| Next changeset 1:2b8b4cacb83d (2022-04-25) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gfastats commit 115f451c7c9e7e30fd1b8df26bfc5362832a6eb7" |
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added:
gfastats.xml macros.xml test-data/dataset_01.fastq.gz test-data/dataset_02.fasta.gz test-data/dataset_03.fasta test-data/dataset_04.gfa test-data/swiss_army.sak test-data/test_01.fasta.gz test-data/test_02_stats.tabular test-data/test_03_stats.tabular test-data/test_04_stats.tabular test-data/test_05_stats.tabular test-data/test_06.fasta.gz test-data/test_07_stats.tabular test-data/test_08.fasta.gz |
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| diff -r 000000000000 -r 5799092ffdff gfastats.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gfastats.xml Wed Mar 09 10:29:20 2022 +0000 |
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| b'@@ -0,0 +1,339 @@\n+<tool id="gfastats" name="gfastats" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">\n+ <description>the swiss army knife for genome assembly</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="biotools"/>\n+ <version_command>gfastats --version</version_command>\n+ <command detect_errors="exit_code"><![CDATA[\n+ gfastats\n+ \'$input_file\'\n+ #if $mode_condition.selector == \'statistics\'\n+ #if $mode_condition.statistics_condition.selector == \'assembly\'\n+ $mode_condition.statistics_condition.expected_genomesize\n+ #end if\n+ #end if\n+ #if $target_condition.target_option == \'true\'\n+ $target_condition.target_sequence\n+ #if $target_condition.include_bed\n+ --include-bed $target_condition.include_bed\n+ #end if\n+ #if $target_condition.exclude_bed\n+ --exclude-bed $target_condition.exclude_bed\n+ #end if\n+ #end if\n+ #if $mode_condition.selector == \'manipulation\'\n+ #if $mode_condition.swiss_army_knife\n+ -k $mode_condition.swiss_army_knife\n+ #end if\n+ #if $mode_condition.sort\n+ --sort $mode_condition.sort\n+ #end if\n+ $mode_condition.homopolymer_compress\n+ -o dataset.$mode_condition.output_condition.out_format\n+ #if $mode_condition.output_condition.out_format == \'fasta\'\n+ #if $mode_condition.output_condition.line_length\n+ --line-length $mode_condition.output_condition.line_length\n+ #end if\n+ #else if $mode_condition.output_condition.out_format == \'fasta.gz\'\n+ #if $mode_condition.output_condition.line_length\n+ --line-length $mode_condition.output_condition.line_length\n+ #end if\n+ #end if\n+ #else\n+ #if $mode_condition.statistics_condition.selector == \'size\'\n+ --out-size $mode_condition.statistics_condition.out_size\n+ #else if $mode_condition.statistics_condition.selector == \'coordinates\'\n+ --out-coord $mode_condition.statistics_condition.out_coord\n+ #else if $mode_condition.statistics_condition.selector == \'assembly\'\n+ --nstar-report\n+ #else\n+ --seq-report\n+ $mode_condition.statistics_condition.out_sequence\n+ #end if\n+ $mode_condition.tabular > \'$stats\' \n+ #end if\n+ #if $mode_condition.selector == \'manipulation\'\n+ && mv dataset* output_dataset\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param name="input_file" argument="--fasta" type="data"\n+ format="fasta,fastq,fastqsanger,gfa1,fasta.gz,fastq.gz,fastqsanger.gz,gfa1.gz"\n+ label="Input file"/>\n+ <conditional name="target_condition">\n+ <param name="target_option" type="select" label="Specify target sequences">\n+ <option value="false">Disabled</option>\n+ <option value="true">Enabled</option>\n+ </param>\n+ <when value="false"/>\n+ <when value="true">\n+ <param name="target_sequence" type="text" value="" label="Target sequence" help="Target specific sequence by header, optionally with coordinates: header[:start-end]">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.digits,string.letters">\n+ <add value=":"/>\n+ <add value="-"/>\n+ <add value="_"/>\n+ <add value="|"/>\n+ <add value=" "/>\n+ </valid>\n+ </sanitizer>\n+ <validator type="regex">[0-9A-Za-z:-_| ]+<'..b' <param name="expected_genomesize" value="600000"/>\n+ </conditional>\n+ </conditional>\n+ <output name="stats" value="test_04_stats.tabular" ftype="tabular"/>\n+ </test>\n+ <!--Test 05 -->\n+ <test expect_num_outputs="1">\n+ <param name="input_file" value="dataset_04.gfa"/>\n+ <conditional name="mode_condition">\n+ <param name="selector" value="statistics"/>\n+ <conditional name="statistics_condition">\n+ <param name="selector" value="coordinates"/>\n+ <param name="out_coord" value="a"/>\n+ </conditional>\n+ </conditional>\n+ <output name="stats" value="test_05_stats.tabular" ftype="tabular"/>\n+ </test>\n+ <!--Test 06 -->\n+ <test expect_num_outputs="1">\n+ <param name="input_file" value="dataset_04.gfa"/>\n+ <conditional name="mode_condition">\n+ <param name="selector" value="manipulation"/>\n+ <conditional name="output_condition">\n+ <param name="out_format" value="fasta.gz"/>\n+ </conditional>\n+ </conditional>\n+ <output name="output" value="test_06.fasta.gz" ftype="fasta.gz"/>\n+ </test>\n+ <!--Test 07 -->\n+ <test expect_num_outputs="1">\n+ <param name="input_file" value="dataset_03.fasta"/>\n+ <conditional name="mode_condition">\n+ <param name="selector" value="statistics"/>\n+ <conditional name="statistics_condition">\n+ <param name="selector" value="assembly"/>\n+ </conditional>\n+ <param name="tabular" value="false"/>\n+ </conditional>\n+ <output name="stats" value="test_07_stats.tabular" ftype="tabular"/>\n+ </test>\n+ <!--Test 08 -->\n+ <test expect_num_outputs="1">\n+ <param name="input_file" value="dataset_01.fastq.gz"/>\n+ <conditional name="mode_condition">\n+ <param name="selector" value="manipulation"/>\n+ <conditional name="output_condition">\n+ <param name="out_format" value="fasta.gz"/>\n+ </conditional>\n+ <param name="sort" value="ascending"/>\n+ <param name="homopolymer_compress" value="true"/>\n+ </conditional>\n+ <output name="output" value="test_08.fasta.gz" ftype="fasta.gz"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+.. class:: infomark\n+\n+**Purpose**\n+\n+gfastats is a single fast and exhaustive tool for summary statistics and simultaneous genome assembly file manipulation. gfastats also allows seamless format conversion.\n+\n+\n+.. class:: infomark\n+\n+**Metrics details**\n+\n+Typical fast* metrics include:\n+\n+- Scaffold, contig and gap size\n+- Number of scaffolds, contigs and gaps\n+- Total length of scaffolds, contigs and gaps\n+- Scaffold, contig, gap N50 and statistics (full N*/NG* statistics with the --nstar-report flag)\n+- Area under the curve (AuN/AuNG) values for scaffolds, contigs and gaps\n+- Average scaffold, contig, gap size\n+- Largest scaffold, contig and gap\n+- Base composition and GC content\n+- Soft-masked base counts (lower case bases)\n+\n+\n+Typical gfa metrics include:\n+\n+- Number of nodes and edges\n+- Average degree\n+- Number of connected components, and length of the largets connected component\n+- Number of dead ends\n+- Number of disconnected components, and their total length\n+\n+\n+.. class:: infomark\n+\n+**Assembly manipulation**\n+\n+gfastats allows extensive assembly manipulation at the sequence level. Manipulation is achieved using a set of instructions provided as an ordered list in a file to the option **swiss army knife**. See the `instruction wiki <https://github.com/vgl-hub/gfastats/tree/main/instructions>`_ for a full list of instructions.\n+\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r 5799092ffdff macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Mar 09 10:29:20 2022 +0000 |
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| @@ -0,0 +1,32 @@ +<macros> + <token name="@TOOL_VERSION@">1.2.0</token> + <token name="@SUFFIX_VERSION@">0</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">gfastats</requirement> + </requirements> + </xml> + <xml name="biotools"> + <xrefs> + <xref type="bio.tools">gfastats</xref> + </xrefs> + </xml> + <xml name="citations"> + <citations> + <citation type="bibtex"> + @misc{githubgfastats, + author = {Formenti, Giulio}, + year = {2022}, + title = {gfastats}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/vgl-hub/gfastats}} + </citation> + </citations> + </xml> + <xml name="length_macro"> + <param argument="--line-length" type="integer" min="0" max="80" value="" + optional="true" label="Especify line length" + help="Specifies line length when output format is fasta. Default has no line breaks."/> + </xml> +</macros> |
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| diff -r 000000000000 -r 5799092ffdff test-data/dataset_01.fastq.gz |
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| Binary file test-data/dataset_01.fastq.gz has changed |
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| diff -r 000000000000 -r 5799092ffdff test-data/dataset_02.fasta.gz |
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| Binary file test-data/dataset_02.fasta.gz has changed |
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| diff -r 000000000000 -r 5799092ffdff test-data/dataset_03.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_03.fasta Wed Mar 09 10:29:20 2022 +0000 |
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| b'@@ -0,0 +1,6996 @@\n+>contig_1\n+TTTCCTTTTCCTACTGTACTTCTCAAATATTCCAGGCGACTTTCGTGATGATTCACAGCA\n+TGTTTCACGATTCGCTAACCCTAATCCGCTACCGCGGTTAGCCGGGAACCCCGCTTTATC\n+AACGCGATAAAAACGCTTCGGTCAGGCCGCGGAATAATGCTCCGGTGCAATGCCCCGGGT\n+CCGTTATCTTCAACGCTAAATTCGGCACCGTGCGGCACTCGCTGCCAGCGTACGGTGATA\n+TGCGTGCCCTTCCGGCGTATGGATTCACGCGTTATTAGACCAGGTTTGAAATCGCACTGC\n+GGTAGCTGATCTTCGTTTGCCAGACACCTTGAGGCCGTTATCTATCTCAAAGGTAAATGT\n+CTGTTTTTCTGACTCAGAGTCTGAGCCTCGCGCTCAACAACGCGCAGCATCATCGGCACA\n+ATCAACCTTTTCATTTGAGGAATGCGTCGGTGCGGCTTCTATTTTCGACAGCGTCAGCAA\n+ATGCTTCACCAGGTCCTTCCATCCCGCTGGGTCTGCTCGCGCATGGTGTGCAACGCTTTT\n+TCGCGTACCGCGCCTTCCAGCGGCTGCTCAATTCATCATCTCCAGGTAACCCCTGTAACA\n+CGGTCCAATGGCGTACGTAACTCATGGCTCACCGTTGGCAAAAAAGTTACGCCGCGCCCC\n+TTCCAGTTGATGCATTTGCGTGACATCACGCGCCACCATCAGCAACTGTTTGTGGGTATA\n+AGGCATGACGCGAATTTCCAGATGCCGCCCGGTGGTTTGAGCACAGATTGAGCGGGCGAG\n+AAAAATCACGCGTTTTCAGATATTGCGTAAACTCCGGGTAAACGCAGTAGTTAAGGATGT\n+TCTGCCCGTTATCTTCCGGCCAGCGCAAACCAAGAAATTTGTTGCGCCAGACCGTTACAC\n+CAGAAAATACCGCCCTTTTCCTNGTCAGCACCACCGCGTCGGGCAGCGACTCCGCGCCGC\n+TACGAAAAGCGTTTAATCAGATTGCCCACTGTTCACGGCGGGCGTTTTTTATTTCCGCAG\n+CTGCATCTGGTGTAAGCCGTATAGTAGCGGTTCCCAGCTACCACCGCCCCGGTGGCGGGG\n+TCATACTGCGATCCCACCCAACAGCCACCATGAAAAGGCGCAATAAATTCCAGAAATGCC\n+AGATAAGCAGTCCTGTTACCGATGCCAGCAAAAACCAGGGCAGGTAACCAAAAAATGCAC\n+CCAAGGATGAAAGCCGGGAGGCAGCAAAGTAGCAGCTCCAGCACCAGGCCTTTCCACGAC\n+AGCCGTTCCAGCACCGTAAGATACTCCAGTTAAGAAAATCATAAGCCCTGCTCTGCGCCG\n+GAGAGCAAGGCGTTAAAAGCGGGGTTGAAAAACGATTATCCTGTACCGCGCACGGTCTGC\n+CACCATGCGGTCATGCCCGCCGGGCTCCAGAGCTTTACGCAGGCGACGAATGTGGACATC\n+GACCGTGCGGTCTTCCACATACACGTTAGTTCCCAGACGTGTTTAACAGCTGCTCGCGCT\n+GTACACGCGCTCAGGATGCGTCATAAAAAAGTGCAGCAGTTTTAAATTCTGTCGGCCCCA\n+TCTCCAGCGGCTCTTCGCCCGCCATCACTCGGTGAGATGTCGGGTCGAGACTTAATCCCT\n+GCATCTTAATCACCTCTTCCACCGCCATTGGCGAAATACGGCGCATTACCGCTTTGATTC\n+>contig_2\n+GCGCCACCAGCTCCTTCGGCGAAAACGGCTTGGTGATATAGTCATCCGCGCCGGTTTCAA\n+GCCGCGCACGCGATCTTCTTCTTTCCCCTCTGGCGGTCAACATCACCACTGGGAATATCC\n+CGGGGTCATCGACTCGCGCTTGAGGTGTTTGATGAACTGGATACCGGAGCCGCCAGGTAA\n+CATCCAGTCGAGGAGAATTAAAATCCGGCCAGGGTTCATTCAGTTTGATTCACAGCACTG\n+TCATAATCTTCCGCTTCGACCGGCTGAAAGCCATTTTGTTCGAGCACGAAGAGAGACCAA\n+TTTCGGCGAATTGGAGCTTCATCTTCTACGACCAGAATACGTCTCGCCATGATTTGCCCT\n+GTTGTAATAAATAGGTTGCGATCATTAATGCGACGTCATTATGCGTCAGATTTATGACAG\n+ATTTATGAAAAGCCTCGTCGCACAATATCTTCAGGTTATTGATTTCCGTGGCGCAGAAAA\n+AAGCAAATGGCACCATCTGTTTGGGTATAATCGCGCCCATGCTTTTTCGCCAGGGAACCG\n+TTATGCGCATCCTTCACACCTCAGACTGGCATCTCTGGCCAGAACTTCTACAGTAAAAGC\n+CGCGAAGCTGAACAATAGGCTTTTCCTTGACTGGCTGCTGGAGACAGCACAAACCCATCA\n+GGTGGATGCGATTATTGTTGCCGGTGATGTTTTCGATACCGGCTCGCCCGCCCAGTTACG\n+CCCGCACGTTATACAACCGTTTTGTTGTCAATTTACAGCAAACTGGCTTTCATCTGGTGG\n+TACTGGCAGGAAACCATGACTCGGTCGCCACGCTGAATGAATCGCGCGATATCATGGCGT\n+CCTCAATACTACCGTGGTCGCCAGCGCCGGACATGCGCCGCAAATCTTGCCTCGTCGCGA\n+CGGGACGGCCAGGCGCAGTGCTGTGCCCCATTCCCGTTTTTACGTCCGCGTGACATTATT\n+ACCAGCCAGGCGGGGCTTAACGGTATTGAAAAACAGCAGCATTTACTGGCAGCGATTACC\n+GATTATTACCAACAACACTATGCCGATGCCTGCAAACTGCGCGGCGATCAGCCTCTGCCC\n+ATCATCGCCACGGGACATTTAACGACCGTGGGGGCCAGTAAAAGTGACGCCGTGCGTGAC\n+CATTTATATTGGCACGCTGGACGCGTTTCCGGCACAAAACTTTCCACCAGCCGACTACAT\n+CGCGCTCGGGCATATTCACCGCGCACAGATTATTGGCGGCATGGAACATGTTCGCTATTG\n+CGGCTCCCCCATTCCACTGAGTTTTGATGAATGCGGTAAGAGTAAATATGTCCATCTGGT\n+GACATTTTCAAACGGCAAATTAGAGAGCGTGGAAAACCTGAACGTACCGGTAACGCAACC\n+CATGGCAGTGCTGAAAGGCGATCTGGCGTCGATTACCGCACAGCTGGAACAGTGGCGCGA\n+TGTATCGCAGGAGCCACCTGTCTGGCTGGATATCGAAATCACTACTGATGAGTATCTGCA\n+TGATATTCAGCGCAAAATCCAGGCATTAACCGAATCATTGCCCTGTCGAAGTATTGCTGG\n+TACGTCGGAGTCGTGAACAGCCCGAGCGTGTGTTAGCCAGCCAACAGCGTGAAACCCTCA\n+GCGAACTCAGCGTCGAAGAGGGTGTTCAATCGCCGTCTGGCACTGGAAGAACTGGATGAA\n+TCGCAGCAGCAACGTCTGCAGCATCTTTTCACCACGACGTTGCATACCCTCGCCGGGAGA\n+ACACGAAGCATGAAAATTCTCAGCCTGCGCCTGAAAAACCTGAACTCATTAAAAGGCGAA\n+TGGAAGATTGATTTCACCCGCGAGCCGTTCGCCAGCAACGGCTGTTTGCTATTACCGGCC\n+CAACAGGTGCGGGGAAAACCACCCTGCTGGACGCCATTTGTCTGGCGCTGTATCACGAAA\n+CTCCGCGTCTCTCTAACGTTTCACAATCGCAAAATGATCTCATGACCCGCGATACCGCCG\n+AATGTCTGGCGGAGGTGGAGTTTGAAGTGAAAGGTGAAGCGTACCGTGCATTCTGGAGCC\n+AGAATCGGGCGCGTAACCAACCCGACGGTAATTTGCAAGGGCCACGCGTAGAGCTGGCGC\n+GCTGCGCCGACGGCAAAATTCTCGCCGACAAAGTGAAAGATAAGCTGGAAC'..b'CCCCTGATTTTTGCCCAAACCCC\n+TGGGTTACGCTTGCGCAAAGCTGACCTGCCTCGTTGTGATCTTTCAGATTGAGGTTTCAT\n+TTAGTTTTCCAGTACTCGTGCGCCCCCCGTATCCAGCCGGCAAATATGACAAAACCTTCC\n+TGATTTTGCAGGTAGTTCTTACCCAACCAGTCGGCAACGCGCGGGGCGGTTTCCGGCTTG\n+TCACACAGAGCGAACAAGGTCCGGGCCGGAGCCGGAGATACCGCTCGCTACCGCGCCATT\n+TCCGCGACCGCCTGCCGCGCCTGCCGGAAGCCTGGCAGTAACCGTTCACGGTAGGTTCAC\n+GCGATAACATCTTTTCATACAGCGTTCGCGGCAAGCTCAGGCTGACGGGAATAGCAGGCG\n+TGAATGAAGCCTGCCAGATGTCGCCCGTGCGCAATGCAATCCTGGCGCGATACTGCCCCG\n+GTAAAATAGCCCTGGCTTTTCCGTCGAGACTTTAATCCCCGGATACGCCAGCACCCACAG\n+CCACTCATCCAAACCTGGCACTTGCTGGCTGATGATGTCGTTTTCTTCGATCATCAACTG\n+CATACCACCGAGAAAACACGGTGCCACGTTGTCGTAATGAATGCTGCCGGAGATACGGCC\n+TTCCAGCTCGCCCATCAAAAGCCAGCGAACGAGTGTCATTAAGCGGCTTGCCGCAGTGTT\n+CAATTTCATCCCATCAGCGCCGCGACCACGAAACAGGCACTGGAGCCTAAGCCCGAACCG\n+ATCGGCATATTCTTTTCCAGGGTCATCGCCACTGGAATTTGCTTACCCAGTTCCTGGCAA\n+AAACGCCTCCCAGCACTGATAAACGATATTTTCCCGTGGTTTCTGACGGCAGCCTTATCC\n+GGGCAAAGCGTCCGAGGTTGTTGAGACTGAATGTCTCTGCCGCCTCAACCGTGACTACAT\n+CTCCGAGCAATGCACCATCAACAGGTGTCACCGCCGCCCCGAGCACATCAAACCCGACGC\n+TCATATTGGCACTGGAAGCCGGGGCATAAACTTTAACCATTTTCAGACTCCTAACTTCCA\n+TGAGAGGGTACGTAGCAGATCAGCAAAGACACCGGCAGCTGTAACCGTCAATTTGCCCGC\n+ACCATATCCGCGCAGTACCAAACGGCAAGCGGCTGATAATAGTGGCTTAAGAGCCAGGGC\n+GTTTTCGCCATTTTTCACTTTGAACAGCGGATCATTACCATCCACTTCGGCAATCTTCAC\n+GCGGCAGACGCCATCTTCATCAATATTGCCAACATAGCGCAAAACCTTTCCCTTCATCAC\n+GGGCCTTCGCCACGCGCGCGGCAAAGAGATCGTCGAGTTGTGACAGATTCGCCATAAAAG\n+CGGCAACATCACCCTCGGCGTTAACCTCTGCGGGGCAGCACAGGTTCAATTTCAATATCC\n+GCCAGCTCCAGTTCACTCCCGTTTCACGAGCGAGAATCAATAGTTTACGCGCCACATCCA\n+TACCAGAAAGATCATCTCGCCGGGTCCGGTTCGGTATAACCCATTTCCCGACGCAGCGTG\n+GTCGCCTCGGAGAAACTCATGCCTTCGTAAACTTGCCGAAGATATAAGAAAGCCGAACCA\n+GACAAGAATGCCGGAGAACTTCATCAATTCATCACCTGCATTGAGCAGATTTTGCAGGTT\n+CTCAATAACCGGTAATCCAGCCCCAACGTTGGTGTCATAGAGGAATTTACGCCGCGATTT\n+TTCCGCCCGCATAACGCAACTGATGGTAGTAATCCATCGACGAGGTGTTTGCCTTTTTGT\n+TCGGCGTGACAACGTGGAAACCTTCGCGCCAGGAAGTCGGCATATTGATCCGCCACCTGC\n+CTGGCTGGAAGTGCAGTCAACAATGACCGGGTTTCAGCAGATGATATTCTTTTCACAAGG\n+CGAGTTAGCGCCCGGGATAAACGGCTCTTGGCTTGCGCCAGTTCTTCCTGCCAGTTTTCC\n+AGATTAAGGCCCATGTAATTGGTGAGCAGAGCCTTCGAGTTGGCAACACCGCAGACACGT\n+AAGTCGATTATTTTATTCTTCAGCCCAGCTTTGCTGACGCGCTTCAGTTGCTCCAGCAGC\n+GGCACCGCCAACGCCACCGACGCCAATCACAAACACTTCGATAACCTGATCGGTATTGAA\n+CAGGCATCTGATGAGTAACGCGCACGCCAGTGGTCGCATCATCGTTATTTACCACGACAC\n+GAGATTGAGCGTTCAGAAGATCCCTGAGCAATGGCGACAATGTTGATATTTGGCGCGGCC\n+AGGCGGCAAAGAATTCTCGCCGAGATCCCACGCAAGGTGCGCATACCATCACCTCCCACG\n+AGATAAATGGCCAGCCGTTCCGCACTGCCAGCGGCTCCCAGTAGCCTTCTTTCAGTTCCA\n+GGTAGAACTCTCCTGGCATGCCCGTTCAGCTCGCACACAGTCGCTTTGTGGAACGCAGAA\n+ACTAATGCGTATTCGGAAAGATGATTGCGTAATCAGCCACACGGAAATACCGGGCGCGTG\n+ACATCGGCTGCAAAGCGCGCCGCCGCCATGCCGACCATCCTATCATCCCCGGACCAGAAC\n+GCTGAAACATGCCATGTTAATTCAGATTGGAAATGGTTCCCTTGACCGGTAATTCGTCTT\n+CAACACGGCTGGCACCAATTAGCGTACCTGGTGCTTGAGGATTTCCGGTATTTTTTAATC\n+AGGCAAAGGGATCTGGAACTGGGCGATGGGGGTAATGGTGCGGGTGAAGAACTTTAGCGC\n+CGAAAGTAGGAAACCCATCGCTTCCTGGTAGGAACATCGACTTCAACAACCTCGCATCGG\n+GGCCACCTGACGCGGGTCGCAGGTATAGACCCCCGTCAACGTCCGCCAAATCTCGCAACA\n+ATCGGGGCCCGTAAACAGGCAGCCAGCACCGCAGCAGAAGTAGTCGGAACCGTTGCGTCC\n+AAGCACCACNAGTTCGCCTTTTTCATTACCGGCGGGGGAACCTGCCATCAGCACGCATGT\n+GATCAGCCGGAATGCAGGGCTTGCCGCAATTAGGCGGGTGGACTCAGGAAATCGACGGTA\n+GATTCGAGGTAATGCCCCACCGCCAGCAGTTTTTCGACCGGATCGATAACCTAAGTACTT\n+GTGACGCCGGCGCCGTCTATACGCCGGCATAAATGGCGAGCGACATTTCTCGCCACGGCC\n+AAAATCGAGCGCCAGCGTTTGATGCTAATCCGGCACTGCCCAACAAACTATTGCCATGGG\n+CAGACATGTTTTATTGGGCCAAATTCCTGATCGACGAAAGTTTTCAATGCGCCAGCGGGA\n+ACCCCCGGCGGGGCGGCGGCGGTCTACCAGGTCAAAAGGTATCGGCAAAAAATACGTTGG\n+CCATCGCGATTATTGGTAAAGCATCCTGGCCCCTAAATGGTATTTTGTCAATTCATCGAC\n+ACCAAGGTGTTGGTGATTTTTGCGGGCGGGTCAGAGAGGGACGGTGGGCCTACCTGCCTC\n+CTGCCTTCGGCTCGGCTTTCTAGAATATCGGCAAACACGCGAAAAAACGTTCTGCATTTG\n+>contig_3\n+CCACTGATGATACCGCCCGAAACTTCAACACTCGCATGGTGTTTACCTCGTTACCTTTGG\n+TCGAAAAAAAAAGCCCCGCACTGTCTAAAGGTGGCGGGCTTNTATTACATGTGTTTCCGT\n+ACGCGTACGGCCCCGCTACCGATACCTGTGGTAATCGGTGAATGTGGGGGTATACGGTGG\n+TGCTATCGTTTTCATGGATGTTGATGAATCTCTGGTATTTTTATCTGTCGGTGCGCTAGG\n+CCTATATTGGTTAAAAATATTTGTGGTTCCGAGTCAATAAAATTTTTAATTTACCACGGG\n+GCCCAAGGAAACCAGTTCAATAAACATGCTATCAGACACCTTTTTTTAGATCCACC\n' 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| diff -r 000000000000 -r 5799092ffdff test-data/dataset_04.gfa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dataset_04.gfa Wed Mar 09 10:29:20 2022 +0000 |
| b |
| b'@@ -0,0 +1,3 @@\n+H\tVN:Z:1.0\n+S\tedge_1\tTTTCCTTTTCCTACTGTACTTCTCAAATATTCCAGGCGACTTTCGTGATGATTCACAGCATGTTTCACGATTCGCTAACCCTAATCCGCTACCGCGGTTAGCCGGGAACCCCGCTTTATCAACGCGATAAAAACGCTTCGGTCAGGCCGCGGAATAATGCTCCGGTGCAATGCCCCGGGTCCGTTATCTTCAACGCTAAATTCGGCACCGTGCGGCACTCGCTGCCAGCGTACGGTGATATGCGTGCCCTTCCGGCGTATGGATTCACGCGTTATTAGACCAGGTTTGAAATCGCACTGCGGTAGCTGATCTTCGTTTGCCAGACACCTTGAGGCCGTTATCTATCTCAAAGGTAAATGTCTGTTTTTCTGACTCAGAGTCTGAGCCTCGCGCTCAACAACGCGCAGCATCATCGGCACAATCAACCTTTTCATTTGAGGAATGCGTCGGTGCGGCTTCTATTTTCGACAGCGTCAGCAAATGCTTCACCAGGTCCTTCCATCCCGCTGGGTCTGCTCGCGCATGGTGTGCAACGCTTTTTCGCGTACCGCGCCTTCCAGCGGCTGCTCAATTCATCATCTCCAGGTAACCCCTGTAACACGGTCCAATGGCGTACGTAACTCATGGCTCACCGTTGGCAAAAAAGTTACGCCGCGCCCCTTCCAGTTGATGCATTTGCGTGACATCACGCGCCACCATCAGCAACTGTTTGTGGGTATAAGGCATGACGCGAATTTCCAGATGCCGCCCGGTGGTTTGAGCACAGATTGAGCGGGCGAGAAAAATCACGCGTTTTCAGATATTGCGTAAACTCCGGGTAAACGCAGTAGTTAAGGATGTTCTGCCCGTTATCTTCCGGCCAGCGCAAACCAAGAAATTTGTTGCGCCAGACCGTTACACCAGAAAATACCGCCCTTTTCCTGGTCAGCACCACCGCGTCGGGCAGCGACTCCGCGCCGCTACGAAAAGCGTTTAATCAGATTGCCCACTGTTCACGGCGGGCGTTTTTTATTTCCGCAGCTGCATCTGGTGTAAGCCGTATAGTAGCGGTTCCCAGCTACCACCGCCCCGGTGGCGGGGTCATACTGCGATCCCACCCAACAGCCACCATGAAAAGGCGCAATAAATTCCAGAAATGCCAGATAAGCAGTCCTGTTACCGATGCCAGCAAAAACCAGGGCAGGTAACCAAAAAATGCACCCAAGGATGAAAGCCGGGAGGCAGCAAAGTAGCAGCTCCAGCACCAGGCCTTTCCACGACAGCCGTTCCAGCACCGTAAGATACTCCAGTTAAGAAAATCATAAGCCCTGCTCTGCGCCGGAGAGCAAGGCGTTAAAAGCGGGGTTGAAAAACGATTATCCTGTACCGCGCACGGTCTGCCACCATGCGGTCATGCCCGCCGGGCTCCAGAGCTTTACGCAGGCGACGAATGTGGACATCGACCGTGCGGTCTTCCACATACACGTTAGTTCCCAGACGTGTTTAACAGCTGCTCGCGCTGTACACGCGCTCAGGATGCGTCATAAAAAAGTGCAGCAGTTTTAAATTCTGTCGGCCCCATCTCCAGCGGCTCTTCGCCCGCCATCACTCGGTGAGATGTCGGGTCGAGACTTAATCCCTGCATCTTAATCACCTCTTCCACCGCCATTGGCGAAATACGGCGCATTACCGCTTTGATTCGCGCCACCAGCTCCTTCGGCGAAAACGGCTTGGTGATATAGTCATCCGCGCCGGTTTCAAGCCGCGCACGCGATCTTCTTCTTTCCCCTCTGGCGGTCAACATCACCACTGGGAATATCCCGGGGTCATCGACTCGCGCTTGAGGTGTTTGATGAACTGGATACCGGAGCCGCCAGGTAACATCCAGTCGAGGAGAATTAAAATCCGGCCAGGGTTCATTCAGTTTGATTCACAGCACTGTCATAATCTTCCGCTTCGACCGGCTGAAAGCCATTTTGTTCGAGCACGAAGAGAGACCAATTTCGGCGAATTGGAGCTTCATCTTCTACGACCAGAATACGTCTCGCCATGATTTGCCCTGTTGTAATAAATAGGTTGCGATCATTAATGCGACGTCATTATGCGTCAGATTTATGACAGATTTATGAAAAGCCTCGTCGCACAATATCTTCAGGTTATTGATTTCCGTGGCGCAGAAAAAAGCAAATGGCACCATCTGTTTGGGTATAATCGCGCCCATGCTTTTTCGCCAGGGAACCGTTATGCGCATCCTTCACACCTCAGACTGGCATCTCTGGCCAGAACTTCTACAGTAAAAGCCGCGAAGCTGAACAATAGGCTTTTCCTTGACTGGCTGCTGGAGACAGCACAAACCCATCAGGTGGATGCGATTATTGTTGCCGGTGATGTTTTCGATACCGGCTCGCCCGCCCAGTTACGCCCGCACGTTATACAACCGTTTTGTTGTCAATTTACAGCAAACTGGCTTTCATCTGGTGGTACTGGCAGGAAACCATGACTCGGTCGCCACGCTGAATGAATCGCGCGATATCATGGCGTCCTCAATACTACCGTGGTCGCCAGCGCCGGACATGCGCCGCAAATCTTGCCTCGTCGCGACGGGACGGCCAGGCGCAGTGCTGTGCCCCATTCCCGTTTTTACGTCCGCGTGACATTATTACCAGCCAGGCGGGGCTTAACGGTATTGAAAAACAGCAGCATTTACTGGCAGCGATTACCGATTATTACCAACAACACTATGCCGATGCCTGCAAACTGCGCGGCGATCAGCCTCTGCCCATCATCGCCACGGGACATTTAACGACCGTGGGGGCCAGTAAAAGTGACGCCGTGCGTGACCATTTATATTGGCACGCTGGACGCGTTTCCGGCACAAAACTTTCCACCAGCCGACTACATCGCGCTCGGGCATATTCACCGCGCACAGATTATTGGCGGCATGGAACATGTTCGCTATTGCGGCTCCCCCATTCCACTGAGTTTTGATGAATGCGGTAAGAGTAAATATGTCCATCTGGTGACATTTTCAAACGGCAAATTAGAGAGCGTGGAAAACCTGAACGTACCGGTAACGCAACCCATGGCAGTGCTGAAAGGCGATCTGGCGTCGATTACCGCACAGCTGGAACAGTGGCGCGATGTATCGCAGGAGCCACCTGTCTGGCTGGATATCGAAATCACTACTGATGAGTATCTGCATGATATTCAGCGCAAAATCCAGGCATTAACCGAATCATTGCCCTGTCGAAGTATTGCTGGTACGTCGGAGTCGTGAACAGCCCGAGCGTGTGTTAGCCAGCCAACAGCGTGAAACCCTCAGCGAACTCAGCGTCGAAGAGGGTGTTCAATCGCCGTCTGGCACTGGAAGAACTGGATGAATCGCAGCAGCAACGTCTGCAGCATCTTTTCACCACGACGTTGCATACCCTCGCCGGGAGAACACGAAGCATGAAAATTCTCAGCCTGCGCCTGAAAAACCTGAACTCATTAAAAGGCGAATGGAAGATTGATTTCACCCGCGAGCCGTTCGCCAGCAACGGCTGTTTGCTATTACCGGCCCAACAGGTGCGGGGAAAACCACCCTGCTGGACGCCATTTGTCTGGCGCTGTATCACGAAACTCCGCGTCTCTCTAACGTTTCACAATCGCAAAATGATCTCATGACCCGCGATACCGCCGAATGTCTGGCGGAGGTGGAGTTTGAAGTGAAAGGTGAAGCGTACCGTGCATTCTGGAGCCAGAATCGGGCGCGTAACCAACCCGACGGTAATTTGCAAGGGCCACGCGTAGAGCTGGCGCGCTGCGCCGACGGCAAAATTCTCGCCGACAAAGTGAAAGATAAGCTGGAACTGACAGCGCGGTTAACCGGGCTGGATTACGGGCGCTTCACCCGTTCGATGCTGCTTTCGCAGGGGCAATTTGCTGCCTTCCTGAATGCCAAACCCAAAGAACGCGCGGGAATTGCTCGAGGAGGTTAACC'..b'CACCAATAAACGCCGAGAGGATCTCGCACTTGCGGGTGACAAAATCCAGCTTCAGCATCTCATCAATTTCAGTCAGGCTGAATTCCGGCAGGTCGTGCGGAAAAAACAGCCCCTGATTTTTGCCCAAACCCCTGGGTTACGCTTGCGCAAAGCTGACCTGCCTCGTTGTGATCTTTCAGATTGAGGTTTCATTTAGTTTTCCAGTACTCGTGCGCCCCCCGTATCCAGCCGGCAAATATGACAAAACCTTCCTGATTTTGCAGGTAGTTCTTACCCAACCAGTCGGCAACGCGCGGGGCGGTTTCCGGCTTGTCACACAGAGCGAACAAGGTCCGGGCCGGAGCCGGAGATACCGCTCGCTACCGCGCCATTTCCGCGACCGCCTGCCGCGCCTGCCGGAAGCCTGGCAGTAACCGTTCACGGTAGGTTCACGCGATAACATCTTTTCATACAGCGTTCGCGGCAAGCTCAGGCTGACGGGAATAGCAGGCGTGAATGAAGCCTGCCAGATGTCGCCCGTGCGCAATGCAATCCTGGCGCGATACTGCCCCGGTAAAATAGCCCTGGCTTTTCCGTCGAGACTTTAATCCCCGGATACGCCAGCACCCACAGCCACTCATCCAAACCTGGCACTTGCTGGCTGATGATGTCGTTTTCTTCGATCATCAACTGCATACCACCGAGAAAACACGGTGCCACGTTGTCGTAATGAATGCTGCCGGAGATACGGCCTTCCAGCTCGCCCATCAAAAGCCAGCGAACGAGTGTCATTAAGCGGCTTGCCGCAGTGTTCAATTTCATCCCATCAGCGCCGCGACCACGAAACAGGCACTGGAGCCTAAGCCCGAACCGATCGGCATATTCTTTTCCAGGGTCATCGCCACTGGAATTTGCTTACCCAGTTCCTGGCAAAAACGCCTCCCAGCACTGATAAACGATATTTTCCCGTGGTTTCTGACGGCAGCCTTATCCGGGCAAAGCGTCCGAGGTTGTTGAGACTGAATGTCTCTGCCGCCTCAACCGTGACTACATCTCCGAGCAATGCACCATCAACAGGTGTCACCGCCGCCCCGAGCACATCAAACCCGACGCTCATATTGGCACTGGAAGCCGGGGCATAAACTTTAACCATTTTCAGACTCCTAACTTCCATGAGAGGGTACGTAGCAGATCAGCAAAGACACCGGCAGCTGTAACCGTCAATTTGCCCGCACCATATCCGCGCAGTACCAAACGGCAAGCGGCTGATAATAGTGGCTTAAGAGCCAGGGCGTTTTCGCCATTTTTCACTTTGAACAGCGGATCATTACCATCCACTTCGGCAATCTTCACGCGGCAGACGCCATCTTCATCAATATTGCCAACATAGCGCAAAACCTTTCCCTTCATCACGGGCCTTCGCCACGCGCGCGGCAAAGAGATCGTCGAGTTGTGACAGATTCGCCATAAAAGCGGCAACATCACCCTCGGCGTTAACCTCTGCGGGGCAGCACAGGTTCAATTTCAATATCCGCCAGCTCCAGTTCACTCCCGTTTCACGAGCGAGAATCAATAGTTTACGCGCCACATCCATACCAGAAAGATCATCTCGCCGGGTCCGGTTCGGTATAACCCATTTCCCGACGCAGCGTGGTCGCCTCGGAGAAACTCATGCCTTCGTAAACTTGCCGAAGATATAAGAAAGCCGAACCAGACAAGAATGCCGGAGAACTTCATCAATTCATCACCTGCATTGAGCAGATTTTGCAGGTTCTCAATAACCGGTAATCCAGCCCCAACGTTGGTGTCATAGAGGAATTTACGCCGCGATTTTTCCGCCCGCATAACGCAACTGATGGTAGTAATCCATCGACGAGGTGTTTGCCTTTTTGTTCGGCGTGACAACGTGGAAACCTTCGCGCCAGGAAGTCGGCATATTGATCCGCCACCTGCCTGGCTGGAAGTGCAGTCAACAATGACCGGGTTTCAGCAGATGATATTCTTTTCACAAGGCGAGTTAGCGCCCGGGATAAACGGCTCTTGGCTTGCGCCAGTTCTTCCTGCCAGTTTTCCAGATTAAGGCCCATGTAATTGGTGAGCAGAGCCTTCGAGTTGGCAACACCGCAGACACGTAAGTCGATTATTTTATTCTTCAGCCCAGCTTTGCTGACGCGCTTCAGTTGCTCCAGCAGCGGCACCGCCAACGCCACCGACGCCAATCACAAACACTTCGATAACCTGATCGGTATTGAACAGGCATCTGATGAGTAACGCGCACGCCAGTGGTCGCATCATCGTTATTTACCACGACACGAGATTGAGCGTTCAGAAGATCCCTGAGCAATGGCGACAATGTTGATATTTGGCGCGGCCAGGCGGCAAAGAATTCTCGCCGAGATCCCACGCAAGGTGCGCATACCATCACCTCCCACGAGATAAATGGCCAGCCGTTCCGCACTGCCAGCGGCTCCCAGTAGCCTTCTTTCAGTTCCAGGTAGAACTCTCCTGGCATGCCCGTTCAGCTCGCACACAGTCGCTTTGTGGAACGCAGAAACTAATGCGTATTCGGAAAGATGATTGCGTAATCAGCCACACGGAAATACCGGGCGCGTGACATCGGCTGCAAAGCGCGCCGCCGCCATGCCGACCATCCTATCATCCCCGGACCAGAACGCTGAAACATGCCATGTTAATTCAGATTGGAAATGGTTCCCTTGACCGGTAATTCGTCTTCAACACGGCTGGCACCAATTAGCGTACCTGGTGCTTGAGGATTTCCGGTATTTTTTAATCAGGCAAAGGGATCTGGAACTGGGCGATGGGGGTAATGGTGCGGGTGAAGAACTTTAGCGCCGAAAGTAGGAAACCCATCGCTTCCTGGTAGGAACATCGACTTCAACAACCTCGCATCGGGGCCACCTGACGCGGGTCGCAGGTATAGACCCCCGTCAACGTCCGCCAAATCTCGCAACAATCGGGGCCCGTAAACAGGCAGCCAGCACCGCAGCAGAAGTAGTCGGAACCGTTGCGTCCAAGCACCACCAGTTCGCCTTTTTCATTACCGGCGGGGGAACCTGCCATCAGCACGCATGTGATCAGCCGGAATGCAGGGCTTGCCGCAATTAGGCGGGTGGACTCAGGAAATCGACGGTAGATTCGAGGTAATGCCCCACCGCCAGCAGTTTTTCGACCGGATCGATAACCTAAGTACTTGTGACGCCGGCGCCGTCTATACGCCGGCATAAATGGCGAGCGACATTTCTCGCCACGGCCAAAATCGAGCGCCAGCGTTTGATGCTAATCCGGCACTGCCCAACAAACTATTGCCATGGGCAGACATGTTTTATTGGGCCAAATTCCTGATCGACGAAAGTTTTCAATGCGCCAGCGGGAACCCCCGGCGGGGCGGCGGCGGTCTACCAGGTCAAAAGGTATCGGCAAAAAATACGTTGGCCATCGCGATTATTGGTAAAGCATCCTGGCCCCTAAATGGTATTTTGTCAATTCATCGACACCAAGGTGTTGGTGATTTTTGCGGGCGGGTCAGAGAGGGACGGTGGGCCTACCTGCCTCCTGCCTTCGGCTCGGCTTTCTAGAATATCGGCAAACACGCGAAAAAACGTTCTGCATTTGCCACTGATGATACCGCCCGAAACTTCAACACTCGCATGGTGTTTACCTCGTTACCTTTGGTCGAAAAAAAAAGCCCCGCACTGTCTAAAGGTGGCGGGCTTTTATTACATGTGTTTCCGTACGCGTACGGCCCCGCTACCGATACCTGTGGTAATCGGTGAATGTGGGGGTATACGGTGGTGCTATCGTTTTCATGGATGTTGATGAATCTCTGGTATTTTTATCTGTCGGTGCGCTAGGCCTATATTGGTTAAAAATATTTGTGGTTCCGAGTCAATAAAATTTTTAATTTACCACGGGGCCCAAGGAAACCAGTTCAATAAACATGCTATCAGACACCTTTTTTTAGATCCACC\tdp:i:14\n+P\tcontig_1\tedge_1+\t*\n' |
| b |
| diff -r 000000000000 -r 5799092ffdff test-data/swiss_army.sak --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/swiss_army.sak Wed Mar 09 10:29:20 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +REMOVE s1_1 |
| b |
| diff -r 000000000000 -r 5799092ffdff test-data/test_01.fasta.gz |
| b |
| Binary file test-data/test_01.fasta.gz has changed |
| b |
| diff -r 000000000000 -r 5799092ffdff test-data/test_02_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_02_stats.tabular Wed Mar 09 10:29:20 2022 +0000 |
| b |
| @@ -0,0 +1,122 @@ +S1_1.1 8550 +S1_2.1 7716 +S1_3.1 11680 +S1_4.1 7905 +S1_5.1 12021 +S1_6.1 7535 +S1_7.1 3774 +S1_8.1 4002 +S1_9.1 818 +S1_10.1 8040 +S1_11.1 4951 +S1_12.1 2777 +S1_13.1 4975 +S1_14.1 1970 +S1_15.1 6421 +S1_16.1 12993 +S1_17.1 9676 +S1_18.1 10457 +S1_19.1 6588 +S1_20.1 9877 +S1_21.1 10161 +S1_22.1 13174 +S1_23.1 10948 +S1_24.1 7299 +S1_25.1 9275 +S1_26.1 8171 +S1_27.1 15460 +S1_28.1 10371 +S1_29.1 7355 +S1_30.1 12962 +S1_31.1 11416 +S1_32.1 2584 +S1_33.1 6403 +S1_34.1 20304 +S1_35.1 2112 +S1_36.1 9403 +S1_37.1 12680 +S1_38.1 5331 +S1_39.1 10575 +S1_40.1 6745 +S1_41.1 1726 +S1_42.1 584 +S1_43.1 12177 +S1_44.1 10685 +S1_45.1 17985 +S1_46.1 6247 +S1_47.1 14541 +S1_48.1 5116 +S1_49.1 13270 +S1_50.1 10349 +S1_51.1 8133 +S1_52.1 17530 +S1_53.1 6769 +S1_54.1 15243 +S1_55.1 3368 +S1_56.1 18590 +S1_57.1 7776 +S1_58.1 9517 +S1_59.1 2536 +S1_60.1 6591 +S1_61.1 2265 +S1_62.1 11983 +S1_63.1 6130 +S1_64.1 18784 +S1_65.1 2916 +S1_66.1 1722 +S1_67.1 7077 +S1_68.1 9185 +S1_69.1 11256 +S1_70.1 8081 +S1_71.1 10480 +S1_72.1 8337 +S1_73.1 23257 +S1_74.1 5090 +S1_75.1 14432 +S1_76.1 9445 +S1_77.1 8632 +S1_78.1 640 +S1_79.1 9024 +S1_80.1 7309 +S1_81.1 7576 +S1_82.1 6137 +S1_83.1 23652 +S1_84.1 8446 +S1_85.1 7779 +S1_86.1 8771 +S1_87.1 2880 +S1_88.1 3736 +S1_89.1 10444 +S1_90.1 7218 +S1_91.1 4958 +S1_92.1 872 +S1_93.1 13572 +S1_94.1 14845 +S1_95.1 721 +S1_96.1 5908 +S1_97.1 6951 +S1_98.1 586 +S1_99.1 3570 +S1_100.1 8100 +S1_101.1 6289 +S1_102.1 11870 +S1_103.1 7613 +S1_104.1 2728 +S1_105.1 13384 +S1_106.1 8650 +S1_107.1 9068 +S1_108.1 15459 +S1_109.1 5180 +S1_110.1 15834 +S1_111.1 3669 +S1_112.1 10059 +S1_113.1 2027 +S1_114.1 4478 +S1_115.1 14554 +S1_116.1 17267 +S1_117.1 7322 +S1_118.1 13737 +S1_119.1 6576 +S1_120.1 5659 +S1_121.1 14423 +S1_122.1 4355 |
| b |
| diff -r 000000000000 -r 5799092ffdff test-data/test_03_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_03_stats.tabular Wed Mar 09 10:29:20 2022 +0000 |
| b |
| b'@@ -0,0 +1,1697 @@\n+Seq\t1\n+Header\tbf06004a-705a-4fe9-942a-2dcabf04766e.1\n+Comment\t\n+Total segment length\t11188\n+Base composition (ACGT)\t2755, 2648, 2783, 3002\n+GC content %\t48.54\n+# soft-masked bases\t0\n+\n+Seq\t2\n+Header\t106a7186-c3b0-43dd-8289-34f8a0494fcf.1\n+Comment\t\n+Total segment length\t15267\n+Base composition (ACGT)\t3870, 3700, 3835, 3862\n+GC content %\t49.35\n+# soft-masked bases\t0\n+\n+Seq\t3\n+Header\te6a172b9-7593-4d0b-9f09-e85edaab94cf.1\n+Comment\t\n+Total segment length\t15699\n+Base composition (ACGT)\t3946, 3779, 3927, 4047\n+GC content %\t49.09\n+# soft-masked bases\t0\n+\n+Seq\t4\n+Header\t48744a56-dcfe-48e0-97ab-3b903ebdb60a.1\n+Comment\t\n+Total segment length\t14688\n+Base composition (ACGT)\t3551, 3670, 3692, 3775\n+GC content %\t50.12\n+# soft-masked bases\t0\n+\n+Seq\t5\n+Header\t94d29bbc-7b1e-4cc5-abaa-d26d744c82bb.1\n+Comment\t\n+Total segment length\t10592\n+Base composition (ACGT)\t2524, 2631, 2678, 2759\n+GC content %\t50.12\n+# soft-masked bases\t0\n+\n+Seq\t6\n+Header\t813565c4-b858-4289-979d-ed8db9603825.1\n+Comment\t\n+Total segment length\t17906\n+Base composition (ACGT)\t4239, 4509, 4722, 4436\n+GC content %\t51.55\n+# soft-masked bases\t0\n+\n+Seq\t7\n+Header\t392f8e7b-42bc-469c-81cd-199b5c068bd7.1\n+Comment\t\n+Total segment length\t14117\n+Base composition (ACGT)\t3392, 3580, 3794, 3351\n+GC content %\t52.23\n+# soft-masked bases\t0\n+\n+Seq\t8\n+Header\t805d527c-db18-465d-be1d-6ef52fa8f84f.1\n+Comment\t\n+Total segment length\t18959\n+Base composition (ACGT)\t4951, 4579, 4593, 4836\n+GC content %\t48.38\n+# soft-masked bases\t0\n+\n+Seq\t9\n+Header\tf4f56757-4761-4f86-a434-3d8c09be3b37.1\n+Comment\t\n+Total segment length\t8044\n+Base composition (ACGT)\t1909, 2034, 2120, 1981\n+GC content %\t51.64\n+# soft-masked bases\t0\n+\n+Seq\t10\n+Header\tc91c7a17-0d05-4248-b677-59617a91d4ce.1\n+Comment\t\n+Total segment length\t12004\n+Base composition (ACGT)\t3080, 3015, 3137, 2772\n+GC content %\t51.25\n+# soft-masked bases\t0\n+\n+Seq\t11\n+Header\t790136e4-0663-4d7a-b7e2-941f5d007754.1\n+Comment\t\n+Total segment length\t6684\n+Base composition (ACGT)\t1594, 1736, 1777, 1577\n+GC content %\t52.56\n+# soft-masked bases\t0\n+\n+Seq\t12\n+Header\te72d1741-ef41-4bc7-a49e-279c9f9b7263.1\n+Comment\t\n+Total segment length\t11195\n+Base composition (ACGT)\t2787, 2843, 3047, 2518\n+GC content %\t52.61\n+# soft-masked bases\t0\n+\n+Seq\t13\n+Header\t78e01914-94ca-4040-bd8e-6c99d7583512.1\n+Comment\t\n+Total segment length\t6987\n+Base composition (ACGT)\t1621, 1818, 1813, 1735\n+GC content %\t51.97\n+# soft-masked bases\t0\n+\n+Seq\t14\n+Header\te76596da-bcc2-4395-aa51-b96a89bf872f.1\n+Comment\t\n+Total segment length\t7674\n+Base composition (ACGT)\t1816, 1949, 1939, 1970\n+GC content %\t50.66\n+# soft-masked bases\t0\n+\n+Seq\t15\n+Header\ta6565705-c7a4-4365-9fd0-3b28c1919cdd.1\n+Comment\t\n+Total segment length\t7530\n+Base composition (ACGT)\t1920, 1881, 1950, 1779\n+GC content %\t50.88\n+# soft-masked bases\t0\n+\n+Seq\t16\n+Header\t81954f91-3ccd-4af8-9bd4-69a43b777235.1\n+Comment\t\n+Total segment length\t8752\n+Base composition (ACGT)\t1968, 2265, 2251, 2268\n+GC content %\t51.60\n+# soft-masked bases\t0\n+\n+Seq\t17\n+Header\t3328f98c-6f8c-4bad-a998-22e81b0f64d0.1\n+Comment\t\n+Total segment length\t7363\n+Base composition (ACGT)\t1868, 1823, 2003, 1669\n+GC content %\t51.96\n+# soft-masked bases\t0\n+\n+Seq\t18\n+Header\t1aff9669-f6d2-4ffd-8f77-4c99cef14421.1\n+Comment\t\n+Total segment length\t9608\n+Base composition (ACGT)\t2517, 2436, 2578, 2077\n+GC content %\t52.19\n+# soft-masked bases\t0\n+\n+Seq\t19\n+Header\tef00aaf4-8ba0-45ff-8df2-bcc01dbf8d50.1\n+Comment\t\n+Total segment length\t8167\n+Base composition (ACGT)\t2187, 2015, 2143, 1822\n+GC content %\t50.91\n+# soft-masked bases\t0\n+\n+Seq\t20\n+Header\tc22489fb-3bdb-484a-8c2a-e9706b7c40b3.1\n+Comment\t\n+Total segment length\t5406\n+Base composition (ACGT)\t1411, 1339, 1455, 1201\n+GC content %\t51.68\n+# soft-masked bases\t0\n+\n+Seq\t21\n+Header\t3c2169f8-24e7-455d-ae9f-44ca5224d990.1\n+Comment\t\n+Total segment length\t4455\n+Base composition (ACGT)\t967, 1187, 1121, 1180\n+GC content %\t51.81\n+# soft-masked bases\t0\n+\n+Seq\t22\n+Header\tdf422228-a7ac-47c4-bfa9-17b9b694b1de.1\n+Comment\t\n+Total segment length\t6143\n+Ba'..b'a-4f64-ae9a-5bac19dfe8eb.1\n+Comment\t\n+Total segment length\t10752\n+Base composition (ACGT)\t3023, 2001, 1932, 3796\n+GC content %\t36.58\n+# soft-masked bases\t0\n+\n+Seq\t192\n+Header\tcf9094c2-11c2-4ed0-acee-68798a448c56.1\n+Comment\t\n+Total segment length\t3135\n+Base composition (ACGT)\t884, 526, 564, 1161\n+GC content %\t34.77\n+# soft-masked bases\t0\n+\n+Seq\t193\n+Header\td6ef2e66-9547-488c-aa53-554531f03cd8.1\n+Comment\t\n+Total segment length\t2970\n+Base composition (ACGT)\t887, 545, 569, 969\n+GC content %\t37.51\n+# soft-masked bases\t0\n+\n+Seq\t194\n+Header\t16faf9c6-9887-41e4-97d2-4b9433c4c6b5.1\n+Comment\t\n+Total segment length\t5256\n+Base composition (ACGT)\t1862, 942, 968, 1484\n+GC content %\t36.34\n+# soft-masked bases\t0\n+\n+Seq\t195\n+Header\t15e1d478-ee33-4a38-99f0-4fce40af07c2.1\n+Comment\t\n+Total segment length\t1103\n+Base composition (ACGT)\t348, 191, 184, 380\n+GC content %\t34.00\n+# soft-masked bases\t0\n+\n+Seq\t196\n+Header\t5aad2a5c-2896-419c-8aab-4bc1238fea95.1\n+Comment\t\n+Total segment length\t5515\n+Base composition (ACGT)\t1489, 987, 1034, 2005\n+GC content %\t36.65\n+# soft-masked bases\t0\n+\n+Seq\t197\n+Header\ta7d909b6-faa4-4bfa-bd82-3e2afd8d2185.1\n+Comment\t\n+Total segment length\t5784\n+Base composition (ACGT)\t1823, 985, 999, 1977\n+GC content %\t34.30\n+# soft-masked bases\t0\n+\n+Seq\t198\n+Header\tce713eb6-99b4-4dc3-83d3-056664bfcd99.1\n+Comment\t\n+Total segment length\t8283\n+Base composition (ACGT)\t2271, 1489, 1481, 3042\n+GC content %\t35.86\n+# soft-masked bases\t0\n+\n+Seq\t199\n+Header\t81f3e7bf-4e15-43f6-8a83-6bd617991df9.1\n+Comment\t\n+Total segment length\t8421\n+Base composition (ACGT)\t3009, 1522, 1533, 2357\n+GC content %\t36.28\n+# soft-masked bases\t0\n+\n+Seq\t200\n+Header\ta281deab-38f6-4e16-9129-a9dd00a14fcf.1\n+Comment\t\n+Total segment length\t5802\n+Base composition (ACGT)\t1537, 1023, 1072, 2170\n+GC content %\t36.11\n+# soft-masked bases\t0\n+\n+Seq\t201\n+Header\t325f1331-dec9-41b8-a69f-028b36681560.1\n+Comment\t\n+Total segment length\t5557\n+Base composition (ACGT)\t1863, 1027, 1028, 1639\n+GC content %\t36.98\n+# soft-masked bases\t0\n+\n+Seq\t202\n+Header\t140e6d68-cc21-4c3c-b854-de9594320be2.1\n+Comment\t\n+Total segment length\t4627\n+Base composition (ACGT)\t1663, 865, 858, 1241\n+GC content %\t37.24\n+# soft-masked bases\t0\n+\n+Seq\t203\n+Header\tbc025485-f152-4e18-ab61-740da71cc8a3.1\n+Comment\t\n+Total segment length\t2941\n+Base composition (ACGT)\t812, 484, 542, 1103\n+GC content %\t34.89\n+# soft-masked bases\t0\n+\n+Seq\t204\n+Header\t751f281c-c196-4257-9580-e203e4da2aeb.1\n+Comment\t\n+Total segment length\t5891\n+Base composition (ACGT)\t1611, 1152, 1164, 1964\n+GC content %\t39.31\n+# soft-masked bases\t0\n+\n+Seq\t205\n+Header\t9035679c-4e33-44f0-8f57-b4e7791d2616.1\n+Comment\t\n+Total segment length\t5428\n+Base composition (ACGT)\t1864, 971, 1118, 1475\n+GC content %\t38.49\n+# soft-masked bases\t0\n+\n+Seq\t206\n+Header\ta2d82a53-518c-4224-8f89-41723c3fa434.1\n+Comment\t\n+Total segment length\t4661\n+Base composition (ACGT)\t1680, 847, 872, 1262\n+GC content %\t36.88\n+# soft-masked bases\t0\n+\n+Seq\t207\n+Header\t48f635ff-a554-4baf-b00d-04b89da3c499.1\n+Comment\t\n+Total segment length\t855\n+Base composition (ACGT)\t304, 156, 159, 236\n+GC content %\t36.84\n+# soft-masked bases\t0\n+\n+Seq\t208\n+Header\t88a5ba1b-a388-48d1-964c-71f836904291.1\n+Comment\t\n+Total segment length\t1435\n+Base composition (ACGT)\t432, 231, 238, 534\n+GC content %\t32.68\n+# soft-masked bases\t0\n+\n+Seq\t209\n+Header\t5f3b0d4d-e80b-4ec9-bc9f-8f642acef345.1\n+Comment\t\n+Total segment length\t2360\n+Base composition (ACGT)\t852, 419, 400, 689\n+GC content %\t34.70\n+# soft-masked bases\t0\n+\n+# scaffolds\t209\n+Total scaffold length\t1466260\n+Average scaffold length\t7015.60\n+Scaffold N50\t9054\n+Scaffold auN\t9961.88\n+Scaffold L50\t59\n+Largest scaffold\t27298\n+# contigs\t209\n+Total contig length\t1466260\n+Average contig length\t7015.60\n+Contig N50\t9054\n+Contig auN\t9961.88\n+Contig L50\t59\n+Largest contig\t27298\n+# gaps\t0\n+Total gap length\t0\n+Average gap length\t-nan\n+Gap N50\t0\n+Gap auN\t0.00\n+Gap L50\t0\n+Largest gap\t0\n+Base composition (ACGT)\t418269, 304935, 314298, 428758\n+GC content %\t42.23\n+# soft-masked bases\t0\n+# paths\t209\n' |
| b |
| diff -r 000000000000 -r 5799092ffdff test-data/test_04_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_04_stats.tabular Wed Mar 09 10:29:20 2022 +0000 |
| b |
| @@ -0,0 +1,132 @@ +Expected genome size 600000 +# scaffolds 3 +Total scaffold length 419576 +Average scaffold length 139858.67 +Scaffold N50 417540 +Scaffold auN 415520.91 +Scaffold L50 1 +Scaffold NG50 417540 +Scaffold auNG 290571.00 +Scaffold LG50 1 +Largest scaffold 417540 +# contigs 6 +Total contig length 419573 +Average contig length 69928.83 +Contig N50 416949 +Contig auN 414345.81 +Contig L50 1 +Contig NG50 416949 +Contig auNG 289747.19 +Contig LG50 1 +Largest contig 416949 +# gaps 3 +Total gap length 3 +Average gap length 1.00 +Gap N50 1 +Gap auN 1.00 +Gap L50 2 +Largest gap 1 +Base composition (ACGT) 102144, 112550, 104859, 100020 +GC content % 51.82 +# soft-masked bases 0 +# paths 3 +Scaffold N10 417540 +Scaffold N20 417540 +Scaffold N30 417540 +Scaffold N40 417540 +Scaffold N50 417540 +Scaffold N60 417540 +Scaffold N70 417540 +Scaffold N80 417540 +Scaffold N90 417540 +Scaffold N100 356 +Scaffold L10 1 +Scaffold L20 1 +Scaffold L30 1 +Scaffold L40 1 +Scaffold L50 1 +Scaffold L60 1 +Scaffold L70 1 +Scaffold L80 1 +Scaffold L90 1 +Scaffold L100 3 +Scaffold NG10 417540 +Scaffold NG20 417540 +Scaffold NG30 417540 +Scaffold NG40 417540 +Scaffold NG50 417540 +Scaffold NG60 417540 +Scaffold NG70 0 +Scaffold NG80 0 +Scaffold NG90 0 +Scaffold NG100 0 +Scaffold LG10 1 +Scaffold LG20 1 +Scaffold LG30 1 +Scaffold LG40 1 +Scaffold LG50 1 +Scaffold LG60 1 +Scaffold LG70 0 +Scaffold LG80 0 +Scaffold LG90 0 +Scaffold LG100 0 +Contig N10 416949 +Contig N20 416949 +Contig N30 416949 +Contig N40 416949 +Contig N50 416949 +Contig N60 416949 +Contig N70 416949 +Contig N80 416949 +Contig N90 416949 +Contig N100 101 +Contig L10 1 +Contig L20 1 +Contig L30 1 +Contig L40 1 +Contig L50 1 +Contig L60 1 +Contig L70 1 +Contig L80 1 +Contig L90 1 +Contig L100 6 +Contig NG10 416949 +Contig NG20 416949 +Contig NG30 416949 +Contig NG40 416949 +Contig NG50 416949 +Contig NG60 416949 +Contig NG70 0 +Contig NG80 0 +Contig NG90 0 +Contig NG100 0 +Contig LG10 1 +Contig LG20 1 +Contig LG30 1 +Contig LG40 1 +Contig LG50 1 +Contig LG60 1 +Contig LG70 0 +Contig LG80 0 +Contig LG90 0 +Contig LG100 0 +Gap N10 1 +Gap N20 1 +Gap N30 1 +Gap N40 1 +Gap N50 1 +Gap N60 1 +Gap N70 1 +Gap N80 1 +Gap N90 1 +Gap N100 1 +Gap L10 1 +Gap L20 1 +Gap L30 1 +Gap L40 2 +Gap L50 2 +Gap L60 2 +Gap L70 3 +Gap L80 3 +Gap L90 3 +Gap L100 3 |
| b |
| diff -r 000000000000 -r 5799092ffdff test-data/test_05_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_05_stats.tabular Wed Mar 09 10:29:20 2022 +0000 |
| b |
| @@ -0,0 +1,1 @@ +edge_1 1 419576 1 W edge_1 1 419576 + |
| b |
| diff -r 000000000000 -r 5799092ffdff test-data/test_06.fasta.gz |
| b |
| Binary file test-data/test_06.fasta.gz has changed |
| b |
| diff -r 000000000000 -r 5799092ffdff test-data/test_07_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_07_stats.tabular Wed Mar 09 10:29:20 2022 +0000 |
| b |
| @@ -0,0 +1,86 @@ ++++Summary+++: +# scaffolds: 3 +Total scaffold length: 419576 +Average scaffold length: 139858.67 +Scaffold N50: 417540 +Scaffold auN: 415520.91 +Scaffold L50: 1 +Largest scaffold: 417540 +# contigs: 6 +Total contig length: 419573 +Average contig length: 69928.83 +Contig N50: 416949 +Contig auN: 414345.81 +Contig L50: 1 +Largest contig: 416949 +# gaps: 3 +Total gap length: 3 +Average gap length: 1.00 +Gap N50: 1 +Gap auN: 1.00 +Gap L50: 2 +Largest gap: 1 +Base composition (ACGT): 102144, 112550, 104859, 100020 +GC content %: 51.82 +# soft-masked bases: 0 +# paths: 3 +Scaffold N10: 417540 +Scaffold N20: 417540 +Scaffold N30: 417540 +Scaffold N40: 417540 +Scaffold N50: 417540 +Scaffold N60: 417540 +Scaffold N70: 417540 +Scaffold N80: 417540 +Scaffold N90: 417540 +Scaffold N100: 356 +Scaffold L10: 1 +Scaffold L20: 1 +Scaffold L30: 1 +Scaffold L40: 1 +Scaffold L50: 1 +Scaffold L60: 1 +Scaffold L70: 1 +Scaffold L80: 1 +Scaffold L90: 1 +Scaffold L100: 3 +Contig N10: 416949 +Contig N20: 416949 +Contig N30: 416949 +Contig N40: 416949 +Contig N50: 416949 +Contig N60: 416949 +Contig N70: 416949 +Contig N80: 416949 +Contig N90: 416949 +Contig N100: 101 +Contig L10: 1 +Contig L20: 1 +Contig L30: 1 +Contig L40: 1 +Contig L50: 1 +Contig L60: 1 +Contig L70: 1 +Contig L80: 1 +Contig L90: 1 +Contig L100: 6 +Gap N10: 1 +Gap N20: 1 +Gap N30: 1 +Gap N40: 1 +Gap N50: 1 +Gap N60: 1 +Gap N70: 1 +Gap N80: 1 +Gap N90: 1 +Gap N100: 1 +Gap L10: 1 +Gap L20: 1 +Gap L30: 1 +Gap L40: 2 +Gap L50: 2 +Gap L60: 2 +Gap L70: 3 +Gap L80: 3 +Gap L90: 3 +Gap L100: 3 |
| b |
| diff -r 000000000000 -r 5799092ffdff test-data/test_08.fasta.gz |
| b |
| Binary file test-data/test_08.fasta.gz has changed |