0\tgene_id "YDL247W"; transcript_id "YDL247W"; exon_number "1"; gene_name "MPH2"; gene_source "ensembl"; gene_biotype "protein_coding"; tra'..b'otein_coding\tgene\t285391\t286695\t.\t-\t.\tgene_id "YDL097C"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n+IV\tprotein_coding\ttranscript\t285391\t286695\t.\t-\t.\tgene_id "YDL097C"; transcript_id "YDL097C"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl";\r\n+IV\tprotein_coding\texon\t285391\t286695\t.\t-\t.\tgene_id "YDL097C"; transcript_id "YDL097C"; exon_number "1"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl"; exon_id "YDL097C.1";\r\n+IV\tprotein_coding\tCDS\t285394\t286695\t.\t-\t0\tgene_id "YDL097C"; transcript_id "YDL097C"; exon_number "1"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl"; protein_id "YDL097C";\r\n+IV\tprotein_coding\tstart_codon\t286693\t286695\t.\t-\t0\tgene_id "YDL097C"; transcript_id "YDL097C"; exon_number "1"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tstop_codon\t285391\t285393\t.\t-\t0\tgene_id "YDL097C"; transcript_id "YDL097C"; exon_number "1"; gene_name "RPN6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "RPN6"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tgene\t286998\t287324\t.\t-\t.\tgene_id "YDL096C"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n+IV\tprotein_coding\ttranscript\t286998\t287324\t.\t-\t.\tgene_id "YDL096C"; transcript_id "YDL096C"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl";\r\n+IV\tprotein_coding\texon\t286998\t287324\t.\t-\t.\tgene_id "YDL096C"; transcript_id "YDL096C"; exon_number "1"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl"; exon_id "YDL096C.1";\r\n+IV\tprotein_coding\tCDS\t287001\t287324\t.\t-\t0\tgene_id "YDL096C"; transcript_id "YDL096C"; exon_number "1"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl"; protein_id "YDL096C";\r\n+IV\tprotein_coding\tstart_codon\t287322\t287324\t.\t-\t0\tgene_id "YDL096C"; transcript_id "YDL096C"; exon_number "1"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tstop_codon\t286998\t287000\t.\t-\t0\tgene_id "YDL096C"; transcript_id "YDL096C"; exon_number "1"; gene_name "OPI6"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "OPI6"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tgene\t287059\t289512\t.\t+\t.\tgene_id "YDL095W"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding";\r\n+IV\tprotein_coding\ttranscript\t287059\t289512\t.\t+\t.\tgene_id "YDL095W"; transcript_id "YDL095W"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl";\r\n+IV\tprotein_coding\texon\t287059\t289512\t.\t+\t.\tgene_id "YDL095W"; transcript_id "YDL095W"; exon_number "1"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl"; exon_id "YDL095W.1";\r\n+IV\tprotein_coding\tCDS\t287059\t289509\t.\t+\t0\tgene_id "YDL095W"; transcript_id "YDL095W"; exon_number "1"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl"; protein_id "YDL095W";\r\n+IV\tprotein_coding\tstart_codon\t287059\t287061\t.\t+\t0\tgene_id "YDL095W"; transcript_id "YDL095W"; exon_number "1"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl";\r\n+IV\tprotein_coding\tstop_codon\t289510\t289512\t.\t+\t0\tgene_id "YDL095W"; transcript_id "YDL095W"; exon_number "1"; gene_name "PMT1"; gene_source "ensembl"; gene_biotype "protein_coding"; transcript_name "PMT1"; transcript_source "ensembl";\r\n' |
| b |
| diff -r 000000000000 -r 33c060ec0ac9 test-data/Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Trinity.fasta Mon Oct 19 08:04:52 2020 +0000 |
| [ |
| b'@@ -0,0 +1,7000 @@\n+>c0_g1_i1 len=344 path=[1:0-295 654:296-343]\n+ATTTATTGGACAGTACAAGTGGCTTCAATGGAACAATTTTAGTACAGGTTCACTGCCCAT\n+TGTTTTAAGCTTAGTACATTTTTACAAAGAATACACCCCTCAGATTTACGAATGGAATAT\n+AAGATTACTAGGACCTCGAGGAGGAGCATCAAGTCACAATGATAACAAGCGAGAAGACAA\n+GAGCGCCGTAGAGTGGAAAATCAACGATCAGTTTCTTTTAAATGGGTTAATTCTCCTGCT\n+TATATTAAATCAGGGGTTTGCAGGAATACTATGCGGATTCATAAGCTGGATGTGTGGTAT\n+TTTCATCGATAAGGGCCTGTTACCGGGATTAGACCATTGGAGAA\n+>c2_g1_i1 len=284 path=[309:0-283]\n+GCCAGCCAGACAATTCGGTTACGTCATCTTGACCACCTCTGCTGGTATCATGGACCATGA\n+AGAAGCCAGAAGAAAGCACGTTTCTGGTAAGATTTTGGGTTTCGTTTACTAAGCTACTTG\n+TTACAACAACCTTTTCGGTAGCTTTATATACTATAATAAACACAAGATAGCCTCATAACT\n+TTACTCATTTCTTATTATACATTTTTTTAGTTTTCCTGTTAAATACTAATATATTTGTAC\n+TTTAAAACTGTTCAAAAGATTAGAAAAAAAAAAAAAAAAAAAAA\n+>c3_g1_i1 len=356 path=[334:0-355]\n+CACGATAATAATACAGCAAAAATGTCAGGTAACGGTGCTCAAGGTACAAAATTCAGAATT\n+TCTTTAGGTTTACCAGTTGGTGCTATCATGAACTGTGCTGACAACAGTGGTGCCAGAAAC\n+TTGTACATCATTGCCGTCAAAGGTTCTGGTTCTAGATTGAACAGATTACCAGCCGCCTCT\n+TTAGGTGACATGGTTATGGCCACTGTTAAAAAGGGTAAGCCAGAATTGAGAAAGAAGGTT\n+ATGCCAGCTATTGTTGTCCGTCAAGCTAAGTCTTGGAGAAGAAGAGACGGTGTCTTTTTG\n+TACTTCGAGGACAATGCTGGTGTCATCGCTAATCCTAAGGGTGAAATGAAGGGGGG\n+>c4_g1_i1 len=368 path=[396:0-367]\n+CAGCAACCTACAAAACAACTCAGATTCAGAATCAGATTCAGACTCGGAAACGAACCACAA\n+AAGCAAAGACAACAATAACGGTGACGACGACGATGAGGATGACGACGAGATTGTGATGCC\n+CGTGCCCAATGTTCGGTCTTCCGTTTTGCAGAAGGTTATCGAATGGGCCGAGCACCACAG\n+AGACTCTAACTTCCCTGACGAAGATGACGACGATTCCAGAAAGAGTGCTCCCGTGGACTC\n+ATGGGACAGAGAATTCCTGAAAGTGGACCAAGAGATGCTATACGAAATTATTCTGGCGGC\n+AAACTACCTCAACATCAAGCCCTTGCTTGACGCTGGCTGCAAGGTGGTTGCTGAAATGAT\n+CAGGGGGG\n+>c5_g1_i1 len=298 path=[161:0-2 160:3-297]\n+CCCCCCTTTCGCGTCTTTTATCTAATCTTTCCTTTTTGTCTTGAATAAACTCTAACTCAG\n+TTGAAAGATTGTTCCATGGTCTTGTGTCGCCTGTACCCGACATGATCAAAATCATAGTAC\n+CTGGTGTAGCATTCTCGTATAATTGTGTTAGATGTTGCCCTATATCATGAAGAACCATGG\n+ACGCATCCAACGAAGGAGTTTCCTTCCGTGGCTTTTTATTATAGTTGCGTGACCTCTCTA\n+AGTTCTTGATTCTCCCCACAATAAGTTTGACATCTTTATTCAGATTCTCGTGAATATG\n+>c6_g1_i1 len=357 path=[53:0-356]\n+ACTGGACAACATCTTACTTGTCCTGGAGTTGATTGATGAATGTATAGACTTTGGTATCGT\n+ACAAGTGACGGATCCAAGTATCATCAAGGACTACATTCGTGTGAAGGTCAACGTACCAAG\n+AGTTACAGTAGACAATGAGGAGTGGAGCCCTGGTGAAGAGAGCAGTAGTAGTAGCGGTAG\n+CGATAGCGATAGCGAGTACAGCAATACTAATAAGAGGAAGGATAAGAAGAAGAAAAGGAA\n+GAAGAAAAAGGGCACTAAAGGGAAAAGCGTGGGCAAAAGTAAATTAAAAAGTATAATGGT\n+AAACAATAAAGAAAATAGGGGCATAAACGTGGTGGAAACTGTCAAGGAGACACTAAG\n+>c12_g1_i1 len=442 path=[362:0-441]\n+CATATTTATATAACTAAGATAGTAACGCACTCAAAAAGATGTTTAGATCTGTTGCTACTA\n+GATTATCTGCCTGCCGTGGGTTAGCATCTAACGCTGCTCGCAAATCACTCACTATTGGTC\n+TTATCCCCGGTGACGGTATCGGTAAGGAAGTCATTCCTGCTGGTAAGCAAGTTTTGGAAA\n+ACCTTAACTCCAAGCACGGCCTAAGCTTCAACTTTATTGATCTCTACGCCGGTTTCCAAA\n+CATTCCAAGAAACAGGAAAGGCGTTGCCTGATGAGACTGTTAAAGTGTTGAAGGAACAAT\n+GTCAAGGTGCTCTTTTCGGTGCAGTTCAGTCTCCAACTACTAAGGTGGAAGGTTACTCCT\n+CACCAATTGTTGCTCTAAGGAGGGAAATGGGCCTTTTCGCTAATGTTCGTCCTGTTAAGT\n+CTGTAGAGGGAGAAAAGGGGGG\n+>c13_g1_i1 len=323 path=[107:0-124 231:125-128 106:129-322]\n+CAACAATTATCAGTAAAAATGGTTAACGTTCCAAAGACCAGAAAGACCTACTGTAAGGGT\n+AAGACCTGTCGTAAGCACACTCAACACAAGGTTACTCAATACAAAGCTGGTAAGGCTTCC\n+TTGTTCGCTCAAGGTAAGAGACGTTATGACCGTAAACAATCTGGTTTCGGTGGTCAAACC\n+AAGCCTGTTTTCCACAAGAAAGCTAAGACTACCAAGAAGGTTGTTTTGAGATTGGAATGT\n+GTCAAATGTAAGACTAGAGCCCAATTAACCTTGAAGAGATGTAAGCACTTCGAATTGGGT\n+GGTGAAAAGAAGCAAAAGGGGGG\n+>c15_g1_i1 len=336 path=[1:0-215 217:216-335]\n+AGCGCTATATACATAAGTAGCTATAGATTATTTATTTCAAGACGGCAACCAACTTTTCGC\n+CAGAATTCCTCCCGTGCTTAATATCATCAAGTAACTGTGGGATATCATCTAACCCGTTCT\n+TGTAAACTTTCACTGGGATGTGGTGGATTTCACCATCATTGATTTTTGGATTGATGAACT\n+TAATAAATTTTATGGCGGCTTCCTTGTATTCAGGGGCTGCTGGCAAAGTAAACGTGCCAA\n+ATGGGACGTCGTTACCTCCTATCAAATATAGAAGGGTTCCTTCAATACTGACGTTTTGCC\n+TCCTGTCTTCCTCCTTGATATCTTTTTCGGTTAAAA\n+>c16_g1_i1 len=356 path=[613:0-161 774:162-355]\n+TTTTTTTTTTTTTTTTTTTTTGAACAAAAAGAAAGTACTGTCTTATTGTATTAAAAGCGA\n+CTATATAGAAAAATTATAAAAAATTTTAAATGTTAGAATATGCAATTTCTTCTAAACAGT\n+GCGGCACTTCTAATCAAATAAACCGAAACCCATGTCGTCATCAGATTCTTCTTCTTCTTC\n+AGCAGCAGCTTCTTCAGCTGGAGCAGCGTCACCGGAAGCAGCGGAGGTAGCAGCTGGAGC\n+AGCAGCAGCGTACTTTTCTGGGTTTTCAATTCTGTCAACCAAATCTTCAATTTCAGGGTA\n+GTGGTAGGAAGCAGCAATGGCAAC'..b'AGTAAGGAATCATGGAGGTATGATTGGTACCAAC\n+CATCTAAGGTGAGCTCCAATGTGCAGCAACCACAACAACAGCTAGGGGACATGGAGAATA\n+ACTTGGAGAAATATCCATTCAGGTATAAAACATGGTTGAGGAACCAGGAAGATGAGAAAA\n+ATCTACAGAGGGAGAGCTGTGAGGATATATTAGATTTGGAAGAATTTGATAGAAGAATAC\n+TGAAAAAGTCGTTGATGACATCGCACACTAAGGGGGG\n+>c1104_g1_i1 len=342 path=[320:0-341]\n+GGCCGATTTGATTAACGTTGGTGGTACCCAATCTGTGATTAAGTATCTATATGAAAACAA\n+CATGTTGCACGGTAACACAATGACTGTTACCGGTGACACTTTGGCAGAACGTGCAAAGAA\n+AGCACCAAGCCTACCTGAAGGACAAGAGATTATTAAGCCACTCTCCCACCCAATCAAGGC\n+CAACGGTCACTTGCAAATTCTGTACGGTTCATTGGCACCAGGTGGAGCTGTGGGTAAAAT\n+TACCGGTAAGGAAGGTACTTACTTCAAGGGTAGAGCACGTGTGTTCGAAGAGGAAGGTGC\n+CTTTATTGAAGCCTTGGAAAGAGGTGAAATCAAGAAGGGGGG\n+>c1105_g1_i1 len=293 path=[1:0-292]\n+GATCCAGAGACCAAAAAACGCAAGAGGAGAGTTGCCACCACAGCCGTTTCACCAAGCACT\n+ATCAGCACGGCAACTGCCGTCAATAATGGCAGGATAGGTACATCTACAGCGTCCAGGGGA\n+GTTAGCAGCGTCGGAAACAGCAACAACAGCAGGATATCAAGACCAAAAACCAACGACTAC\n+GGCGAACCGCTCTACTGCTACTGTAACCAAGTGGCATACGGGGAAATGGTGGGGTGTGAT\n+GGCGCAGACTGTGAGCTAGAATGGTTCCATTTGCCATGTATTGGACTCGAAAC\n+>c1106_g1_i1 len=312 path=[290:0-311]\n+TTATCATGGATGCCCTTTCCGTGATTGGAGTCACGAGAGACTATCTGCAGAATTGCGCTC\n+TATGAAGTTGACCCAAGCGCAGATCATCAGTGTTCTGGATTCCTGCCAGAAAGGTGAATA\n+CACAATTGCTTGCACTAAAGTGTTTGAAATGACACACAACTCTGCATCAGCGGATTTGGA\n+AATTGGCGAGCAAACGCATATCGCGCATCCTAACCTATACTTCGAAAGATCAAGGCAACT\n+GCAAAAGAAACAGCAGAAGCTGGAAAAGGAAAAACTATTCAATAATGGTAATCATTAGTG\n+CAGAAAGGGGGG\n+>c1107_g1_i1 len=298 path=[1:0-297]\n+TGCAAAGACAAGGTAAATTAGAAGTCCCAGGTTACGTTGACATTGTCAAGACCTCTTCTG\n+GTAATGAAATGCCACCACAAGACGCTGAAGGTTGGTTCTACAAGCGTGCTGCCTCCGTTG\n+CTAGACACATTTACATGAGAAAGCAAGTCGGTGTTGGTAAGTTGAACAAATTGTACGGTG\n+GTGCCAAGAGCAGAGGTGTCAGACCATACAAGCACATTGATGCTTCCGGTTCTATCAACA\n+GAAAGGTCTTGCAAGCTTTGGAAAAAATCGGTATTGTCGAAATCTCTCCAAAGGGGGG\n+>c1108_g1_i1 len=487 path=[465:0-486]\n+GCTACGCATCGTACCCAGAGCACACCATTATTGGTATGCCGGCACTGTCTCCTACGATGA\n+CGCAAGGTAATCTTGCTGCTTGGACTAAGAAGGAAGGTGACCAATTGTCTCCCGGTGAAG\n+TTATTGCCGAAATAGAAACAGACAAGGCTCAAATGGACTTTGAGTTCCAAGAAGATGGTT\n+ACTTAGCCAAGATTCTAGTTCCTGAAGGTACAAAGGACATTCCTGTCAACAAGCCTATTG\n+CCGTCTATGTGGAGGACAAAGCTGATGTGCCAGCTTTTAAGGACTTTAAGCTGGAGGATT\n+CAGGTTCTGATTCAAAGACCAGTACGAAGGCTCAGCCTGCCGAACCACAGGCAGAAAAGA\n+AACAAGAAGCGCCAGCTGAAGAGACCAAGACTTCTGCACCTGAAGCTAAGAAATCTGACG\n+TTGCTGCTCCTCAAGGTAGGATTTTTGCCTCTCCACTTGCCAAGACTATCGCCTTGGAAA\n+AGGGGGG\n+>c1109_g1_i1 len=278 path=[1:0-277]\n+TTTTGCCTTTAAAAATTGAGTTTCTAGTTAATTAGTAAATAGCGCTAAACACAATTAAAT\n+AATACCGAATTGGCAGTGGTAGAGGAAAGAATGTACGTTACATATATCATTAAAAAAACA\n+TCTATTTCTTGTTAACTTCTCTTCTTTGTCTGACAGCAGCAGCCAATTTCCTCAAGACGT\n+CTTCAGTAGTTTCCCAACCTATACAAGCATCAGTGATGGAAACACCATATTTCAAGCCGG\n+CTTTACCTTCGGCTGGGATGCCTTGGTTACCTTCGTTG\n+>c1110_g1_i1 len=292 path=[270:0-291]\n+ACTCCTTTTTGAATCTGTATGTACCACCGTATGACCCGCCTGTATTGTCGTGCTTGTCCC\n+AGGTCCCTGAAGTGTGCCAAGCAAGACGGACTAATACGGGCCCATAGCCTATATAGTTGT\n+CATATTCGTCATCTTCCCTCAGCTTGAGTGCAATCGCATTGTACACCTTTTGGAAGTCCT\n+CGTATGCCCTCCCTTTTTCGACAGAGGCGACATGAACGAGCGGTGTAGTGGAAGCCAAAG\n+CAGCTGCCTTCCCCCAGTTGTTCCATCCGTGGTTACTACCACCCCCGGGAGA\n+>c1111_g1_i1 len=284 path=[1:0-283]\n+GTCTGAACAGTATGTTACACCATACCTTCCGAAATCTTTGCAACCTATTGCAAAAATTAG\n+TGCAGAGGAACAAAGGCGTATACAAAGTGAACAGGAAGAAGCCGAATTGAAGCAATCTTT\n+AGAGGGAGAGGCCATTAGAAATGCCACCGTGAATGCCATTAAGGAAAAGATCAAATCTTA\n+TGGTGGTAATGAAACGACGCTAGGGTTCATGGTGCCATCGTATATCAATCATAGAGGATC\n+ACCACCAAAGGCGTGCTTTGTCTCACTAATTACTGAAAGGGGGG\n+>c1112_g1_i1 len=353 path=[331:0-352]\n+CAGCATTTCAGAAGTGCATTGGGTGAAACCCAAAAAGATACATATCAAGTTCTTCTGAGA\n+AGAAATAAGCTTCCCATGTCATTGTTGGAAGAAAAGGACGCAGATGAATCCCCAAAAGCC\n+AGAATTTTGGATACCGAAAGTTATGCTGATGCGTTTGGGCCCAAAGCCCAAAGAAAGAGA\n+CCACGTCTTGCTGCATCCAATCTAGAGGACTTGGTCAAGGCTACAAATGAAGACATTACC\n+AAGTATGAGGAAAAGCAAGTCTTAGATGCCACATTAGGACTAATGGGGAACCAGGAAGAC\n+AAAGAAAATGGGTGGACCTCCGCAGCAAAAGAAGCTATTTTCAGTAAGGGGGG\n+>c1113_g1_i1 len=265 path=[243:0-264]\n+GGCTACACAGGCCTTCTCTGAGATAGAACCTTGAACAGGCTTGTTATCTGGAGTATAAGG\n+GATTTGACCAGACACGTACACAAAATTGTTGGCCTTCATAGCTTGGGAGTAAGAGGCGGC\n+AGCGGGTGGGGCCAACTTGGTGCTGACCGGGGTCAATGTTGTTATACCCCTCCTCAAGAC\n+TGGAGCTGTTCTCAAAACGGAATTTCTTAAAAACATTATTGGTAATATATTTGTGTGTAT\n+GTGTTGTCCTTTTTACCTGTAAATC\n+>c1114_g1_i1 len=269 path=[247:0-268]\n' |
| b |
| diff -r 000000000000 -r 33c060ec0ac9 test-data/idba.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/idba.fasta Mon Oct 19 08:04:52 2020 +0000 |
| b |
| b'@@ -0,0 +1,3000 @@\n+>contig-60_0 length_1811 read_count_3587\n+AACAATTTCACACAGGAAACAGCTATGACCATGATTACGCCAAGCGCGCAATTAACCCTCACTAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGATGTGGAAAGGACTTATCCATCAATATAAAGAATTTTTACCTGTAACAGATCAAACACCGGCGCTAACTTTACATGAAGGAAACACACCTCTTATTCACCTGCCGAAGCTGTCTGAGCAGCTCGGAATTGAGCTTCATGTCAAAACGGAAGGCGTCAATCCTACGGGATCATTTAAAGATCGCGGAATGGTTATGGCTGTGGCAAAGGCAAAAGAAGAAGGCAATGACACGATTATGTGCGCGTCAACAGGTAACACTTCCGCTGCTGCGGCAGCATATGCAGCCCGTGCTAACATGAAATGCATTGTCATCATCCCGAACGGAAAAATTGCATTTGGAAAACTCGCTCAAGCTGTCATGTACGGAGCCGAGATTATCGCAATTGACGGAAACTTTGACGATGCGCTTAAAATTGTCCGTTCCATCTGTGAGAAATCACCGATTGCCCTTGTCAACTCAGTCAACCCTTACCGCATTGAAGGCCAAAAAACTGCTGCCTTCGAAGTGTGCGAACAGCTGGGGGAAGCGCCTGATGTTTTAGCGATCCCGGTCGGAAATGCTGGAAACATCACTGCGTACTGGAAGGGCTTCAAGGAATATCATGAGAAAAACGGCACAGGCCTTCCGAAAATGCGCGGCTTTGAAGCTGAGGGTGCGGCGGCAATCGTGCGCAATGAAGTGATTGAAAATCCGGAAACAATAGCGACAGCCATTCGTATCGGAAACCCGGCAAGCTGGGACAAAGCTGTAAAGGCAGCCGAGGAATCCAATGGGAAAATTGACGAAGTCACTGATGATGAAATCCTTCACGCATATCAGCTGATCGCCCGTGTAGAAGGCGTGTTTGCAGAACCAGGTTCTTGCGCGTCTATCGCAGGAGTGCTGAAACAGGTGAAATCCGGAGAAATTCCGAAAGGCAGCAAGGTCGTAGCTGTGTTAACAGGAAACGGACTGAAAGATCCGAACACAGCGGTCGACATTTCAGAAATCAAGCCTGTCACATTGCCGACTGATGAAGACAGCATCCTTGAATATGTAAAAGGAGCGGCCCGTGTATGAACGAAGCCGACATGCTGTTCTCTGTCACTGTTCCCGGAAGCACAGCTAACCTAGGCCCCGGCTTTGATTCAGTCGGAATGGCGCTCAGCAGATATTTGAAGCTGACCGTCTTTGAAAGCGACAAATGGTCTTTTGAGGCTGAAACAGAAACAGTCGCCGGAATTCCGGCGGGTACAGATAACCTGATCTACCAAGTGGCTAAACGGACCGCAGATTTGTACGGAAAAGAAATGCCTCCTGTCCATGTGAAGGTGTGGAGCGACATCCCGCTTGCACGCGGCCTTGGCAGCAGCGCCGCAGCGATTGTAGCGGCCATTGAACTGGCTGATGAATTATGCGGCTTAAAGCTGTCTGAAGCGGACAAGCTGCATTTAGCGAGTCTAGAAGAAGGACACCCGGACAATGCTGGCGCTTCTCTCGTCGGCGGACTTGTGATCGGCCTGCATGAGGATGACGAGACCCAAATGATCCGCGTCCCGAATGCTGACATTGACGTAGTCGTTGTCATTCCTTTTTATGAAGTGCTGACAAGAGACGCGAGAGACGTGCTTCCGAAGGAGTTTCCATATGCCGATGCCGTAAAAGCAAGTGCTGTCAGCAATATCCTCATTGCTGCGATCATGTCCAAGGATTGGCCGCTTGTCGGGAAAA\n+>contig-60_1 length_1662 read_count_1507\n+AAACTGCTCACAACATGAAGGTCATGAAATTCTCTGTCTCTCCAGTTGTGCAAGTCGCTGTCGAAGTCAAGAACGCTAACGACTTACCAAAATTGGTCGAAGGTTTGAAGAGATTGTCCAAGTCTGATCCATGTGTCTTGACCTATATGTCTGAATCCGGTGAACATATCGTTGCTGGTACCGGTGAATTGCATTTGGAAATTTGTTTGCAAGATTTGGAACACGACCACGCTGGTGTTCCATTGAAGATCTCCCCACCAGTTGTCGCTTACAGAGAAACTGTTGAAAGTGAATCTTCTCAAACTGCTTTGTCCAAGTCTCCAAACAAGCATAACAGAATCTACTTGAAGGCTGAACCAATTGACGAAGAAGTCTCTTTGGCTATTGAAAACGGTATCATCAACCCAAGAGATGATTTCAAGGCCAGAGCTAGAATCATGGCTGACGACTACGGTTGGGATGTCACCGATGCCAGAAAGATCTGGTGTTTCGGTCCAGACGGTAACGGTCCAAACTTGGTTATTGACCAAACTAAGGCTGTCCAATACTTGCACGAAATCAAGGATTCCGTTGTTGCTGCTTTCCAATGGGCTACCAAGGAAGGTCCAATTTTCGGTGAAGAAATGAGATCTGTCAGAGTTAACATTTTGGATGTTACTTTACATGCCGATGCTATCCACAGAGGTGGTGGTCAAATCATCCCAACCATGAGAAGAGCTACTTACGCTGGTTTCTTGTTGGCTGATCCAAAGATCCAAGAACCAGTTTTCTTGGTCGAAATTCAATGTCCAGAACAAGCCGTCGGTGGTATCTACTCCGTCTTAAACAAGAAGAGAGGTCAAGTCGTTTCTGAAGAACAAAGACCAGGTACTCCATTGTTTACCGTCAAGGCCTACTTGCCAGTTAACGAATCTTTCGGTTTCACTGGTGAATTGAGACAAGCTACCGGTGGTCAAGCTTTCCCACAAATGGTTTTCGACCATTGGTCCACTTTAGGTTCTGACCCATTGGACCCAACCTCTAAGGCTGGTGAAATTGTTCTTGCTGCTCGTAAGAGACACGGTATGAAGGAAGAAGTTCCAGGCTGGCAAGAATATTACGACAAATTGTAAGAAGTCTAAATGAGAAAAGGTGGTTCTGTAAGAGCAAACCTTACCGCCTTATGATCTTTTTCATTTATTCTCTGCTTTAAAATTTTGTCGTAATAAAAATAGTATGGTAATAGACTTATATATTATTTTCTTACACATTTTTGTCATATAGTTATATTCCGAATGTTTACAATCGAACCCATCATAAAAATGGACCTTTTCGTATTACCGCCCCCTTTGTAGAGGGGGAGGAACGGCAACTTCTTGACTATTACGACGTATCACCACCCCGTTAGATATACTATGGAAAAAACTATTAAAAACCATTATAATTCATTAATGACATCGGTCCTGAGGTAGTATTACGTATAACTTACCTGGCTCTTGGTCATAGCTTTTTATCCGTTTACGAAAAAAGGAGAAGAAGATTGGGCTTCCGCGGCTATTGTTTGGTTTATACCCCGCCGTATGTTGGTGCTTCTATAATTAGAGCGAAATAGGAAATACAAAAAATCCTTGGAGGGGAGGACCAGCCTCATCGGGCTAAAACTCCCTCAAAACCGTTGGGGGG\n+>contig-60_2 length_1112 read_count_3123\n+TAAAGGGAACAAAAGCTGGGTACCGGGCCCCCCCTCGAGCTGTCCTTTCATCCATAAGCGGAGAAAAAGGGAATGACATTGTTCTTACACGGCACAAGCAGACAAAATCAACATGGTCATTTAGAAATCGGAGGTGTGGATGCTCTCTATTTAGCGGAGAAATATGGTACACCTCTTTACGTATATGATGTGGCTTTAATACGTGAGCGTGCTAAAAGCTTTAAGCAGGCGTTTATTTCTGCAGGGCTGAAAGCACAGGTGGCATATGCGAGCAAAGCATTCTCATCAGTCGCAATGATTCAGCTCGCTGAGGAAGGGGGGCTTTCTTTAGATGTCGTATCCGGAGGAGAGCTATATACGGCTGTTGCAGCAGGCT'..b'CCGGACTTATGTGGCTCCCTTTAGAATATAAGGGTCTTCCCTTTAACGGAACAGTAAGGTTCCACAAGGTGGCAAAAAAGGCAATCCAACCGACACTTCGGCAAATTTCTTTCA\n+>contig-60_1488 length_279 read_count_87\n+CCCCCCAAGACTATTCGTTTGGTGGCTATCTTTATAATTCGAATCAGTTCGCAAATTTTTTGGTGAAGAGCTATTCAATTATTAGCTAATTATGGAAACTATTTTGCAGCCAAAGGCTAGACCATTTGAGTCTTTGAAAAGAAAACGTTTTAGAGAATGGTTGAGGCCGTCGACTGCGCATGGATCCCTGTTGCATTCTGATACATTAGATTTGCGTGACTTTGCAAAACCTAATCCCGCTGACACATTTTCTAATCTTGATTCTGGTCATTGTCCTTT\n+>contig-60_1489 length_279 read_count_658\n+CGGCAAAGTAAAGCTTCTGAAAGAAGACATGTCAATTTCTCTATTAGGTAGAATTGTTTCACAACAATTCTCCGGCATACGGGCGGCTGAGCCAGGGAGATCTCTATATTTACCGTTTACCTTACTATTGAAACAGCCCGGTGCTTACAAGGTGAGCCTACACAGATATGTACATAGCACCCAAACGAAGAGCCACTTGAGCTTTTTAATGAATAATAACGATATAACACCTTTTCAAAAATTTACAGTTAAAGTTTTCAAAGAGCAGTGCAAATCTTG\n+>contig-60_1490 length_279 read_count_99\n+AGGTTTCAAATGAGATGGTAAAACCTTATATCTTTAGTTCTGATCCAGTTTTAGAAGCTTACCTTATTAAAGCTGCGGAAATTCACAAAGAAGCTGAATTTGAGTATTGGAGAAAGCAATACCCAGAGGTTGATTTGCCTTAGGGCCGAATTTTTGGTATTTATCTAGTATATTCTAATATAAAATGTACGAGCATCATTAACTTCAAGAACATTACGAAGCCCGCAATTAAGTGTCAGTCCATCTGGGTGTAAAAGTTATGTACGCTCGAAACAAATT\n+>contig-60_1491 length_279 read_count_498\n+CCAAGGTTTGATTCCATGGGCATGGATCGAAGCCTCCACTAAAGGTGCTGTGTTGCTGTTCGTGTCAGCTGAGGCTGAGTATCGTTTCAAAAGTTTGGGGTTGAACAACTTTGCCTCAGGTATATTAGGTGGTGTCACGGGTGGTGTCACTCAAGCCTACTTAACCATGGGGTTCTGTACCTGTATGAAAACGGTGGAAATTACAAGACATAAATCTGCCTCCGCAGGTGGTGTCCCACAATCTTCTTGGAGTGTGTTCAAGAATATTTATAAAAAGGT\n+>contig-60_1492 length_279 read_count_1472\n+GGATTACAAACCAGGCATGCCCCATCTCCACGCTCAAGAGGAGAATAATAACTTCAGCATCTTTAGATGGGACCAGGTACAACAACCATTACCAGGCGAAGGTAACATTCTGCCTCCAGGAGTCAGCTTACCAAACGATGGTGGTCGGAAATCGAAAAGCGCCGATGTAGCTGCAGGGCTACACAAGCAAACCGGTGTAGATCCGGATTATATCACTAGAAAGTTGACTATGAAGCCGCTGGTGATGAAAATTGTGTCAAATCAGACTGGGTTGGGGGG\n+>contig-60_1493 length_279 read_count_992\n+AGTAGTGGTTATTTGGCTGACTATTATTGGCTCCAGAGTATTGGTTATCATGAGGAGGAAATTTCTTGTAGCCATTGGCTTGCTGCGGGTGTGGGGGCGGTGGACCTCTTTGGTCAGTCATAGTGCCTACAATTGATCTATTGTTCTTTGTAATAAATTCTTTCTTTCAGGAACAGTAAAAACAGCCTAAAAATATGAAGTCGCCGTAGTAAACGTTATCTTCTAGTTACTATCAACACAGACGCCTTTTTAAATTCGAGGGTCAAGGCTGTTAGGCTG\n+>contig-60_1494 length_278 read_count_151\n+GTTCACTGTCAGTGATATCAAAGCAGAATGGAGAGGCCGTATGTAGAACTATCTTGATATCCTTGCCGTGCTTTTGGAAAACATGGTCAAATGCGTCCAGCTTAGATATGTCTGGGACAACTTCCATGGAGAATTTTGGGTTGTTACCAAAGGCCTCCGTTAAATTCTCGGCCTTTTCTTGACTTCTGGCAGAACCGATGACCTTATAGTCTTCCTTCAACAGGAGATCGACAATGTGTTGGGCAATGAACCCGTTAGCACCTGAAACGAAAACTGAC\n+>contig-60_1495 length_278 read_count_832\n+ATAATAAAAGAAGATACAAAAGTAAAGAAATCGAATTGGTCAAATTACTTCAAATCGTGATTTTAAATGTCGAAATTATGCCTGGCCTGCGTTTCTTCATGGCACTTTCGGAAAAGGCGGAAGAACACAGGTAAATGTTCTTACGACCGAGGTCCTACAGCCTCCCTTTTTTCTTATTTTACATATTAATATACATAAATATACCATAATGCATTCTTTTTCTAATGATTTAGCTCTCCTTTTTTTGACATTTTTGAAAATAAATATATATTGGGGGG\n+>contig-60_1496 length_278 read_count_1311\n+ATCGAATCATGCCTGACTCTAAGTACACAATGCAAGGTTATAACCTTGTTAAGCTATTAAAAAGGCTAGAAGAAGCCACTGCAAGATTAGAGGATGTCACCATCTATCAAGAAGGTTATATTCAGAATAAATTGGAGGCATCTAAAAATAACAAGCCTTCCGACTCCGGGGCCGATGCGAATACTACGAATGAACCTTCTGCAGAAAATGCTCCTGAAGTAGAACAAGATCCGAAATGCATAACTGCGTTCCAATCTTACATCGGTGAGAATATTGAT\n+>contig-60_1497 length_278 read_count_206\n+TGAAAACCGAAAGGTTATTTTGAGAAATCTAAACAAATTGAAATGGATTAGAGTTCCAATATACATAAAGGCTGTAAATGCGCATGGCGTGATTGTGGCACGTAGAGGAATGGACGAGAATACAGCTGCTACTGGGATTGCTTGTATCGAATTTACGGCCCAATTACTAGCATACTTGATGCACAAGAGTAATTGAGCACTTGATTTACACGAAATAGTATATATTTTTGAATGAACACTCTCATGTGATTAAAATGTATTACTACCACTAATGCTTG\n+>contig-60_1498 length_278 read_count_1999\n+GACAACCAAATCTATGCTATTGAAAAGCCAGAAGTCTTCAGATCTGCCGGTGGTAACTACGTTGTCTTCGGTGAAGCTAAGGTTGACAACTTTACCCAAAAGCTAGCCGCTGCTCAACAACAAGCTCAAGCTAGCGGTATTATGCCATCTAACGAAGACGTCGCTACCAAGTCCCCAGAAGACATCCAAGCTGACATGCAAGCCGCCGCAGAAGGCAGTGTCAACGCCGCAGCAGAAGAAGATGACGAAGAAGGTGAAGTTGATGCCGGTGACTTGAA\n+>contig-60_1499 length_278 read_count_2179\n+TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAGCAAATAAATGATAATATTCGTACGACACTAGAGAATATGATATTGTATTAAGTAAATATATATATATAGAGAAGGAGAGAGAAAGACAAGAACAGGGCGGCTATTAAGCGTCGTCTTCGTCATTCATAGAGATAGCTGTCTGTGGCTTTTCTTCTTCTGCAACCTCAGGCTTTGCTTCCGGCTCTTCCGCAAATGAGTTGGATAGGAACTCTTTCATTAGGCCAGCCGAGGTTTCAAAAT\n' |