| Next changeset 1:37b5e1f0b544 (2020-07-16) |
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Commit message:
planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6 |
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added:
spaln.xml test-data/genome.fasta test-data/output1.bed12 test-data/output1.tabular test-data/output1_gff_genes.gff3 test-data/output1_gff_matches.gff3 test-data/query.fasta |
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| diff -r 000000000000 -r 95ea8d97abb4 spaln.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/spaln.xml Fri Jan 11 18:15:21 2019 -0500 |
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| @@ -0,0 +1,84 @@ +<tool id="spaln" name="Spaln: align cDNA or Protein to genome" version="@TOOL_VERSION@+galaxy0"> + <description>Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</description> + <macros> + <token name="@TOOL_VERSION@">2.3.2</token> + </macros> + <edam_topics> + <edam_topic>topic_3512</edam_topic> + </edam_topics> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">spaln</requirement> + </requirements> + <command detect_errors="aggressive"><![CDATA[ + spaln -t\${GALAXY_SLOTS:-1} -O$format -o '$output1' '$genome' '$query' + ]]></command> + <inputs> + <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" /> + <param type="data" name="query" format="fasta" label="Query sequence(s) (protein or cDNA)" /> + <param argument="-O" type="select" name="format" label="Output format"> + <option value="0">GFF3 format genes</option> + <option value="2">GFF3 format matches</option> + <option value="3">BED format</option> + <option value="4">Tabular format exon information</option> + </param> + </inputs> + <outputs> + <data name="output1" format="tabular"> + <change_format> + <!-- these values correspond with the format options of the spaln command, not all of which are current supported --> + <when input="format" value="0" format="gff3" /> + <when input="format" value="2" format="gff3" /> + <when input="format" value="3" format="bed12" /> + <when input="format" value="4" format="tabular" /> + </change_format> + <!-- <actions> .. <conditional> .. <when> .. <action> current does not work in Galaxy, + something that https://github.com/galaxyproject/galaxy/pull/7197 is addressing, so this is + commented out till that is merged + <actions> + <conditional name="format"> + <when value="4"> + <action type="metadata" name="column_names" default="rID,gID,%id,ExonL,MisMch,Unpair,ref_l,ref_r,tgt_l,tgt_r,eScore,IntrnL,iScore,Sig3/I,Sig5/T # - X P DiNuc" /> + </when> + </conditional> + </actions> + --> + </data> + </outputs> + <tests> + <test> + <param name="genome" ftype="fasta" value="genome.fasta" /> + <param name="query" ftype="fasta" value="query.fasta" /> + <param name="format" value="0"/> + <output name="output1" value="output1_gff_genes.gff3" /> + </test> + <test> + <param name="genome" ftype="fasta" value="genome.fasta" /> + <param name="query" ftype="fasta" value="query.fasta" /> + <param name="format" value="2"/> + <output name="output1" value="output1_gff_matches.gff3" /> + </test> + <test> + <param name="genome" ftype="fasta" value="genome.fasta" /> + <param name="query" ftype="fasta" value="query.fasta" /> + <param name="format" value="3"/> + <output name="output1" value="output1.bed12" /> + </test> + <test> + <param name="genome" ftype="fasta" value="genome.fasta" /> + <param name="query" ftype="fasta" value="query.fasta" /> + <param name="format" value="4"/> + <output name="output1" value="output1.tabular" /> + </test> + </tests> + <help><![CDATA[ + Spaln_ (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or + protein sequences onto a whole genomic sequence in a single job. + + This Galaxy wrapper currently only supports the default (i.e. *-O3*) algorithm for Spaln with default parameters. + + .. _Spaln: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ + ]]></help> + <citations> + <citation type="doi">0.1093/nar/gkn105</citation> + </citations> +</tool> |
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| diff -r 000000000000 -r 95ea8d97abb4 test-data/genome.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fasta Fri Jan 11 18:15:21 2019 -0500 |
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| b'@@ -0,0 +1,1000 @@\n+>scaffold_1\n+TGCTTTTCTGAGATTTATGTCAGCTCCCCATTGGGAGATACAGGAGAATCCAATATATTC\n+CTGTCTCGCTTCTTTTATATTTATCCTTTCTACACCTGACATCCTCAGTGATTGAAGTGA\n+CAAAAAGTGGAGCGCACGCAGTGGTCATTACCCTCCAATGGTACTTCTAATTAAGGAAAG\n+ATTTTTTGCATTCACTGAGCAAAACACTTATTTGCATGAATGGAAAATCATAAATGAGGG\n+GTCCATTAAACAAATTTCCTAATTGTTTGCTTTTTTTTCTTCCTACTTCACCATCCCTCT\n+AAAGCTATTACTCTCTATTCTACCCCATTATCGAGTGCACAAACACCAGCCCCAAATTGT\n+CTTATCTCTGCTTTGATAAATGATATTTTTTTCTCTTATAATTGTGTTTCTCTCTAGATG\n+TGCGGTGTCCATCAAGACACTGGATGTCACGTGGTCACTCCTGTGAAGAGCGAACTGTGT\n+GGAACCCGAAGTACTGTGTGGTTGCTGACTGTCAGATGCTGCTTCTGAATGAGGAGGAGG\n+TGGTGAGAGCAGACAGCACAATCTCTTGTCTGGCATGTTCCTCTGTGTCACCATTGTCTC\n+TCTCATCTGCTCGTGTGTGTGTGTGTGTGTGTCCTTGTCAATGTCATTACACAATTTATG\n+TTGGTGCACTGCATGTCAGAGTCTGAACTTTGTTGGACATCTACTTTCTGTCACCTGATA\n+CCTCATACTTTACACTCTAATCCCTTTTTCCTTTCTAACTGCTGCTGTGTTAAGCTGTCA\n+TATTAATATACTAAATAATGATAATATTAATTCTAATAATGATAGTGAATGGAGATTCAC\n+AATGAAGAAACACAAGGTCCAGACTGAACCCCTGTGCTGTGTGAAGAGTTCACTCTACAT\n+TTACATTCATCCCACATCAGAGACCAGCAATAGCCAGGTTAAGCAGAGCAAGGCTGAGTC\n+TGGCTCTTTGCCTCTGTTGTTTTGATTAGTGTCACACTGGATTATGCTAGTTTGTGTGAG\n+ATTAGAGGTCCTGTTGTTACGAGCAAATCAGCAGTCAGCAGGGTAATCTAAATTACATTG\n+TTCTGTCGGCAATATCCTCTCCTCGCTCAACAGCTTTGTGTGAGCTCATATTTAAAGCCC\n+CCACAGTAGTGCAGTGCATAAAATCATGCAGATACAGATCAGAAGCTTCAGGTAATGTTT\n+ACATCAAACATCAGGGGGAAAATGTGATCTCAGTGCCTCTGACCGTGGTGTGATTGTTGG\n+TGCCGGACAGGCTGGTTTGAGTATTTCTAAAACTGCTGATCTCCTGGGATTTTCACACAC\n+GGCATTCTCTAGAGTTTACTCAGAACGGTGTGGAAAGCAAAAAAACATCCCGCGAGCTGC\n+AATCCTGCGGATGGAAACACCTTGTTGATGGGATATGTCAGAGGAATGGCCAGGCTGGAT\n+CAATCTGACAGAAAGGCGGTAACTCAGATAAGCACTCTCTACAACTGTGGTGAGCAGAAA\n+AGCGTTCTCAGAATGCACAACACGTTCAACCTTGAGGAAGATGTTGCTACAGCAGCAGAT\n+GAAGACCACGTCTGGTTCCACTCCTGTCAGCCAAGAACATCTCAGACTGCACAGGACACC\n+AAAACAAAAACACATCCTGTTTTCTACTGGTGGTAGAGTCACAATTTGGCAATAAGATAA\n+ATCCATGGACCCAACTTGCCTTGTGTCAATAGACCAAGCTGCTGGTGGTCTTGGGGAATG\n+TTTTCTTTACACTTTCACACTATCGGCCTATATAAAATCCTATTATAAACTGCTGTACAG\n+TGCATTGGGTTTGATAAGCCCTCTAAGTCTGTATATCATGATCTCATTGATACCTGCGGC\n+AATACACCCCCACAAACGCAGCTCCCTGCATTTTAAGTATTATAGAGAGTAATTTCACTG\n+TCCATGTCTTTTTTGATCATAAAGCAGGTCTAGGTGCTGTATACAACACTGTATTGAAAT\n+GCTGAAGCAGGTCTAGGTGCTGTATACAACACTGTATTGAAATGCTGAAGCCAATATATC\n+AATCTATCTGTCTATATTTTATGAAATATCAGAGCATTTTAGTCCAAATTTGTCTGTTTT\n+GTTCATTGCAATGCTGACTGCTTAACATTTTCCTCAGTGGTGGCCATCACCACAGCATTT\n+ACTGGTGAGTTTTACCAAGCTACAGTGGGCCACAATGAGTTACCTGTTATTGGCCTGGCT\n+CTATGGCATGCAGAAAACAGTCAGCCAATCAGAGGACAGACTCAGAGACAGACACAAAGT\n+GCCCTGTTCTTGTTAGAGCAGAGATAAATGAGACAGAGGAGATGTAAAACTATACTGAGA\n+TGGTTTTTTGGTTCTTAAAACCACAAATATATTGTATTACGGATATCAAAACTTCAAATA\n+AAACCAGTAAAGTGTAAAACATGGGACCTCTAAATGAAGGGCTGTTTTGTTTCGTAGTTC\n+TAGATTATGTCACTATGTGGCCTCGGTCTCTGTCTGCGTAAAGCGGCTACATGTAGAATT\n+TGACCCACTTTGGTGCCCACATATGGTAACTAAAACACTACAGACAGTATGCACTCCAAC\n+CCTATATAATTTATGTCCTTCAGTGAAGCCTACAAAATGTGCAGCATGATTTGCTATGAT\n+TAATACCTAGAATTATATTAAATTTTAGAAGTTTAGAGAGATGGCTTATACCTTTTTCTG\n+AGCATGGAGTCATCTCATGTAATTTGTCACATACCTTTGGCCAGCTTAAACCTGGTCATT\n+CCAGTGAGAGCTGCTCACCCAAATGTTTCTGTATGCACCTCCTGCTGTGGGTGCCAATAG\n+CTCATGCAAGTTGGTGTCTTTCAACTAAGGCCACTATGTGAGGACCATCAGCAGCAAATT\n+AAATTAGAAGTGCCTTGGAGTTTCTCAGGCCCTCTTCTATGATCATTAAGGTCTCAGTGA\n+CAGAACAGTGCCCCTTTGAGGGACTATGGCATCTTGAGCACTTAAGTTGGCCGAATGTTT\n+GATCTCAAATATGAGTGCACTGTTTCAAAGTCACAAAAGCCTCTGGACAAGGCATAGTTA\n+CTGGGCTTGGTTAACCTTTTTTTCATACCGGCGTGACTGCTGGAACTTGGAACATGTAGC\n+CTAAGTTTCCCTTTGTCTGCAATTACTGAGGTATGCCATGTTGAAATAGAACAATAATTG\n+CAGGGAGGAATTATTCCAATCGACCCATCGGCAGGCTTTCCAATACAGTGCTTTTTGTTT\n+CACAGCAACAAAGAACAAGAGCTTTTAAATGCATCCATCTGGACCCTGACTATGAAAGGT\n+CATTGGTAACGCTGCTGGATTTCTGTTATGTCAGCAAACTGCAGGTCAAAGCGATGATAC\n+AGTCTTATAATGGCTTTCTCCAAGTGAAGGTGGGATAACATGGTTTAAACAAGCTCAGTT\n+AAATGGATCAGAGCATCAACTGCTGTGAACAAGCAATCACACGGTCAAGGTCAAACATTT\n+ACACTTCTGAGAGATCTGGAGAGTATGTCATGGCAGTATTGCTTTTCAGTTATTTCAGTA\n+ACTGATTACGCCTTGTACTTAGTCTCAGAATTAGTGATTTGATTCAAAGTGTTTTATATA\n+TGTATATTTCAAAGCAAAAATACAGCTTAGGTAAAGCTCCTTAGACTCATGCAGCCTAAT\n+TTACTGTAGACATTCCTCCATGTACAGTACTGTGCAAATGTTTTAGGCAGTTTTAGGCAC\n+TAAAGGTGAACTGAGGATGCAGTCCCACGATTAATTTTTATTCATCAGTTAACCTCATGT\n+GAAGTGTAGTAAACAGAAAAAACCTAAATCAGATCAGTATTTCTTATGACCCCCCTCCCC'..b'AACATACATTATATACTACAGTGTAGTGTG\n+TGTGAGTGTGAGAAGGATTTACTTTATAATGCAGTTTCATCTTGATGAGTCACACTGCCA\n+CACATGATTAACACTAATTTCATTAGTTTCCAATGTTGCACACAGTCAGAGATCTCATTT\n+AAATAATCTAACATTGCCTCAGTGATGCAATGACCGCATATGTTTTACAAAGGCTGATGA\n+TTATATCACCGTATCTGACCTAGTTAGACACATTTTTTACATTTTTATTCATGTTGTTAG\n+AATGCCTTGTACTCAAAGCTATAATACATGTACAGATCATAGCAGCCTACACAACTTTCC\n+ATTTATCACACAGGGTTACATAAGTCCACCAGCTGCCTCCAATATAACATACTGATAATT\n+TGCTCTGTACCTATGAGTTAGCAGTTAGCAGTGATGGCTATCTGAAATCTGTGGGGACTT\n+GCACGCTCAACAACACTTGCATTCCACTTGGACATGTCCAGATTTGCTGCTTCCACACAT\n+ATGCTCTGGAGCTCTTTCACATCTCTTTCATGCTGACCTGATACTGTGCTGTACTGTGTC\n+TCCAGGTTAAAAAAAGAAATTATATAGAAACACACAGGTTAAAAAGATAACAGATACAGA\n+CAAGTTCAGACAAGTTCAGTTAACACGGAAAGGAATGTGAAAAATAAGGAACTGAAAGCT\n+ACAGGCTTTTTACATATTTATGGAGGAATAGGTAATAGTACGCAATCCTGTGTTAACGTC\n+TTTGAATCAAATCAAATATAAAGTCAAGAAATAAATTGAAGATATGACCAACAAACACTT\n+TTTTTTTCAATTTCATGAAACTTTTGCCTTTGATCAATACGAACAGATGTTGAAAGCTTT\n+GAACATCTTAAGCTAAGGTTTGGGTTTATTACGTTTGAATAAAAAAGTTGAACCTTTATC\n+AGAACTGTCACTTACAAAGCATAAATTTCTTGAGTTTGAAATTGAGCCAGGTCAGACTAG\n+TTTGAGTGCAGGCCTGTTTGGCACCTCAGACTCCACACCCTTATTTCCAACACAGTTTGT\n+GCCAAAGCTCTACCTTTGGTTCAGTGGTGTAGCTCAGTTTGAAGCTCTGTCTGTGTTGTT\n+TCTGCTTGGAGTTTGTATATTCTCCTGTGGGTTTGAGTGAGTTTCTTCAGACAGTGTGGA\n+GGCAGGCAGGTCAAGTGAATTGGGAATTTTAAGAGGGATACACACAGTCTCTATTGCAAT\n+ACACAATAATGTCAACTAGGAATAATTTGAAATTTTGGGAATTACACCTTATTGTTTTCA\n+TGTGGAGAGTTAAATGAGAAGGTTGATATAATTTGTATGTTGGATAGCTTTGTTTATTAT\n+CCTTTTTTCCTTTAAATAAAAAGCTAGAGCCAGTGTCCAATTAGCTTGTCTTAGCATTAA\n+GACTGAAAACAGGTGGAACAAACTAGCCTGGTTTTGTCCAAAGCTTAAAAATACACCTTT\n+GGGATTAAACAAATGACAAACAACATGCTAATTAATGAGCTTAGAGATGCTGATAGGATT\n+CTATTTTATTTACTTTTCTACTTTATAGTGAGCCAAGCTAGCTGTTTCCTTTTGCTTCCA\n+GTCTTTAGTCTGAGCCAGTTGTCTCCTGGCACCATAGTTAACAGATAGAAATAGAACCAA\n+TTTCGATCTTCTCATCTAACTGTTGGCAAGAAAGCAAATAATTGCATTTCCCAAAACGTT\n+GAGCTACTCTTTAAACATGTACTTTTCAAAAGACCAATTCCACTATGTAAAGATCTCTCT\n+GTTTGCAGAGTCTCCTCCAGAGAGGACAGGACGCCGACGCAGTATGCCAGGCAGCTCCTC\n+TGACAAGACCACACCCGCCATGGAGGCCACGTCCACTGCTGCCACACCTTTTAGAGTCAC\n+CGTGAGTACTGTGAGTGTGTTCTTCTGTACTGCCTCTGTCTTCTCTATTTGTTTTACCCT\n+CTGGCTTTCTCTTTGTATCCACCTTAGTTTGCCTGAGCAGGCTGTTAGTTATATATCAGT\n+GTCGACAGAATCCTGGTCTGGTGTCCAGATGGACCCATGCCAATCTGAAACTCGTTTACT\n+TCAAATATTGGAATGGGACCTTTGATGTTTGGCGTCTGCACATCATGCATCTTGGGCTTA\n+TGTTCAGCACAGTATCCTCCATTGACTTTTCACATCCGGTGTGATTTCACATTGCATTTC\n+ACGCTGAATTATGTTCACGTGCTTCAAGCAAGCTAACACACACACACACACACTTCCACA\n+CCTGTGCACACACACAACGTCGTCACTCACTAACTTCTAAGCACACTGTCTCTCCTCGTC\n+TCTGTCAAACATGCACGCACATGCAGCAGGCCTTTGTCTGTCATCTTGCTCTAATTCAAA\n+ACCAGTATGCTTTCTGCCATGTTTAATTCAACAGATAAACAGCCAGTTAATGAAGCAAAA\n+AATTCTGTTATGAGTCATCAATTTAAAGCTAATTAGCAGTGCATATTCCCATTAATAAAT\n+AATGAGTGGGGAGATGACGACCCAGAGGTGAACTGTAAACAGTAGATGTTAAGCCAGCAG\n+GGCCAGGGACATGCAGCACTCAGTCTCTCATAAACAATCCTCCAACTTCATGTAAACTTT\n+CTGCTTTTTGAAATTACACTAATGGGCCAAGTTAAGTGCTAAAACACATTATATTACTAT\n+AATACTAAACTATACTCTGAAAATAGAAAAGATATTCTTATTTCTTTCAGTTCCTCCTTT\n+TTGATTCCTTTTTTTAATCACTTCAGCACTCGGTTTCGCTAAAAGATCGTGTTCAGTCTC\n+AAAAACCCCAAAAAACCCAAAGTGGGATGCCTCCAAGGCTTAGTAAAAGCTCACAGTAAG\n+TAAAAAAAACAAAAGTAGGCTAGACCCACTGTTATTGGACCACCAGCTGAGTGAGAATAG\n+AGTCTTTCACTGAACTGAAACAGTTGTAACTTTATTTTTGGAGTAACACATATAAATTAC\n+CACAGCTTGATGATGCCAAACTCTCATCTGTTCATATAAAAAAGTGTAAATGATGTTTCC\n+GGGGGAATGGTTACCCGCTGTGTGTGTGTGACTGCATGCATTTTTGTGTCTCTCTCTGAC\n+TGATTTATTCCAATTTAAATTTGTTTTTCATAGGGATGTGAATTTAGTCACCGAGCAGTG\n+TTTTTTTTTACATGACTAGGAATGAATGAGTAGATATATAGAGAGAGATGTAAAAAAGAA\n+AAGAAGAACGGAAAGCTAGTAGGAGGCACATAGGGTCAGATGGAAGGGCTAAATATTGAT\n+TAAGTGTCTCTTAAGCAGCTCCTCGTACTCTCCGGGGAAGAGAGAGCGAAGAGGAACACT\n+GCAGCAAAGTCATCCTGTCTCAATCACATGACCACTTCACTTACTTCTGTGGGCTTATTG\n+CTAAGCAGCACTTCTTGCACAAAGATTCCTCAGACAGTGTTTGACCCTCTCCTGCACTTT\n+TCCTCATACTGCCCCCTTCTGGCCTCTGATTGTAGCACAGCTAACTTTTTGATCTGTTGG\n+GTTCCGTTGAATACAAACAAATAAACTAATAAGATTTGACTTAAATAGAGTTGATTTTCA\n+GCTTAAATTGTTTAATTTTAAGGACAACAAGTAAAAAATGTGTAAGGACACCAGTATGAT\n+TTTGCAGATCTATCAAATTCTGAGTATAGATAGTACTGTAGAAAGACACAATACAGTATA\n+TGGATGGATGGACAGAGGAAAAGGATGCAGGCATGGTGGCACACACAAATGTTGGAATGA\n+AAACAGGAAGACAAGTAGGCAGGCACTCGTTTTCTCCTCCTTCTCTCCTGCATCTCCCAC\n+TTTTAGCAATGACAAACCACCCCTCACTTTTCTCCCTCCAGTGAAAAGAGTTGTGGTGAC\n' 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| diff -r 000000000000 -r 95ea8d97abb4 test-data/output1.bed12 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.bed12 Fri Jan 11 18:15:21 2019 -0500 |
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| @@ -0,0 +1,2 @@ +track name=Spaln description="NP_001121846.1" useScore=1 +scaffold_1 233 29800 NP_001121846.1 1000 + 233 29800 255,0,0 43 31,30,125,9,9,106,4,9,5,37,8,18,12,18,9,4,30,18,8,3,2,3,15,6,10,7,5,7,14,2,11,20,12,12,2,19,23,26,5,7,9,23,5, 0,71,184,1922,2587,6911,7425,7504,7626,8016,8114,8185,8347,8632,8746,9149,9725,15480,15549,15615,16511,16714,16848,17115,17191,18118,18504,19271,19365,19443,20377,22213,22440,25892,25951,26121,26227,26308,26406,28178,28715,28868,29562 |
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| diff -r 000000000000 -r 95ea8d97abb4 test-data/output1.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1.tabular Fri Jan 11 18:15:21 2019 -0500 |
| b |
| @@ -0,0 +1,45 @@ +# rID gID %id ExonL MisMch Unpair ref_l ref_r tgt_l tgt_r eScore IntrnL iScore Sig3/I Sig5/T # - X P DiNuc +NP_001121846.1 scaffold_1 30.00 31 7 0 1 10 234 264 71.9 0 0.0 67.90 -1.80 0 0 0 0 . +NP_001121846.1 scaffold_1 16.67 30 6 9 11 27 305 334 -9.0 40 -8.2 9.90 -2.20 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 64.29 125 15 0 28 69 418 542 226.4 83 8.4 22.20 16.00 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 66.67 9 1 0 70 72 2156 2164 37.9 1613 -6.6 4.40 21.90 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 66.67 9 1 0 73 75 2821 2829 32.3 656 7.5 7.20 12.10 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 62.86 106 13 0 76 110 7145 7250 176.6 4315 4.0 25.10 25.30 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 0.00 4 2 0 111 112 7659 7662 22.9 408 11.8 5.70 17.50 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 0.00 9 2 1 113 114 7738 7746 4.9 75 20.0 13.50 2.90 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 0.00 5 1 0 115 115 7860 7864 24.0 113 -3.9 7.30 16.20 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 30.00 37 7 0 116 125 8250 8286 15.8 385 9.7 12.50 11.50 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 100.00 8 0 0 126 127 8348 8355 28.3 61 18.0 16.20 -0.80 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 33.33 18 4 0 128 133 8419 8436 26.2 63 1.5 12.10 6.70 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 0.00 12 4 0 134 137 8581 8592 29.2 144 9.9 18.20 9.20 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 0.00 18 6 0 138 143 8866 8883 29.1 273 5.7 14.00 24.90 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 0.00 9 3 0 144 146 8980 8988 28.2 96 33.9 21.70 10.20 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 50.00 4 1 0 147 148 9383 9386 33.7 394 -5.5 3.40 14.10 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 10.00 30 5 4 149 154 9959 9988 21.1 572 3.1 10.30 20.60 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 16.67 18 5 0 155 160 15714 15731 43.6 5725 3.9 18.20 22.40 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 50.00 8 1 0 161 162 15783 15790 19.0 51 8.8 -3.20 17.10 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 0.00 3 1 0 163 163 15849 15851 17.0 58 20.8 13.40 3.40 0 0 0 1 GC.AG +NP_001121846.1 scaffold_1 0.00 2 1 0 164 164 16745 16746 20.9 893 -5.3 14.60 8.20 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 0.00 3 1 0 165 165 16948 16950 27.2 201 14.2 22.30 9.10 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 100.00 15 0 0 166 166 17082 17096 13.3 131 17.9 23.40 2.50 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 0.00 6 1 1 167 167 17349 17354 28.3 252 -9.3 5.30 22.50 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 33.33 10 2 0 168 170 17425 17434 15.0 70 22.3 10.10 2.30 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 33.33 7 2 0 171 173 18352 18358 24.7 917 -18.2 2.90 16.40 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 100.00 5 0 0 174 174 18738 18742 17.0 379 19.5 12.40 0.60 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 66.67 7 1 0 175 177 19505 19511 32.6 762 -14.2 7.60 16.10 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 0.00 14 4 0 178 181 19599 19612 16.1 87 15.0 1.90 18.00 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 0.00 2 1 0 182 182 19677 19678 17.1 64 18.2 10.00 3.60 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 50.00 11 1 0 183 184 20611 20621 30.0 932 -2.8 17.10 15.00 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 33.33 20 2 2 185 188 22447 22466 27.3 1825 -5.3 7.50 15.80 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 50.00 12 2 0 189 192 22674 22685 31.9 207 4.4 5.00 7.70 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 20.00 12 3 1 193 197 26126 26137 31.8 3440 -1.3 22.70 14.00 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 0.00 2 1 0 198 198 26185 26186 22.5 47 14.8 12.40 8.30 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 33.33 19 4 0 199 204 26355 26373 33.1 168 7.8 15.10 7.10 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 0.00 23 3 0 205 207 26461 26483 8.0 87 11.9 16.80 8.10 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 33.33 26 2 4 208 212 26542 26567 22.6 58 18.9 20.50 -0.50 0 0 0 0 GT.AG +NP_001121846.1 scaffold_1 0.00 5 1 0 213 213 26640 26644 24.6 72 3.9 14.90 11.30 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 33.33 7 2 0 214 216 28412 28418 28.0 1767 -4.5 11.80 12.30 0 0 0 1 GT.AG +NP_001121846.1 scaffold_1 100.00 9 0 0 217 217 28949 28957 26.9 530 17.1 25.30 10.30 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 28.57 23 2 3 218 221 29102 29124 36.1 144 16.5 21.20 10.60 0 0 0 2 GT.AG +NP_001121846.1 scaffold_1 0.00 5 1 1 222 222 29796 29800 24.4 671 8.0 19.10 10.60 0 0 0 1 GT.AG +@ scaffold_1 + ( 234 29800 ) NP_001121846.1 222 ( 1 222 ) S: 1357.3 =: 38.1 C: 110.8 T#: 122 T-: 26 B#: 0 B-: 0 X: 0 Pam: 0 |
| b |
| diff -r 000000000000 -r 95ea8d97abb4 test-data/output1_gff_genes.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1_gff_genes.gff3 Fri Jan 11 18:15:21 2019 -0500 |
| b |
| @@ -0,0 +1,47 @@ +##gff-version 3 +##sequence-region scaffold_1 1 59940 +scaffold_1 ALN gene 234 29800 1357 + . ID=gene00001;Name=scaffold_1_15 +scaffold_1 ALN mRNA 234 29800 1357 + . ID=mRNA00001;Parent=gene00001;Name=scaffold_1_15 +scaffold_1 ALN cds 234 264 71 + 0 ID=cds00001;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 1 10 + +scaffold_1 ALN cds 305 334 -9 + 2 ID=cds00002;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 11 27 + +scaffold_1 ALN cds 418 542 226 + 2 ID=cds00003;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 28 69 + +scaffold_1 ALN cds 2156 2164 37 + 0 ID=cds00004;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 70 72 + +scaffold_1 ALN cds 2821 2829 32 + 0 ID=cds00005;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 73 75 + +scaffold_1 ALN cds 7145 7250 176 + 0 ID=cds00006;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 76 110 + +scaffold_1 ALN cds 7659 7662 22 + 2 ID=cds00007;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 111 112 + +scaffold_1 ALN cds 7738 7746 4 + 1 ID=cds00008;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 113 114 + +scaffold_1 ALN cds 7860 7864 24 + 1 ID=cds00009;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 115 115 + +scaffold_1 ALN cds 8250 8286 15 + 2 ID=cds00010;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 116 125 + +scaffold_1 ALN cds 8348 8355 28 + 1 ID=cds00011;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 126 127 + +scaffold_1 ALN cds 8419 8436 26 + 2 ID=cds00012;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 128 133 + +scaffold_1 ALN cds 8581 8592 29 + 2 ID=cds00013;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 134 137 + +scaffold_1 ALN cds 8866 8883 29 + 2 ID=cds00014;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 138 143 + +scaffold_1 ALN cds 8980 8988 28 + 2 ID=cds00015;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 144 146 + +scaffold_1 ALN cds 9383 9386 33 + 2 ID=cds00016;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 147 148 + +scaffold_1 ALN cds 9959 9988 21 + 1 ID=cds00017;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 149 154 + +scaffold_1 ALN cds 15714 15731 43 + 1 ID=cds00018;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 155 160 + +scaffold_1 ALN cds 15783 15790 19 + 1 ID=cds00019;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 161 162 + +scaffold_1 ALN cds 15849 15851 17 + 2 ID=cds00020;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 163 163 + +scaffold_1 ALN cds 16745 16746 20 + 2 ID=cds00021;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 164 164 + +scaffold_1 ALN cds 16948 16950 27 + 0 ID=cds00022;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 165 165 + +scaffold_1 ALN cds 17082 17096 13 + 0 ID=cds00023;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 166 166 + +scaffold_1 ALN cds 17349 17354 28 + 0 ID=cds00024;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 167 167 + +scaffold_1 ALN cds 17425 17434 15 + 0 ID=cds00025;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 168 170 + +scaffold_1 ALN cds 18352 18358 24 + 2 ID=cds00026;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 171 173 + +scaffold_1 ALN cds 18738 18742 17 + 1 ID=cds00027;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 174 174 + +scaffold_1 ALN cds 19505 19511 32 + 2 ID=cds00028;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 175 177 + +scaffold_1 ALN cds 19599 19612 16 + 1 ID=cds00029;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 178 181 + +scaffold_1 ALN cds 19677 19678 17 + 2 ID=cds00030;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 182 182 + +scaffold_1 ALN cds 20611 20621 30 + 0 ID=cds00031;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 183 184 + +scaffold_1 ALN cds 22447 22466 27 + 1 ID=cds00032;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 185 188 + +scaffold_1 ALN cds 22674 22685 31 + 2 ID=cds00033;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 189 192 + +scaffold_1 ALN cds 26126 26137 31 + 2 ID=cds00034;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 193 197 + +scaffold_1 ALN cds 26185 26186 22 + 2 ID=cds00035;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 198 198 + +scaffold_1 ALN cds 26355 26373 33 + 0 ID=cds00036;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 199 204 + +scaffold_1 ALN cds 26461 26483 8 + 2 ID=cds00037;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 205 207 + +scaffold_1 ALN cds 26542 26567 22 + 0 ID=cds00038;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 208 212 + +scaffold_1 ALN cds 26640 26644 24 + 1 ID=cds00039;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 213 213 + +scaffold_1 ALN cds 28412 28418 28 + 2 ID=cds00040;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 214 216 + +scaffold_1 ALN cds 28949 28957 26 + 1 ID=cds00041;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 217 217 + +scaffold_1 ALN cds 29102 29124 36 + 1 ID=cds00042;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 218 221 + +scaffold_1 ALN cds 29796 29800 24 + 2 ID=cds00043;Parent=mRNA00001;Name=scaffold_1_15;Target=NP_001121846.1 222 222 + |
| b |
| diff -r 000000000000 -r 95ea8d97abb4 test-data/output1_gff_matches.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output1_gff_matches.gff3 Fri Jan 11 18:15:21 2019 -0500 |
| b |
| @@ -0,0 +1,45 @@ +##gff-version 3 +##sequence-region scaffold_1 1 59940 +scaffold_1 ALN nucleotide_to_protein_match 234 264 71 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 1 10 +;Gap=M10 +scaffold_1 ALN nucleotide_to_protein_match 305 334 -9 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 11 27 +;Gap=M2 D1 M5 I8 M2 +scaffold_1 ALN nucleotide_to_protein_match 418 542 226 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 28 69 +;Gap=M42 +scaffold_1 ALN nucleotide_to_protein_match 2156 2164 37 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 70 72 +;Gap=M3 +scaffold_1 ALN nucleotide_to_protein_match 2821 2829 32 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 73 75 +;Gap=M3 +scaffold_1 ALN nucleotide_to_protein_match 7145 7250 176 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 76 110 +;Gap=M35 +scaffold_1 ALN nucleotide_to_protein_match 7659 7662 22 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 111 112 +;Gap=M2 +scaffold_1 ALN nucleotide_to_protein_match 7738 7746 4 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 113 114 +;Gap=D1 M2 +scaffold_1 ALN nucleotide_to_protein_match 7860 7864 24 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 115 115 +;Gap=M1 +scaffold_1 ALN nucleotide_to_protein_match 8250 8286 15 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 116 125 +;Gap=M10 D3 +scaffold_1 ALN nucleotide_to_protein_match 8348 8355 28 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 126 127 +;Gap=M2 +scaffold_1 ALN nucleotide_to_protein_match 8419 8436 26 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 128 133 +;Gap=M6 +scaffold_1 ALN nucleotide_to_protein_match 8581 8592 29 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 134 137 +;Gap=M4 +scaffold_1 ALN nucleotide_to_protein_match 8866 8883 29 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 138 143 +;Gap=M6 +scaffold_1 ALN nucleotide_to_protein_match 8980 8988 28 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 144 146 +;Gap=M3 +scaffold_1 ALN nucleotide_to_protein_match 9383 9386 33 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 147 148 +;Gap=M2 +scaffold_1 ALN nucleotide_to_protein_match 9959 9988 21 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 149 154 +;Gap=D4 M6 +scaffold_1 ALN nucleotide_to_protein_match 15714 15731 43 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 155 160 +;Gap=M6 +scaffold_1 ALN nucleotide_to_protein_match 15783 15790 19 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 161 162 +;Gap=M2 +scaffold_1 ALN nucleotide_to_protein_match 15849 15851 17 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 163 163 +;Gap=M1 +scaffold_1 ALN nucleotide_to_protein_match 16745 16746 20 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 164 164 +;Gap=M1 +scaffold_1 ALN nucleotide_to_protein_match 16948 16950 27 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 165 165 +;Gap=M1 +scaffold_1 ALN nucleotide_to_protein_match 17082 17096 13 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 166 166 +;Gap=M1 D4 +scaffold_1 ALN nucleotide_to_protein_match 17349 17354 28 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 167 167 +;Gap=D1 M1 +scaffold_1 ALN nucleotide_to_protein_match 17425 17434 15 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 168 170 +;Gap=M3 +scaffold_1 ALN nucleotide_to_protein_match 18352 18358 24 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 171 173 +;Gap=M3 +scaffold_1 ALN nucleotide_to_protein_match 18738 18742 17 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 174 174 +;Gap=M1 +scaffold_1 ALN nucleotide_to_protein_match 19505 19511 32 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 175 177 +;Gap=M3 +scaffold_1 ALN nucleotide_to_protein_match 19599 19612 16 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 178 181 +;Gap=M4 +scaffold_1 ALN nucleotide_to_protein_match 19677 19678 17 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 182 182 +;Gap=M1 +scaffold_1 ALN nucleotide_to_protein_match 20611 20621 30 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 183 184 +;Gap=M2 D2 +scaffold_1 ALN nucleotide_to_protein_match 22447 22466 27 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 185 188 +;Gap=D2 M4 +scaffold_1 ALN nucleotide_to_protein_match 22674 22685 31 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 189 192 +;Gap=M4 +scaffold_1 ALN nucleotide_to_protein_match 26126 26137 31 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 193 197 +;Gap=I1 M4 +scaffold_1 ALN nucleotide_to_protein_match 26185 26186 22 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 198 198 +;Gap=M1 +scaffold_1 ALN nucleotide_to_protein_match 26355 26373 33 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 199 204 +;Gap=M6 +scaffold_1 ALN nucleotide_to_protein_match 26461 26483 8 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 205 207 +;Gap=M3 D5 +scaffold_1 ALN nucleotide_to_protein_match 26542 26567 22 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 208 212 +;Gap=D4 M5 +scaffold_1 ALN nucleotide_to_protein_match 26640 26644 24 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 213 213 +;Gap=M1 +scaffold_1 ALN nucleotide_to_protein_match 28412 28418 28 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 214 216 +;Gap=M3 +scaffold_1 ALN nucleotide_to_protein_match 28949 28957 26 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 217 217 +;Gap=M1 D2 +scaffold_1 ALN nucleotide_to_protein_match 29102 29124 36 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 218 221 +;Gap=D3 M4 +scaffold_1 ALN nucleotide_to_protein_match 29796 29800 24 + . ID=match00001;Name=scaffold_1_15;Target=NP_001121846.1 222 222 +;Gap=M1 D1 |
| b |
| diff -r 000000000000 -r 95ea8d97abb4 test-data/query.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/query.fasta Fri Jan 11 18:15:21 2019 -0500 |
| [ |
| @@ -0,0 +1,6 @@ +>NP_001121846.1 uncharacterized protein LOC100148058 [Danio rerio] +MQRRRNTMENPLFCSSPNQHHGWIQVSDMRSPPGHWMSCGHSCAEHAVWNPKFCVVTDYQMLLLDKEEIH +PLLLQEKRTDSSKSRLLRRTISVPVETHFPGFQSHLSVDNNERASGAGEGRREDEGFLQFFTVINKRIFQ +SFSLSHFWPMGTACMSALTEGDSLIIRPKTKDCVFACSHLTECLVARISLYYLSSFRVFACKKLSRLVSR +VTLSLQKPMRTV + |