| Next changeset 1:7355bbf5e05f (2018-06-10) |
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Commit message:
planemo upload commit 6d089b07b7a1d50b619e2ac6f33cd2bfe2a793c1 |
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added:
barrnap.xml test-data/bacteria.fna test-data/small.fna test-data/test_1.gff test-data/test_2.gff test-data/test_3.gff |
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| diff -r 000000000000 -r 8fd427007e93 barrnap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/barrnap.xml Mon Aug 28 14:14:41 2017 -0400 |
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| @@ -0,0 +1,97 @@ +<tool id="barrnap" name="barrnap" version="1.2.0"> + <description>Locate ribosomal RNA's in a fasta file. (GFF output)</description> + <requirements> + <requirement type="package" version="0.8">barrnap</requirement> + </requirements> + <version_command>barrnap --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + barrnap + --quiet + --threads \${GALAXY_SLOTS:-1} + --reject $reject + --lencutoff $lencutoff + --evalue $evalue + #if $incseq + --incseq + #end if + --kingdom $kingdom + '$fasta_file' + > '$gff' + ]]> + </command> + + <inputs> + <param name="fasta_file" type="data" format="fasta" label="Fasta file" help="Fasta file to look for rRNA's in" /> + <param name="kingdom" type="select" label="Kingdom"> + <option value="bac" selected="true">Bacteria</option> + <option value="euk">Eukaryote</option> + <option value="mito">Mitochondria</option> + <option value="arc">Archaea</option> + </param> + <param name="reject" type="float" value="0.5" label="Reject length threshold" help="Proportional length threshold to reject prediction" /> + <param name="lencutoff" type="float" value="0.8" label="Length cutoff" help="Proportional length threshold to tag a find as pseudo" /> + <param name="evalue" type="float" value="1e-06" label="e-value" help="Similarity e-value cutoff" /> + <param name="incseq" type="boolean" label="Include Sequences in GFF" help="Include the fasta sequences in the GFF output file" /> + </inputs> + + <outputs> + <data name="gff" format="gff3" label="${tool.name} on ${on_string}: rRNA GFF"/> + </outputs> + + <tests> + <test><!-- Test 1 --> + <param name="fasta_file" value="bacteria.fna" ftype="fasta" /> + <param name="kingdom" value="bac" /> + <output name="gff" value="test_1.gff" ftype="gff3" /> + </test> + <test> <!-- Test 2 --> + <param name="fasta_file" value="small.fna" ftype="fasta" /> + <param name="kingdom" value="bac" /> + <param name="incseq" value="true" /> + <output name="gff" value="test_2.gff" ftype="gff3" /> + </test> + <test> <!-- Test 3 --> + <param name="fasta_file" value="small.fna" ftype="fasta" /> + <param name="kingdom" value="bac" /> + <param name="evalue" value="0.00000001" /> + <output name="gff" value="test_3.gff" ftype="gff3" /> + </test> + </tests> + +<help> + +**barrnap** + +barrnap_ predicts the location of 5S, 16S and 23S ribosomal RNA genes in Bacterial genome sequences. Barrnap now supports Archaea, Eukaryota and Mitochondria. It takes FASTA DNA sequence as input, and write GFF3 as output. It uses the new NHMMER tool that comes with HMMER 3.1-dev for HMM searching in DNA:DNA style. NHMMER binaries for 64-bit Linux and Mac OS X are included and will be auto-detected. Multithreading is supported and one can expect roughly linear speed-ups with more CPUs. +This tool is designed to be a substitute for RNAmmer. It was motivated by my desire to remove Prokka's dependency on RNAmmer which is encumbered by an free-for-academic sign-up license, and by the needed legacy HMMER 2.x which conflicts with HMMER 3.x that most people are using now. + +RNAmmer is more sophisticated than Barrnap, and more accurate. because it uses HMMER 2.x in glocal alignment mode, whereas HMMER 3.x currently only supports local alignment (Sean Eddy expects glocal to be supported in 2014). In practice, Barrnap will find all the typical 5/16/23S genes in bacteria, but may get the end points out by a few bases and will probably miss wierd rRNAs. The HMM models it uses are derived from RFAM, Silva, and GreenGenes. + +The name Barrnap is derived from BActerial Ribosomal RNA Predictor. It was spawned at CodeFest 2013 in Berlin, Germany by Torsten Seemann and Tim Booth. + +.. _barrnap: https://github.com/tseemann/barrnap + +**Inputs/Parameters** + +*Fasta file*: The fasta file whose contents you want to search for ribosomal RNA's. + +*Kingdom*: Select the Kingdom of the organism: Bacteria, Eukarote, Mitochondria or Archaea. + +*Length cutoff*: Proportional length threshold to tag a possible rRNA as pseudo. + +*Reject length threshold*: Proportional length threshold to reject prediction + +*E-value*: Similarity cutoff e-value. + +*Include Sequences in GFF*: This includes the original fasta sequence in the GFF file below the #FASTA tag + +</help> +<citations> + <citation type="bibtex">@UNPUBLISHED{Seemann2013, + author = "Torsten Seemann", + title = "barrnap 0.8 : rapid ribosomal RNA prediction", + year = "2013", + note = "https://github.com/tseemann/barrnap"} + </citation> +</citations> +</tool> |
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| diff -r 000000000000 -r 8fd427007e93 test-data/bacteria.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bacteria.fna Mon Aug 28 14:14:41 2017 -0400 |
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| b'@@ -0,0 +1,66284 @@\n+>E.coli Escherichia coli str. K-12 substr. MG1655, complete genome\n+AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATAGCAGC\n+TTCTGAACTGGTTACCTGCCGTGAGTAAATTAAAATTTTATTGACTTAGGTCACTAAATACTTTAACCAA\n+TATAGGCATAGCGCACAGACAGATAAAAATTACAGAGTACACAACATCCATGAAACGCATTAGCACCACC\n+ATTACCACCACCATCACCATTACCACAGGTAACGGTGCGGGCTGACGCGTACAGGAAACACAGAAAAAAG\n+CCCGCACCTGACAGTGCGGGCTTTTTTTTTCGACCAAAGGTAACGAGGTAACAACCATGCGAGTGTTGAA\n+GTTCGGCGGTACATCAGTGGCAAATGCAGAACGTTTTCTGCGTGTTGCCGATATTCTGGAAAGCAATGCC\n+AGGCAGGGGCAGGTGGCCACCGTCCTCTCTGCCCCCGCCAAAATCACCAACCACCTGGTGGCGATGATTG\n+AAAAAACCATTAGCGGCCAGGATGCTTTACCCAATATCAGCGATGCCGAACGTATTTTTGCCGAACTTTT\n+GACGGGACTCGCCGCCGCCCAGCCGGGGTTCCCGCTGGCGCAATTGAAAACTTTCGTCGATCAGGAATTT\n+GCCCAAATAAAACATGTCCTGCATGGCATTAGTTTGTTGGGGCAGTGCCCGGATAGCATCAACGCTGCGC\n+TGATTTGCCGTGGCGAGAAAATGTCGATCGCCATTATGGCCGGCGTATTAGAAGCGCGCGGTCACAACGT\n+TACTGTTATCGATCCGGTCGAAAAACTGCTGGCAGTGGGGCATTACCTCGAATCTACCGTCGATATTGCT\n+GAGTCCACCCGCCGTATTGCGGCAAGCCGCATTCCGGCTGATCACATGGTGCTGATGGCAGGTTTCACCG\n+CCGGTAATGAAAAAGGCGAACTGGTGGTGCTTGGACGCAACGGTTCCGACTACTCTGCTGCGGTGCTGGC\n+TGCCTGTTTACGCGCCGATTGTTGCGAGATTTGGACGGACGTTGACGGGGTCTATACCTGCGACCCGCGT\n+CAGGTGCCCGATGCGAGGTTGTTGAAGTCGATGTCCTACCAGGAAGCGATGGAGCTTTCCTACTTCGGCG\n+CTAAAGTTCTTCACCCCCGCACCATTACCCCCATCGCCCAGTTCCAGATCCCTTGCCTGATTAAAAATAC\n+CGGAAATCCTCAAGCACCAGGTACGCTCATTGGTGCCAGCCGTGATGAAGACGAATTACCGGTCAAGGGC\n+ATTTCCAATCTGAATAACATGGCAATGTTCAGCGTTTCTGGTCCGGGGATGAAAGGGATGGTCGGCATGG\n+CGGCGCGCGTCTTTGCAGCGATGTCACGCGCCCGTATTTCCGTGGTGCTGATTACGCAATCATCTTCCGA\n+ATACAGCATCAGTTTCTGCGTTCCACAAAGCGACTGTGTGCGAGCTGAACGGGCAATGCAGGAAGAGTTC\n+TACCTGGAACTGAAAGAAGGCTTACTGGAGCCGCTGGCAGTGACGGAACGGCTGGCCATTATCTCGGTGG\n+TAGGTGATGGTATGCGCACCTTGCGTGGGATCTCGGCGAAATTCTTTGCCGCACTGGCCCGCGCCAATAT\n+CAACATTGTCGCCATTGCTCAGGGATCTTCTGAACGCTCAATCTCTGTCGTGGTAAATAACGATGATGCG\n+ACCACTGGCGTGCGCGTTACTCATCAGATGCTGTTCAATACCGATCAGGTTATCGAAGTGTTTGTGATTG\n+GCGTCGGTGGCGTTGGCGGTGCGCTGCTGGAGCAACTGAAGCGTCAGCAAAGCTGGCTGAAGAATAAACA\n+TATCGACTTACGTGTCTGCGGTGTTGCCAACTCGAAGGCTCTGCTCACCAATGTACATGGCCTTAATCTG\n+GAAAACTGGCAGGAAGAACTGGCGCAAGCCAAAGAGCCGTTTAATCTCGGGCGCTTAATTCGCCTCGTGA\n+AAGAATATCATCTGCTGAACCCGGTCATTGTTGACTGCACTTCCAGCCAGGCAGTGGCGGATCAATATGC\n+CGACTTCCTGCGCGAAGGTTTCCACGTTGTCACGCCGAACAAAAAGGCCAACACCTCGTCGATGGATTAC\n+TACCATCAGTTGCGTTATGCGGCGGAAAAATCGCGGCGTAAATTCCTCTATGACACCAACGTTGGGGCTG\n+GATTACCGGTTATTGAGAACCTGCAAAATCTGCTCAATGCAGGTGATGAATTGATGAAGTTCTCCGGCAT\n+TCTTTCTGGTTCGCTTTCTTATATCTTCGGCAAGTTAGACGAAGGCATGAGTTTCTCCGAGGCGACCACG\n+CTGGCGCGGGAAATGGGTTATACCGAACCGGACCCGCGAGATGATCTTTCTGGTATGGATGTGGCGCGTA\n+AACTATTGATTCTCGCTCGTGAAACGGGACGTGAACTGGAGCTGGCGGATATTGAAATTGAACCTGTGCT\n+GCCCGCAGAGTTTAACGCCGAGGGTGATGTTGCCGCTTTTATGGCGAATCTGTCACAACTCGACGATCTC\n+TTTGCCGCGCGCGTGGCGAAGGCCCGTGATGAAGGAAAAGTTTTGCGCTATGTTGGCAATATTGATGAAG\n+ATGGCGTCTGCCGCGTGAAGATTGCCGAAGTGGATGGTAATGATCCGCTGTTCAAAGTGAAAAATGGCGA\n+AAACGCCCTGGCCTTCTATAGCCACTATTATCAGCCGCTGCCGTTGGTACTGCGCGGATATGGTGCGGGC\n+AATGACGTTACAGCTGCCGGTGTCTTTGCTGATCTGCTACGTACCCTCTCATGGAAGTTAGGAGTCTGAC\n+ATGGTTAAAGTTTATGCCCCGGCTTCCAGTGCCAATATGAGCGTCGGGTTTGATGTGCTCGGGGCGGCGG\n+TGACACCTGTTGATGGTGCATTGCTCGGAGATGTAGTCACGGTTGAGGCGGCAGAGACATTCAGTCTCAA\n+CAACCTCGGACGCTTTGCCGATAAGCTGCCGTCAGAACCACGGGAAAATATCGTTTATCAGTGCTGGGAG\n+CGTTTTTGCCAGGAACTGGGTAAGCAAATTCCAGTGGCGATGACCCTGGAAAAGAATATGCCGATCGGTT\n+CGGGCTTAGGCTCCAGTGCCTGTTCGGTGGTCGCGGCGCTGATGGCGATGAATGAACACTGCGGCAAGCC\n+GCTTAATGACACTCGTTTGCTGGCTTTGATGGGCGAGCTGGAAGGCCGTATCTCCGGCAGCATTCATTAC\n+GACAACGTGGCACCGTGTTTTCTCGGTGGTATGCAGTTGATGATCGAAGAAAACGACATCATCAGCCAGC\n+AAGTGCCAGGGTTTGATGAGTGGCTGTGGGTGCTGGCGTATCCGGGGATTAAAGTCTCGACGGCAGAAGC\n+CAGGGCTATTTTACCGGCGCAGTATCGCCGCCAGGATTGCATTGCGCACGGGCGACATCTGGCAGGCTTC\n+ATTCACGCCTGCTATTCCCGTCAGCCTGAGCTTGCCGCGAAGCTGATGAAAGATGTTATCGCTGAACCCT\n+ACCGTGAACGGTTACTGCCAGGCTTCCGGCAGGCGCGGCAGGCGGTCGCGGAAATCGGCGCGGTAGCGAG\n+CGGTATCTCCGGCTCCGGCCCGACCTTGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCC\n+GACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGG\n+GCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGC\n+GCAAGCCGTAACCCAGGGGTTG'..b'GGTTAACGTTGCTGCTGAACCGGCGTTAC\n+TGGAGCAGGCGCTGGGAAATTTACTGGATAACGCCATCGATTTTACCCCCGAGAGCGGTTGCATCACGCT\n+AAGCGCCGAAGTGGATCAGGAACACGTCACGCTTAAGGTGCTGGATACCGGTAGTGGTATTCCTGACTAC\n+GCGCTTTCACGTATTTTTGAACGCTTTTACTCTTTGCCTCGTGCAAATGGGCAAAAAAGCAGCGGTCTGG\n+GGTTGGCGTTCGTCAGTGAGGTCGCCCGTTTGTTTAACGGCGAAGTCACGCTGCGCAACGTGCAGGAAGG\n+TGGCGTGCTGGCCTCGCTTCGACTTCACCGTCACTTCACATAGCTTCAAATTCTTCCCACATAGTCTTCG\n+TATCCTGCTGCCATTGCAAAGGAGAAGACTATGTTGAAATCCCCCCTGTTCTGGAAAATGACTAGCCTGT\n+TTGGTGCAGTATTGCTGTTGTTGATTCCGATAATGCTGATTCGGCAGGTGATTGTCGAACGTGCTGATTA\n+CCGTAGCGATGTGGAAGATGCGATTCGCCAAAGTACCAGCGGGCCGCAAAAACTCGTTGGGCCGCTCATC\n+GCTATTCCTGTGACCGAGCTTTATACGGTGCAGGAAGAGGATAAAACCGTGGAGCGGAAACGAAGTTTTA\n+TCCATTTTTGGTTACCTGAGTCATTGATGGTTGATGGCAATCAGAACGTGGAAGAACGCAAGATAGGGAT\n+TTATACCGGTCAGGTCTGGCACAGTGATTTAACGTTAAAAGCCGATTTCGATGTTTCGCGTCTTAGCGAA\n+CTCAACGCGCCAAATATCACCTTAGGCAAGCCATTTATTGTGATTAGCGTCGGGGATGCGCGTGGTATTG\n+GTGTGGTGAAAGCGCCTGAAGTTAACGGAACGGCGCTGACCATTGAACCCGGCACCGGGTTAGAGCAAGG\n+CGGGCAGGGCGTGCATATCCCTTTACCTGAAGGGGACTGGCGGAAGCAGAACCTGAAGCTGAATATGGCC\n+CTGAATTTAAGCGGTACCGGCGATCTTTCTGTGGTGCCTGGCGGGCGTAATAGCGAAATGACCTTAACCA\n+GCAACTGGCCGCATCCCAGTTTTTTAGGTGATTTTCTACCAGCCAAACGGGAAGTTAGCGAGTCAGGTTT\n+TCAGGCGCACTGGCAAAGCAGCTGGTTTGCTAATAATCTCGGTGAGCGTTTTGCTTCAGGCAATGATACC\n+GGCTGGGAAAACTTCCCGGCGTTTAGCGTCGCAGTAACGACGCCAGCCGATCAATACCAATTAACTGACC\n+GGGCGACTAAGTACGCCATTCTGCTGATTGCACTGACTTTTATGGCGTTCTTTGTTTTTGAAACGCTCAC\n+CGCGCAACGTTTACACCCAATGCAATATTTGCTGGTGGGGCTTTCATTGGTGATGTTTTATTTGCTCTTG\n+CTGGCGCTTTCTGAACATACCGGTTTTACCGTGGCATGGATAATCGCCAGTCTGATTGGGGCGATAATGA\n+ACGGTATTTATTTGCAAGCGGTATTGAAAGGTTGGTGCAACAGCATGTTGTTTACCCTCGCGCTGTTGTT\n+GCTGGATGGTGTGATGTGGGGACTGCTCAACTCTGCCGATAGCGCGCTGTTGTTGGGAACCAGTGTGCTG\n+GTGGTGGCGCTGGCCGGCATGATGTTTGTGACCCGTAATATCGACTGGTATGCGTTTTCACTGCCGAAAA\n+TGAAAGCCAGTAAAGAAGTTACAACGGACGATGAGTTACGTATCTGGAAATAAGGTTGAAAAATAAAAAC\n+GGCGCTAAAAAGCGCCGTTTTTTTTGACGGTGGTAAAGCCGATTAATCTTCCAGATCACCGCAGAAGCGA\n+TAACCTTCACCGTGAATGGTGGCGATGATTTCCGGCGTATCCGGCGTAGATTCGAAATGTTTACGAATAC\n+GGCGGATCGTCACGTCTACAGTACGGTCGTGCGGTTTCAGCTCACGGCCGGTCATTTTCTTCAGCAGTTC\n+AGCACGGGACTGAATTTTGCCTGGGTTTTCACAGAAGTGAAGCATGGCGCGGAACTCGCTGCGCGGCAGC\n+TTGTACTGCTCGCCATCAGGGCCGATCAACGAACGGCTGTTGATGTCCAGTTCCCAACCATTGAACTTGT\n+AGCTTTCAACGCTACGACGTTCTTCGCTGACAGTACCCAGATTCATGGTACGGGACAGTAGGTTGCGTGC\n+ACGAATCGTCAGTTCACGCGGGTTGAACGGTTTGGTGATGTAGTCATCTGCACCGATTTCGAGGCCGAGA\n+ATTTTATCGACTTCGTTGTCACGGCCAGTCAGGAACATCAACGCAACATTCGCCTGCTCGCGCAGTTCAC\n+GCGCTAACAGAAGACCGTTCTTACCCGGCAGATTGATATCCATGATCACCAGGTTGATGTCATATTCAGA\n+GAGGATCTGATGCATTTCCGCGCCATCTGTCGCTTCGAAAACATCATAGCCTTCCGCTTCGAAAATACTT\n+TTCAACGTGTTGCGTGTTACCAACTCGTCTTCAACGATAAGAATGTGCGGGGTCTGCATGTTTGCTACCT\n+AAATTGCCAACTAAATCGAAACAGGAAGTACAAAAGTCCCTGACCTGCCTGATGCATGCTGCAAATTAAC\n+ATGATCGGCGTAACATGACTAAAGTACGTAATTGCGTTCTTGATGCACTTTCCATCAACGTCAACAACAT\n+CATTAGCTTGGTCGTGGGTACTTTCCCTCAGGACCCGACAGTGTCAAAAACGGCTGTCATCCTAACCATT\n+TTAACAGCAACATAACAGGCTAAGAGGGGCCGGACACCCAATAAAACTACGCTTCGTTGACATATATCAA\n+GTTCAATTGTAGCACGTTAACAGTTTGATGAAATCATCGTATCTAAATGCTAGCTTTCGTCACATTATTT\n+TAATAATCCAACTAGTTGCATCATACAACTAATAAACGTGGTGAATCCAATTGTCGAGATTTATTTTTTA\n+TAAAATTATCCTAAGTAAACAGAAGGATATGTAGCATTTTTTAACAACTCAACCGTTAGTACAGTCAGGA\n+AATAGTTTAGCCTTTTTTAAGCTAAGTAAAGGGCTTTTTCTGCGACTTACGTTAAGAATTTGTAAATTCG\n+CACCGCGTAATAAGTTGACAGTGATCACCCGGTTCGCGGTTATTTGATCAAGAAGAGTGGCAATATGCGT\n+ATAACGATTATTCTGGTCGCACCCGCCAGAGCAGAAAATATTGGGGCAGCGGCGCGGGCAATGAAAACGA\n+TGGGGTTTAGCGATCTGCGGATTGTCGATAGTCAGGCACACCTGGAGCCAGCCACCCGCTGGGTCGCACA\n+TGGATCTGGTGATATTATTGATAATATTAAAGTTTTCCCGACATTGGCTGAATCGTTACACGATGTCGAT\n+TTCACTGTCGCCACCACTGCGCGCAGTCGGGCGAAATATCATTACTACGCCACGCCAGTTGAACTGGTGC\n+CGCTGTTAGAGGAAAAATCTTCATGGATGAGCCATGCCGCGCTGGTGTTTGGTCGCGAAGATTCCGGGTT\n+GACTAACGAAGAGTTAGCGTTGGCTGACGTTCTTACTGGTGTGCCGATGGTGGCGGATTATCCTTCGCTC\n+AATCTGGGGCAGGCGGTGATGGTCTATTGCTATCAATTAGCAACATTAATACAACAACCGGCGAAAAGTG\n+ATGCAACGGCAGACCAACATCAACTGCAAGCTTTACGCGAACGAGCCATGACATTGCTGACGACTCTGGC\n+AGTGGCAGATGACATAAAACTGGTCGACTGGTTACAACAACGCCTGGGGCTTTTAGAGCAACGAGACACG\n+GCAATGTTGCACCGTTTGCTGCATGATATTGAAAAAAATATCACCAAATAAAAAACGCCTTAGTAAGTAT\n+TTTTC\n+\n' 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| diff -r 000000000000 -r 8fd427007e93 test-data/small.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/small.fna Mon Aug 28 14:14:41 2017 -0400 |
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| b'@@ -0,0 +1,25018 @@\n+>P.marinus Prochlorococcus marinus subsp. marinus str. CCMP1375 chromosome, complete genome\n+AAAGCTAGATGGCAGAAAGGTTTTTGAATAATTTCCACAGATTCCACAAGACCTACTACTACTGTATTAA\n+TTTCATATAATTAAATTAGAATTACTAGAAGAAGAGAAAACTTTTATTAAAGCTATGAAAACTTTTTGTT\n+CCTTTTTTGGTATTTCGTAGTTATGTTGAACCGATGAAACTTGTTTGTTCTCAAATTGAGCTCAATACAG\n+CTCTTCAACTAGTTAGTAGAGCTGTAGCCACTAGGCCTTCGCATCCAGTATTGGCAAATGTATTGCTTAC\n+TGCTGATGCGGGAACTGGAAAACTAAGCTTAACTGGATTTGATCTTAATTTAGGAATTCAAACATCGCTT\n+AGTGCTTCTATCGAAAGTAGTGGAGCAATTACAGTTCCCTCAAAACTTTTCGGAGAAATAATATCAAAAT\n+TATCTAGTGAATCTTCTATAACTTTATCAACAGATGATTCTAGTGAACAAGTTAATTTAAAGAGTAAAAG\n+TGGAAATTATCAGGTAAGAGCTATGAGTGCTGATGATTTTCCTGATTTGCCTATGGTAGAAAATGGAGCT\n+TTTTTAAAGGTTAATGCTAATTCTTTTGCTGTTTCATTAAAATCTACTTTATTTGCTAGTAGTACAGATG\n+AGGCGAAACAGATTTTAACAGGTGTTAATTTATGTTTTGAAGGTAATTCCTTAAAGTCAGCTGCTACAGA\n+TGGTCATAGATTAGCTGTTTTAGATCTTCAGAATGTAATAGCTTCTGAAACTAATCCTGAAATTAATAAT\n+TTATCTGAAAAATTAGAAGTAACTCTACCATCTAGATCATTAAGAGAGTTAGAACGTTTTCTATCTGGAT\n+GCAAATCGGATTCTGAAATAAGTTGTTTTTATGATCAAGGTCAATTTGTTTTTATTTCTTCTGGGCAAAT\n+TATAACGACAAGAACACTAGATGGTAATTACCCTAATTATAATCAATTAATTCCTGATCAATTTAGTAAT\n+CAATTAGTTTTAGATAAAAAATATTTTATAGCAGCTTTAGAGCGTATTGCTGTTTTGGCAGAGCAACATA\n+ACAATGTGGTTAAAATTTCAACTAATAAGGAATTACAAATTTTGAATATCTCTGCTGATGCGCAAGATCT\n+TGGTAGTGGTTCGGAATCTATACCTATAAAATATGATTCTGAAGATATTCAAATTGCTTTTAATTCAAGA\n+TATTTATTAGAAGGTTTAAAAATTATAGAAACAAATACGATTTTATTAAAGTTTAACGCTCCTACAACTC\n+CAGCAATATTTACACCTAATGATGAAACTAATTTTGTATATTTAGTTATGCCTGTACAGATTCGTTCTTA\n+AATTGAATATTCCAAGTCAATTTTTATTGAGCAATCTATTGAAGCTTAATGCTCGTTGTAGTAATGGTAT\n+TGATCATGGTATTGGAACAACGGCTTGGATGTATCCTCCTGTTCATCGGCTTTTAGGTTGGGCAAGCAGA\n+CCTTCTAAATTAAGTCTTAAGAGATCTGTTTGGCGTTTAGATCAAATAAAAGCAATTACTGATAAAGATT\n+TATTTGTTAAGGGTGTTCCAGCAGAATCAGATCAGGCTACAATAAATCGATTTCCAACTTTGCTTGAAGC\n+TTCTTTGTTGAGTAAACAATCAGAAAAAATAGCTAATATTGCTGATCTTGTATTTGATACTAAAACAGGT\n+AATATTATTTATTATTTAGTTGCGCGTAGTAATCCTAAATTACCTGGAACTAGTCGATGGCGTTTTGATT\n+TAGATAAAATTATTGATCAACAGCCTGGCTGTGTTTTTTCTACGTTAGAGACTTTAGATGAATTGCCTTT\n+AGTTAAAAGTAGTATTAAGGAAGATTTTTTAAAAAGAAGTAAAGAAATTCGAGAAAATGTTTTAGAGTTT\n+TCAAATATAGCTAATGAAAGATTAGAAGGATGGTTAGACGAAAATCAATTTGATAATCCTATTAATACTA\n+ACGATAATTGGGTTGATGATTATTCTAATAATAGAATAAATGATGACGAATATTATAATTCATCAGATTA\n+TGAGAGATCTAAGAATGTTTTTAATAATGGAGAAGATCCATGGATTTAGATATGATTGATATTTCATTTA\n+ATAGATTGATTAAATCTAAAGATTATTTAGTTGATTATAATGTTGAATTAGCTTTAAAAAAGGAAGGTTT\n+AACGAAGGCTGATTATATTGAAATTTGTAATCGATTAAAAAGATCTCCTAATAGAACTGAATTAGGAATG\n+TTTGGAGTTATGTGGTCTGAGCATTGTTGTTACCGTAATTCACGTTCTTTATTGTCCAATTTTCCAACAA\n+CAGGAAAAAATATTTTAGTTGGACCTGGTGAAAATGCTGGCGTTGTTGATTTAGGTGAAGGACAAAGATT\n+AGCTTTTAAGATAGAAAGTCATAATCATCCTTCTGCTATTGAACCTTTTCAAGGAGCAGCTACTGGTGTA\n+GGTGGCATATTGCGAGACATTTTTACTATGGGAGCACGTCCTATTGCTTTACTGAATTCATTAAGATTTG\n+GTCCATTGGATACTCCTATAAATGTAGGTTTATTGGAAGGTGTTGTTTCAGGAATAGCCCATTATGGAAA\n+TTGTGTTGGTGTTCCTACTGTTGGGGGTGAAGTAGCTTTTGATAAAAGTTATTCAGGAAATCCTTTAGTA\n+AATGCAATGGCTTTAGGCATTATGGAAACTAAGGAGATTGTTTGTTCAGGTGCAAAAGGAATAGATTTTC\n+CTGTTATTTATGTCGGTAGCACTACAGGTAGAGATGGTATGGGAGGAGCTAGTTTTGCAAGTTCGGAGCT\n+TACTCAAGCTTCTATAGATGATAGACCTGCTGTACAAGTTGGCGACCCTTTTCTAGAAAAGGGTCTTATT\n+GAAGGATGCTTAGAAGCCTTTAAAACAGGTTATGTTGTCGCAGCTCAAGATATGGGAGCGGCAGGTCTTA\n+CTTGCAGTTGTTCTGAAATGGCTGCAAAAGGTGGTGTTGGTATTGAACTAGATCTGGATTTAGTTCCAGC\n+AAGAGAAAAAAATATGACAGCATACGAATTTTTGCTTTCTGAATCACAAGAACGCATGCTTTTTGTTGTT\n+GAACCAGGTAAAGAAGAGCTTATAATGAATAAATTTAGAAAATGGGGATTACAAGCTAAGGTGGTAGGGA\n+AAGTATTAGAAGAAAATATTGTTCGTGTTATTCATGAAAAACAAATTGTTGTTAATTTACCTGCAGATTC\n+TTTAGCTGAAGATACTCCTGTGAATAAACATGAATTGCTTGAAGAGCCTCCTGGCTTCATTAAAGATCAT\n+TGGAAATGGGATGAAACATCTCTTCCTAAAGTTTCAATTAAAGGAGTTCATTTTAAGGAAAATAACACTA\n+TTTTAGATTGGAATCAAATTATCTTGAGATTATTAGATGATCCCACAATTGCATCAAAAAGATGGATTTA\n+TAATCAATATGATTATCAAGTACAAAATAATACAATTATTGCTCCTGGTATAGGAGATGCAGCTCTGATT\n+CGATTAAGAGAAATAGAGAATCAAAATCAAAATTCTAATCGTGGAATTGCTGCAGTAGTTGATTGCCCTA\n+ATAGATGGGTTGCTTTAGATCCAGAACGTGGTGCTATTGCTGCAGTAGCAGAGGCATCCCGAAATATTAG\n+TTGTGTAGGAGCTAAACCTCTTGCTGTTACAGATAATTTAAATTTTTCTTCACCTGAAGATCCAATTGGG\n+TATTGGCAATTAGCAAAGGCATGTAAGGGTTTATCAAAAGCTTGTGTAGTTTTAGAAACACCTGTTACA'..b'TACC\n+AGCCCCTGTTTCTCCTGTGAAGACTGAGAAACCCTGTTCAAAAGAAAGATTGATACTTTCTATAAGCGCA\n+ATGTTATGGAGTCGAAGACCTAGAAGCACAGTATTCAAGTAATCTATTAAAAGCTAGCTAATACCCCAAT\n+GATTTAGAAGGGGTATTGAAGCCACCATCGCAAAATGAAAGAAGAACTTGGTGATTTCATTGAAGCTGCT\n+GGATTGCAGTCATATGACCCTAATGAAATCAGTAATATCTACAAAAAGAACCCCAGTCGACTTATAAAAA\n+GATTATGGGAAACGTTAATTCCAATTTGTTTATTTCTCATAGGTGTTGGATGGGACAAATTAATAGGACT\n+ACTGAACAATGAAACTAGAGCGAGAGAAAGAGCTAAAGAGTTTACAAACCTCCTTGTGGAACTGGGTCCC\n+GCTTTCATAAAAGCAGGACAAGCATTATCAACACGCCCTGATGTAGTCCCAAGAATAGTCTTAGAAGAAT\n+TAGCACAATTACAAGATCAACTGCCAGGTTTTGCAAGCGAATTAGCAATAGCATGTATTAAAGAAGACCT\n+TGGAAAAACATATGAAGAAGTTTTTAAATCATTTGAACTAGATCCAATATCAGCAGCTTCACTAGGACAA\n+GTTCATCAAGCAATCTTGCACAGTGGCGAGAAAGTAGCAGTAAAAATACAAAGGCCAGGGCTTAGGGAAC\n+AAATCACTCTCGATTTATATATTGTTAGAAATATCGCTATATGGCTAAAAAAATATGTTGGATTTATTAG\n+AAGTGATCTAGTTGCATTAATTGATGAACTAGGAAAAAGAGTTTTTGAAGAAATGGATTATATCAATGAA\n+GCAAATAATGCTGAAAAATTTGAAACACTACATCAAAAGAATAAAAAAATAACAGTACCTAAAATGTATA\n+AAAATCTAACTAGCAAAAGAGTATTAACAATGGAATGGATTGATGGTATCAAATTAACAAATATAGATGG\n+GGTCAAAAAGCTTGGAATTAATCCTAATGAGCTAATTGAAATAGGTGTAAATTGTAGTCTTCAACAACTA\n+CTTGAGCATGGATACTTTCATGCTGATCCACACCCAGGAAATATACTTGCTTTAAACGATGGTAGACTTT\n+GTTACTTAGACTTCGGGATGATGAGTGAAGTCACTGATAAATCTAGAACAGGATTGATACAAGCTGTTGT\n+TCATTTGGTAAATAGGAATTTTGATAAATTATCAAAAGATTTTGTTGAATTAGGTTTTCTTAATGAAGAT\n+GTAAACCTAGAACCAATTGTTCCAGCTTTTGAAAAGGTTTTTGATGGAGCCTTAACTATGGGAGTGAGTA\n+AAATGGATTTTAAAACAGTGACTGATGACATGTCAGGCTTAATGTATAAATTTCCTTTTCAATTACCACC\n+ATATTACGCTCTAATTATTAGATCTTTAATAACACTTGAAGGAATAGCATTAAGTGTAGATCCAGATTTC\n+AAGATTCTAGGCGCAGCATATCCTTATTTTGCAAGAAGATTAATGGAAGATCCAGACCCTAAACTAAGAA\n+AAAGTTTAAAAGAAATGCTTTTTGATGGCGGGATTTTTAAATGGAATAGATTAGAAAATCTTGTATCAAA\n+TGCATCTAAACAAAAAGAAATAAATATAGAAAACCTATTAGACCAGGTTATAGATTTTCTATTTTCAGAA\n+AATGGTGGAATATTAAGAGAAGAAATAATCGAAACTATTGCTGAAAGATTCGACTTATTGAATTTGTATG\n+CTATAAAAAATATAAATAAAAGACTACCTAATACCCTTAAATTAAATAATCTAAATCTAGATGCTGGAAT\n+GATAAACGAAATAGAGCCACTTCAAAAATTAATTGGAATATTAAGTAACATCCCAGAATTAAATACAAAT\n+CTCATTTTCAAAAAACTAAATAGAATAATAAAAGAGCCACTAACAAGAGTTATGAGTATAAAAATAGCTA\n+AAAAAGTAACTAAGAAAAGTGTTGTAAGGATTATTAAGCTAGCAGCTGGAGTGAAGCAATAATGAACATA\n+AACAAAGCAAAAGGTTATCTAATTAGCATGATGTTAATTGTTACCAATTTAATCTTTTACCCTGCATATT\n+CTGCAGAGAAAATAACTTTTTATATCAGCATACTAAGTCGAAGTATTACTGTAGAAGAATTAGAGAACTT\n+TAGTAAAAGAGGTGTTAAATCACAATTTTTAAAAAGAGTTCTTAAAAATCAAAATGAAAGAGAGATTAGA\n+GAGATATTAAGAAAAGAGTATAAGGCACCAATAAAGCTTACTAGTAGATTGTTATATAGCAAAATTGGTG\n+GTGTAATTCTAAAAAGAGTATCTAAAATTATATATCCTTATAGAATACCTGAAGAATCAATTAGTATAGT\n+TGCTTTAAAAGCAGCAACTATAGAAGCAATTGCAAAAGGTGATGAAACAATAAATATAATTAGTTTTATC\n+AAGGCATATCCAAGCAAAGTTATTGCAATAGATGTAAGTGAGTTATTAAAAGTTATTAACAAAGTAGAAT\n+CTACAAATGAACTTGTAAGATTTTTCTCTAATGCACCATTAGATAAACTCAAAAAAGATTCTAATTAAAT\n+TATGGCAAGGTCATTTTTCAAAAAATTTATTACAAAACAGAATCATCAAGCTGTTCACAAGCATTGGCCT\n+GGGATTATAGAAGCATATAAGCATTGGCTTCCTGTTACTAAAAAAACACCTATTATTACCCTACAAGAAG\n+GTGCAACTCCACTAATTGAACTTCAATATATAAATAAAATAATCGGAAAAGATGTCAAGGTATATGCAAA\n+ATATGATGGATTAAACCCAACAGGATCTTTTAAAGATAGAGGTATGACAATGGCAATAAGTAAAGCTAAA\n+GAAAATGGTACTAAAGTTGTAATTTGTGCAAGCACTGGAAATACATCTGCATCTGCAGCTGCATATGCAA\n+AAAAAGGGGGAATGAGAAGTTTTGTTTTAATCCCAGAAGGTTATGTAGCACAAGGAAAATTAGCACAAGC\n+TTTAGTATATGGAGCAGAGGTATTAGCAATAAAAGGCAACTTTGATGAAGCATTAAAAATTGTGCAAAAT\n+ATATCAAATAAATTTCCAGTAACACTGGTCAATTCTGTAAATCCATATCGTCTTCAAGGACAAAAAACAG\n+CCGCATTTGAAATAATTGAATCCTTAGGAGAAGCACCAGATTGGTTATGTATACCAATGGGCAATGCTGG\n+AAATATTACTGCCTATTGGATGGGTTTTAATGAATATTATATTGCAGGCATATCTAAAAAACTTCCTAAA\n+ATGATGGGTTTCCAAGCTAAAGGTTCAGCACCATTAGTACTAGGAAAAACTATAGACAATCCAGATACAA\n+TTGCTACAGCAATTAGAATAGGAAATCCAGTGAATAAGGAAAATGCTTATAAAGTCAAAAAAGAATCAAA\n+AGGAAAATTTACAGATGTTACTGATGAAGAAATTATAAATGCCTATAAAATATTGGGTAAAGAAGAAGGT\n+ATTTTTTGTGAACCTGCTAGCGCATCATCAGTTGCAGGTTTATTAAAAGTCAAAGAGAGCATACCTAGTA\n+ATTCTAAAATAGTTTGTGTTTTAACTGGAAATGGTCTAAAAGATCCTGATTGTGCGATTAAAAATAATGA\n+TGCTGTGTTTAAAGAGGGAATAAGTCCAGACATTAAAACAGTTGCAGAAAATATGGGGTTTTAAAAACAA\n+AAAAAGTAGACAATCAGATTTGTGCCTGGGGAAGAGCAAAAACACAACAGTGATATTCTGTGGAAAAACA\n+AGAAATCCTTCTTGTTTTTTCAACAAAAATATTTTAATAGTGGATTTCAGTTTTTAATCCACAATTGAAG\n+AAAATCAAATCCACAAATTTAAAAAAAGAA\n+\n' |
| b |
| diff -r 000000000000 -r 8fd427007e93 test-data/test_1.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1.gff Mon Aug 28 14:14:41 2017 -0400 |
| b |
| @@ -0,0 +1,23 @@ +##gff-version 3 +E.coli barrnap:0.8 rRNA 223774 225311 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.8 rRNA 225761 228661 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.8 rRNA 228760 228870 1.9e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.8 rRNA 2724096 2724206 1.9e-11 - . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.8 rRNA 2724304 2727204 0 - . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.8 rRNA 2727639 2729176 0 - . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.8 rRNA 3421450 3421560 4.4e-11 - . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.8 rRNA 3421695 3421805 1.9e-11 - . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.8 rRNA 3421903 3424803 0 - . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.8 rRNA 3425244 3426781 0 - . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.8 rRNA 3939834 3941371 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.8 rRNA 3941729 3944629 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.8 rRNA 3944727 3944837 1.9e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.8 rRNA 4033557 4035094 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.8 rRNA 4035544 4038445 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.8 rRNA 4038544 4038654 2.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.8 rRNA 4164685 4166222 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.8 rRNA 4166666 4169566 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.8 rRNA 4169664 4169774 6.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA +E.coli barrnap:0.8 rRNA 4206173 4207710 0 + . Name=16S_rRNA;product=16S ribosomal RNA +E.coli barrnap:0.8 rRNA 4208068 4210968 0 + . Name=23S_rRNA;product=23S ribosomal RNA +E.coli barrnap:0.8 rRNA 4211067 4211177 6.5e-11 + . Name=5S_rRNA;product=5S ribosomal RNA |
| b |
| diff -r 000000000000 -r 8fd427007e93 test-data/test_2.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2.gff Mon Aug 28 14:14:41 2017 -0400 |
| b |
| b'@@ -0,0 +1,25023 @@\n+##gff-version 3\n+P.marinus\tbarrnap:0.8\trRNA\t353314\t354793\t0\t+\t.\tName=16S_rRNA;product=16S ribosomal RNA\n+P.marinus\tbarrnap:0.8\trRNA\t355464\t358334\t0\t+\t.\tName=23S_rRNA;product=23S ribosomal RNA\n+P.marinus\tbarrnap:0.8\trRNA\t358433\t358536\t9.6e-07\t+\t.\tName=5S_rRNA;product=5S ribosomal RNA\n+##FASTA\n+>P.marinus Prochlorococcus marinus subsp. marinus str. CCMP1375 chromosome, complete genome\n+AAAGCTAGATGGCAGAAAGGTTTTTGAATAATTTCCACAGATTCCACAAGACCTACTACTACTGTATTAA\n+TTTCATATAATTAAATTAGAATTACTAGAAGAAGAGAAAACTTTTATTAAAGCTATGAAAACTTTTTGTT\n+CCTTTTTTGGTATTTCGTAGTTATGTTGAACCGATGAAACTTGTTTGTTCTCAAATTGAGCTCAATACAG\n+CTCTTCAACTAGTTAGTAGAGCTGTAGCCACTAGGCCTTCGCATCCAGTATTGGCAAATGTATTGCTTAC\n+TGCTGATGCGGGAACTGGAAAACTAAGCTTAACTGGATTTGATCTTAATTTAGGAATTCAAACATCGCTT\n+AGTGCTTCTATCGAAAGTAGTGGAGCAATTACAGTTCCCTCAAAACTTTTCGGAGAAATAATATCAAAAT\n+TATCTAGTGAATCTTCTATAACTTTATCAACAGATGATTCTAGTGAACAAGTTAATTTAAAGAGTAAAAG\n+TGGAAATTATCAGGTAAGAGCTATGAGTGCTGATGATTTTCCTGATTTGCCTATGGTAGAAAATGGAGCT\n+TTTTTAAAGGTTAATGCTAATTCTTTTGCTGTTTCATTAAAATCTACTTTATTTGCTAGTAGTACAGATG\n+AGGCGAAACAGATTTTAACAGGTGTTAATTTATGTTTTGAAGGTAATTCCTTAAAGTCAGCTGCTACAGA\n+TGGTCATAGATTAGCTGTTTTAGATCTTCAGAATGTAATAGCTTCTGAAACTAATCCTGAAATTAATAAT\n+TTATCTGAAAAATTAGAAGTAACTCTACCATCTAGATCATTAAGAGAGTTAGAACGTTTTCTATCTGGAT\n+GCAAATCGGATTCTGAAATAAGTTGTTTTTATGATCAAGGTCAATTTGTTTTTATTTCTTCTGGGCAAAT\n+TATAACGACAAGAACACTAGATGGTAATTACCCTAATTATAATCAATTAATTCCTGATCAATTTAGTAAT\n+CAATTAGTTTTAGATAAAAAATATTTTATAGCAGCTTTAGAGCGTATTGCTGTTTTGGCAGAGCAACATA\n+ACAATGTGGTTAAAATTTCAACTAATAAGGAATTACAAATTTTGAATATCTCTGCTGATGCGCAAGATCT\n+TGGTAGTGGTTCGGAATCTATACCTATAAAATATGATTCTGAAGATATTCAAATTGCTTTTAATTCAAGA\n+TATTTATTAGAAGGTTTAAAAATTATAGAAACAAATACGATTTTATTAAAGTTTAACGCTCCTACAACTC\n+CAGCAATATTTACACCTAATGATGAAACTAATTTTGTATATTTAGTTATGCCTGTACAGATTCGTTCTTA\n+AATTGAATATTCCAAGTCAATTTTTATTGAGCAATCTATTGAAGCTTAATGCTCGTTGTAGTAATGGTAT\n+TGATCATGGTATTGGAACAACGGCTTGGATGTATCCTCCTGTTCATCGGCTTTTAGGTTGGGCAAGCAGA\n+CCTTCTAAATTAAGTCTTAAGAGATCTGTTTGGCGTTTAGATCAAATAAAAGCAATTACTGATAAAGATT\n+TATTTGTTAAGGGTGTTCCAGCAGAATCAGATCAGGCTACAATAAATCGATTTCCAACTTTGCTTGAAGC\n+TTCTTTGTTGAGTAAACAATCAGAAAAAATAGCTAATATTGCTGATCTTGTATTTGATACTAAAACAGGT\n+AATATTATTTATTATTTAGTTGCGCGTAGTAATCCTAAATTACCTGGAACTAGTCGATGGCGTTTTGATT\n+TAGATAAAATTATTGATCAACAGCCTGGCTGTGTTTTTTCTACGTTAGAGACTTTAGATGAATTGCCTTT\n+AGTTAAAAGTAGTATTAAGGAAGATTTTTTAAAAAGAAGTAAAGAAATTCGAGAAAATGTTTTAGAGTTT\n+TCAAATATAGCTAATGAAAGATTAGAAGGATGGTTAGACGAAAATCAATTTGATAATCCTATTAATACTA\n+ACGATAATTGGGTTGATGATTATTCTAATAATAGAATAAATGATGACGAATATTATAATTCATCAGATTA\n+TGAGAGATCTAAGAATGTTTTTAATAATGGAGAAGATCCATGGATTTAGATATGATTGATATTTCATTTA\n+ATAGATTGATTAAATCTAAAGATTATTTAGTTGATTATAATGTTGAATTAGCTTTAAAAAAGGAAGGTTT\n+AACGAAGGCTGATTATATTGAAATTTGTAATCGATTAAAAAGATCTCCTAATAGAACTGAATTAGGAATG\n+TTTGGAGTTATGTGGTCTGAGCATTGTTGTTACCGTAATTCACGTTCTTTATTGTCCAATTTTCCAACAA\n+CAGGAAAAAATATTTTAGTTGGACCTGGTGAAAATGCTGGCGTTGTTGATTTAGGTGAAGGACAAAGATT\n+AGCTTTTAAGATAGAAAGTCATAATCATCCTTCTGCTATTGAACCTTTTCAAGGAGCAGCTACTGGTGTA\n+GGTGGCATATTGCGAGACATTTTTACTATGGGAGCACGTCCTATTGCTTTACTGAATTCATTAAGATTTG\n+GTCCATTGGATACTCCTATAAATGTAGGTTTATTGGAAGGTGTTGTTTCAGGAATAGCCCATTATGGAAA\n+TTGTGTTGGTGTTCCTACTGTTGGGGGTGAAGTAGCTTTTGATAAAAGTTATTCAGGAAATCCTTTAGTA\n+AATGCAATGGCTTTAGGCATTATGGAAACTAAGGAGATTGTTTGTTCAGGTGCAAAAGGAATAGATTTTC\n+CTGTTATTTATGTCGGTAGCACTACAGGTAGAGATGGTATGGGAGGAGCTAGTTTTGCAAGTTCGGAGCT\n+TACTCAAGCTTCTATAGATGATAGACCTGCTGTACAAGTTGGCGACCCTTTTCTAGAAAAGGGTCTTATT\n+GAAGGATGCTTAGAAGCCTTTAAAACAGGTTATGTTGTCGCAGCTCAAGATATGGGAGCGGCAGGTCTTA\n+CTTGCAGTTGTTCTGAAATGGCTGCAAAAGGTGGTGTTGGTATTGAACTAGATCTGGATTTAGTTCCAGC\n+AAGAGAAAAAAATATGACAGCATACGAATTTTTGCTTTCTGAATCACAAGAACGCATGCTTTTTGTTGTT\n+GAACCAGGTAAAGAAGAGCTTATAATGAATAAATTTAGAAAATGGGGATTACAAGCTAAGGTGGTAGGGA\n+AAGTATTAGAAGAAAATATTGTTCGTGTTATTCATGAAAAACAAATTGTTGTTAATTTACCTGCAGATTC\n+TTTAGCTGAAGATACTCCTGTGAATAAACATGAATTGCTTGAAGAGCCTCCTGGCTTCATTAAAGATCAT\n+TGGAAATGGGATGAAACATCTCTTCCTAAAGTTTCAATTAAAGGAGTTCATTTTAAGGAAAATAACACTA\n+TTTTAGATTGGAATCAAATTATCTTGAGATTATTAGATGATCCCACAATTGCATCAAAAAGATGGATTTA\n+TAATCAATATGATTATCAAGTACAAAATAATACAATTATTGCTCCTGGTATAGGAGATGCAGC'..b'TACC\n+AGCCCCTGTTTCTCCTGTGAAGACTGAGAAACCCTGTTCAAAAGAAAGATTGATACTTTCTATAAGCGCA\n+ATGTTATGGAGTCGAAGACCTAGAAGCACAGTATTCAAGTAATCTATTAAAAGCTAGCTAATACCCCAAT\n+GATTTAGAAGGGGTATTGAAGCCACCATCGCAAAATGAAAGAAGAACTTGGTGATTTCATTGAAGCTGCT\n+GGATTGCAGTCATATGACCCTAATGAAATCAGTAATATCTACAAAAAGAACCCCAGTCGACTTATAAAAA\n+GATTATGGGAAACGTTAATTCCAATTTGTTTATTTCTCATAGGTGTTGGATGGGACAAATTAATAGGACT\n+ACTGAACAATGAAACTAGAGCGAGAGAAAGAGCTAAAGAGTTTACAAACCTCCTTGTGGAACTGGGTCCC\n+GCTTTCATAAAAGCAGGACAAGCATTATCAACACGCCCTGATGTAGTCCCAAGAATAGTCTTAGAAGAAT\n+TAGCACAATTACAAGATCAACTGCCAGGTTTTGCAAGCGAATTAGCAATAGCATGTATTAAAGAAGACCT\n+TGGAAAAACATATGAAGAAGTTTTTAAATCATTTGAACTAGATCCAATATCAGCAGCTTCACTAGGACAA\n+GTTCATCAAGCAATCTTGCACAGTGGCGAGAAAGTAGCAGTAAAAATACAAAGGCCAGGGCTTAGGGAAC\n+AAATCACTCTCGATTTATATATTGTTAGAAATATCGCTATATGGCTAAAAAAATATGTTGGATTTATTAG\n+AAGTGATCTAGTTGCATTAATTGATGAACTAGGAAAAAGAGTTTTTGAAGAAATGGATTATATCAATGAA\n+GCAAATAATGCTGAAAAATTTGAAACACTACATCAAAAGAATAAAAAAATAACAGTACCTAAAATGTATA\n+AAAATCTAACTAGCAAAAGAGTATTAACAATGGAATGGATTGATGGTATCAAATTAACAAATATAGATGG\n+GGTCAAAAAGCTTGGAATTAATCCTAATGAGCTAATTGAAATAGGTGTAAATTGTAGTCTTCAACAACTA\n+CTTGAGCATGGATACTTTCATGCTGATCCACACCCAGGAAATATACTTGCTTTAAACGATGGTAGACTTT\n+GTTACTTAGACTTCGGGATGATGAGTGAAGTCACTGATAAATCTAGAACAGGATTGATACAAGCTGTTGT\n+TCATTTGGTAAATAGGAATTTTGATAAATTATCAAAAGATTTTGTTGAATTAGGTTTTCTTAATGAAGAT\n+GTAAACCTAGAACCAATTGTTCCAGCTTTTGAAAAGGTTTTTGATGGAGCCTTAACTATGGGAGTGAGTA\n+AAATGGATTTTAAAACAGTGACTGATGACATGTCAGGCTTAATGTATAAATTTCCTTTTCAATTACCACC\n+ATATTACGCTCTAATTATTAGATCTTTAATAACACTTGAAGGAATAGCATTAAGTGTAGATCCAGATTTC\n+AAGATTCTAGGCGCAGCATATCCTTATTTTGCAAGAAGATTAATGGAAGATCCAGACCCTAAACTAAGAA\n+AAAGTTTAAAAGAAATGCTTTTTGATGGCGGGATTTTTAAATGGAATAGATTAGAAAATCTTGTATCAAA\n+TGCATCTAAACAAAAAGAAATAAATATAGAAAACCTATTAGACCAGGTTATAGATTTTCTATTTTCAGAA\n+AATGGTGGAATATTAAGAGAAGAAATAATCGAAACTATTGCTGAAAGATTCGACTTATTGAATTTGTATG\n+CTATAAAAAATATAAATAAAAGACTACCTAATACCCTTAAATTAAATAATCTAAATCTAGATGCTGGAAT\n+GATAAACGAAATAGAGCCACTTCAAAAATTAATTGGAATATTAAGTAACATCCCAGAATTAAATACAAAT\n+CTCATTTTCAAAAAACTAAATAGAATAATAAAAGAGCCACTAACAAGAGTTATGAGTATAAAAATAGCTA\n+AAAAAGTAACTAAGAAAAGTGTTGTAAGGATTATTAAGCTAGCAGCTGGAGTGAAGCAATAATGAACATA\n+AACAAAGCAAAAGGTTATCTAATTAGCATGATGTTAATTGTTACCAATTTAATCTTTTACCCTGCATATT\n+CTGCAGAGAAAATAACTTTTTATATCAGCATACTAAGTCGAAGTATTACTGTAGAAGAATTAGAGAACTT\n+TAGTAAAAGAGGTGTTAAATCACAATTTTTAAAAAGAGTTCTTAAAAATCAAAATGAAAGAGAGATTAGA\n+GAGATATTAAGAAAAGAGTATAAGGCACCAATAAAGCTTACTAGTAGATTGTTATATAGCAAAATTGGTG\n+GTGTAATTCTAAAAAGAGTATCTAAAATTATATATCCTTATAGAATACCTGAAGAATCAATTAGTATAGT\n+TGCTTTAAAAGCAGCAACTATAGAAGCAATTGCAAAAGGTGATGAAACAATAAATATAATTAGTTTTATC\n+AAGGCATATCCAAGCAAAGTTATTGCAATAGATGTAAGTGAGTTATTAAAAGTTATTAACAAAGTAGAAT\n+CTACAAATGAACTTGTAAGATTTTTCTCTAATGCACCATTAGATAAACTCAAAAAAGATTCTAATTAAAT\n+TATGGCAAGGTCATTTTTCAAAAAATTTATTACAAAACAGAATCATCAAGCTGTTCACAAGCATTGGCCT\n+GGGATTATAGAAGCATATAAGCATTGGCTTCCTGTTACTAAAAAAACACCTATTATTACCCTACAAGAAG\n+GTGCAACTCCACTAATTGAACTTCAATATATAAATAAAATAATCGGAAAAGATGTCAAGGTATATGCAAA\n+ATATGATGGATTAAACCCAACAGGATCTTTTAAAGATAGAGGTATGACAATGGCAATAAGTAAAGCTAAA\n+GAAAATGGTACTAAAGTTGTAATTTGTGCAAGCACTGGAAATACATCTGCATCTGCAGCTGCATATGCAA\n+AAAAAGGGGGAATGAGAAGTTTTGTTTTAATCCCAGAAGGTTATGTAGCACAAGGAAAATTAGCACAAGC\n+TTTAGTATATGGAGCAGAGGTATTAGCAATAAAAGGCAACTTTGATGAAGCATTAAAAATTGTGCAAAAT\n+ATATCAAATAAATTTCCAGTAACACTGGTCAATTCTGTAAATCCATATCGTCTTCAAGGACAAAAAACAG\n+CCGCATTTGAAATAATTGAATCCTTAGGAGAAGCACCAGATTGGTTATGTATACCAATGGGCAATGCTGG\n+AAATATTACTGCCTATTGGATGGGTTTTAATGAATATTATATTGCAGGCATATCTAAAAAACTTCCTAAA\n+ATGATGGGTTTCCAAGCTAAAGGTTCAGCACCATTAGTACTAGGAAAAACTATAGACAATCCAGATACAA\n+TTGCTACAGCAATTAGAATAGGAAATCCAGTGAATAAGGAAAATGCTTATAAAGTCAAAAAAGAATCAAA\n+AGGAAAATTTACAGATGTTACTGATGAAGAAATTATAAATGCCTATAAAATATTGGGTAAAGAAGAAGGT\n+ATTTTTTGTGAACCTGCTAGCGCATCATCAGTTGCAGGTTTATTAAAAGTCAAAGAGAGCATACCTAGTA\n+ATTCTAAAATAGTTTGTGTTTTAACTGGAAATGGTCTAAAAGATCCTGATTGTGCGATTAAAAATAATGA\n+TGCTGTGTTTAAAGAGGGAATAAGTCCAGACATTAAAACAGTTGCAGAAAATATGGGGTTTTAAAAACAA\n+AAAAAGTAGACAATCAGATTTGTGCCTGGGGAAGAGCAAAAACACAACAGTGATATTCTGTGGAAAAACA\n+AGAAATCCTTCTTGTTTTTTCAACAAAAATATTTTAATAGTGGATTTCAGTTTTTAATCCACAATTGAAG\n+AAAATCAAATCCACAAATTTAAAAAAAGAA\n+\n' |
| b |
| diff -r 000000000000 -r 8fd427007e93 test-data/test_3.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_3.gff Mon Aug 28 14:14:41 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +##gff-version 3 +P.marinus barrnap:0.8 rRNA 353314 354793 0 + . Name=16S_rRNA;product=16S ribosomal RNA +P.marinus barrnap:0.8 rRNA 355464 358334 0 + . Name=23S_rRNA;product=23S ribosomal RNA |