Galaxy |

Changeset 0:c147914c9f02 (2022-05-25)

Next changeset 1:45d4d26e01b5 (2022-09-22)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/orfipy commit 9815d91c049d03a29d5d0f9040b0cbd7ea2d6a13

added:
macros.xml
orfipy.xml
test-data/orfipy.fa
test-data/orfipy.fa.gz
test-data/test1.bed
test-data/test2.fa

diff -r 000000000000 -r c147914c9f02 macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Wed May 25 14:53:03 2022 +0000

@@ -0,0 +1,8 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.0.4</token>
+    <xml name="xrefs">
+        <xrefs>
+            <xref type="bio.tools">orfipy</xref>
+        </xrefs>
+    </xml>
+</macros>

diff -r 000000000000 -r c147914c9f02 orfipy.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/orfipy.xml Wed May 25 14:53:03 2022 +0000

[

b'@@ -0,0 +1,193 @@\n+<tool id="orfipy" name="ORFipy" version="@TOOL_VERSION@+galaxy0" profile="21.05">\n+ <description>a versatile ORF finder</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="xrefs"/>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">orfipy</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+orfipy \n+--procs "\\${GALAXY_SLOTS:-1}"\n+--outdir ./ \n+#for $o in str($out_files).split(\',\'):\n+ #if $o == \'BED\':\n+ --bed \'$out_bed\'\n+ #else if $o == \'BED12\':\n+ --bed12 \'$out_bed12\'\n+ #else if $o == \'DNA\':\n+ --dna \'$out_dna\'\n+ #else if $o == \'RNA\':\n+ --rna \'$out_rna\'\n+ #else if $o == \'PEP\':\n+ --pep \'$out_pep\'\n+ #end if\n+#end for\n+--strand $strand\n+#if $min:\n+ --min $min\n+#end if\n+--table $table\n+#if $start:\n+ --start \'$start\'\n+#end if\n+#if $stop:\n+ --stop \'$stop\'\n+#end if\n+$ignore_case\n+$partial_3\n+$partial_5\n+$between_stops\n+$include_stop\n+\'$input1\'\n+ ]]></command>\n+ <inputs>\n+ <param name="input1" type="data" format="fasta,fasta.gz" label="Find ORFs in:" help="ORFs will be detected in this sequence"/>\n+ <param type="select" argument="--table" label="Specify genetic code">\n+ <option value="1" selected="true">1 Standard</option>\n+ <option value="2">2 Vertebrate mitochondrial</option>\n+ <option value="3">3 Yeast mitochondrial</option>\n+ <option value="4">4 Mold, Protozoan, Coelenterate, Mycoplasma, Spiroplasma mitochondrial</option>\n+ <option value="5">5 Invertebrate Mitochondrial</option>\n+ <option value="6">6 Ciliate, Dasycladacean, Hexamita Nuclear</option>\n+ <option value="7">7 Echinoderm and Flatworm Mitochondrial</option>\n+ <option value="8">8 Euplotid Nuclear</option>\n+ <option value="9">9 Bacterial, Archaeal and Plant Plastid</option>\n+ <option value="10">10 Alternative Yeast nuclear</option>\n+ <option value="11">11 Ascidian mitochondrial</option>\n+ <option value="12">12 Alternative Flatworm mitochondrial</option>\n+ <option value="13">13 Chlorophycean mitochondrial</option>\n+ <option value="14">14 Trematode mitochondrial</option>\n+ <option value="15">15 Scenedesmus obliquus mitochondrial</option>\n+ <option value="16">16 Thraustochytrium mitochondrial code</option>\n+ <option value="17">17 Pterobranchia mitochondrial</option>\n+ <option value="18">18 Candidate Division SR1 and Gracilibacteria</option>\n+ <option value="19">19 Pachysolen tannophilus Nuclear Code</option>\n+ <option value="20">20 Karyorelict nuclear</option>\n+ <option value="21">21 Condylostoma nuclear</option>\n+ <option value="22">22 Mesodinium nuclear</option>\n+ <option value="23">23 Peritrich nuclear</option>\n+ </param>\n+ <param name="out_files" argument="--bed,--bed12,--dna,--rna,--pep" type="select" multiple="true" display="checkboxes" label="Select outputs"\n+ help="DNA, RNA, and Peptide options will produce FASTA outputs">\n+ <option value="BED" selected="true">BED</option>\n+ <option value="BED12">BED12</option>\n+ <option value="DNA">DNA</option>\n+ <option value="RNA">RNA</option>\n+ <option value="PEP">Peptides</option>\n+ </param>\n+ <param argument="--strand" type="select" display="radio" label="Select strand" help="Identify ORFs on which strand">\n+ <option value="b" selected="true">Both</option>\n+ <option value="f">Forward</option>\n+ <option value="r">Reverse</option>\n+ </param>\n+ <param argument="--min" type="integer" min="0" optional="true" label="Minimum length of ORFs"\n+ help="No ORFs below this value will be reported. All ORFs will be reported if this paramet'..b'ing} (FASTA RNA)">\n+ <filter>"RNA" in out_files</filter>\n+ </data>\n+ <data name="out_pep" format="fasta" label="ORFs on ${on_string} (FASTA Protein)">\n+ <filter>"PEP" in out_files</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="1">\n+ <param name="input1" value="orfipy.fa"/>\n+ <param name="out_files" value="BED"/>\n+ <output name="out_bed" file="test1.bed"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="input1" value="orfipy.fa"/>\n+ <param name="out_files" value="DNA"/>\n+ <param name="min" value="100"/>\n+ <param name="partial_5" value="true"/>\n+ <output name="out_dna" file="test2.fa"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="input1" value="orfipy.fa.gz"/>\n+ <param name="out_files" value="DNA"/>\n+ <param name="min" value="100"/>\n+ <param name="partial_5" value="true"/>\n+ <output name="out_dna" file="test2.fa"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+Orfipy is a tool for finding open reading frames (ORFs). \n+\n+**Parameters**\n+\n+Galaxy interface of Orfipy supports the following parameters (the following is taken from the tool help)::\n+ \n+ --table TABLE The codon table number to use or path to .json file\n+ with codon table. Use --show-tables to see available\n+ tables compiled from: https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=cgencodes Default: 1\n+ --start START Comma-separated list of start-codons. This will\n+ override start codons described in translation table.\n+ E.g. "--start ATG,ATT" Default: Derived from the\n+ translation table selected\n+ --stop STOP Comma-separated list of stop codons. This will\n+ override stop codons described in translation table.\n+ E.g. "--start TAG,TTT" Default: Derived from the\n+ translation table selected\n+ --outdir OUTDIR Path to outdir default: orfipy_<infasta>_out\n+ --bed12 BED12 bed12 out file Default: None\n+ --bed BED bed out file Default: None\n+ --dna DNA fasta (DNA) out file Default: None\n+ --rna RNA fasta (RNA) out file Default: None\n+ --pep PEP fasta (peptide) out file Default: None\n+ --min MIN Minimum length of ORF, excluding stop codon\n+ (nucleotide) Default: 30\n+ --max MAX Maximum length of ORF, excluding stop codon\n+ (nucleotide) Default: 1,000,000,000\n+ --strand {f,r,b} Strands to find ORFs [(f)orward,(r)everse,(b)oth]\n+ Default: b\n+ --ignore-case Ignore case and find ORFs in lower case sequences too.\n+ Useful for soft-masked sequences. Default: False\n+ --partial-3 Output ORFs with a start codon but lacking an inframe\n+ stop codon. E.g. "ATG TTT AAA" Default: False\n+ --partial-5 Output ORFs with an inframe stop codon lacking an\n+ inframe start codon. E.g. "TTT AAA TAG" Default: False\n+ --between-stops Output ORFs defined as regions between stop codons\n+ (regions free of stop codon). This will set\n+ --partial-3 and --partial-5 true. Default: False\n+ --include-stop Include stop codon in the results, if a stop codon\n+ exists. This output format is compatible with\n+ TransDecoder\'s which includes stop codon coordinates\n+ Default: False\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btab090</citation>\n+ </citations>\n+</tool>\n'

diff -r 000000000000 -r c147914c9f02 test-data/orfipy.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/orfipy.fa Wed May 25 14:53:03 2022 +0000

b'@@ -0,0 +1,132 @@\n+>pbr322\n+TTCTCATGTTTGACAGCTTATCATCGATAAGCTTTAATGCGGTAGTTTATCACAGTTAAATTGCTAACGC\n+AGTCAGGCACCGTGTATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTG\n+TAGGCATAGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCGC\n+CAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTTCTCGGAGCA\n+CTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGCCACTATCGACTACGCGA\n+TCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCAC\n+AGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTC\n+ATGAGCGCTTGTTTCGGCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCT\n+TGCATGCACCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCA\n+GGAGTCGCATAAGGGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGG\n+GCGCGGGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGGTGC\n+CGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCT\n+TGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGTTTCGGC\n+GAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCTGGCGTTCGCGACGC\n+GAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGC\n+CATGCTGTCCAGGCAGGTAGATGACGACCATCAGGGACAGCTTCAAGGATCGCTCGCGGCTCTTACCAGC\n+CTAACTTCGATCACTGGACCGCTGATCGTCACGGCGATTTATGCCGCCTCGGCGAGCACATGGAACGGGT\n+TGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGCGTCGCGGTGCATGGAGCCG\n+GGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACGGATTCACCACTCCAAGAATTGGAGCCA\n+ATCAATTCTTGCGGAGAACTGTGAATGCGCAAACCAACCCTTGGCAGAACATATCCATCGCGTCCGCCAT\n+CTCCAGCAGCCGCACGCGGCGCATCTCGGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTC\n+CTGTCGTTGAGGACCCGGCTAGGCTGGCGGGGTTGCCTTACTGGTTAGCAGAATGAATCACCGATACGCG\n+AGCGAACGTGAAGCGACTGCTGCTGCAAAACGTCTGCGACCTGAGCAACAACATGAATGGTCTTCGGTTT\n+CCGTGTTTCGTAAAGTCTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCA\n+GGATGCTGCTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCATTGACCCTGAGTGA\n+TTTTTCTCTGGTCCCGCCGCATCCATACCGCCAGTTGTTTACCCTCACAACGTTCCAGTAACCGGGCATG\n+TTCATCATCAGTAACCCGTATCGTGAGCATCCTCTCTCGTTTCATCGGTATCATTACCCCCATGAACAGA\n+AATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAACATGGCCCGCTTTATCA\n+GAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACGCGGATGAACAGGCAGACATCTGTGA\n+ATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGCTGCCTCGCGCGTTTCGGTGATGACGGTGAAAAC\n+CTCTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCC\n+GTCAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCGCAGCCATGACCCAGTCACGTAGCGATAGCGG\n+AGTGTATACTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAA\n+TACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCT\n+GCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAA\n+TCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCG\n+CGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAG\n+GTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCT\n+GTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATA\n+GCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCC\n+CGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTA\n+TCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCT\n+TGAAGTGGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGT\n+TACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTT\n+GTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGT\n+CTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCAC\n+CTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGAC\n+AGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCT\n+GACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACC\n+GCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGA\n+AGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTT\n+CGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGG\n+TATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAA\n+GCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTA\n+TGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTC\n+AACCAAGTCAT'..b'TTTTCGTTCCACTGAGCGTCAGACCCC\n+AATTACACGCCACTGGCTGTGCTTGCTGGGGTGACGGTGGCAACGGTGGCGGCCTTGCTGGGCTATCGCG\n+TTGGAAAGAAACGAGGGAAAGGGGACTGATAAACCGGTCTTAGCCCCTCCCCTTGGTGTCCAACCGCTCT\n+GTAGGCCTCTCAGGCGCCGCTGGTGCCGCTGGTTGGACGCCAAGGGTGAATCCGCCTCGATACCCTGATT\n+ACTCGCTTCCTGCGCCCTCTCAGGCGGCGATAGGGGACTGGTAAAACGGGGATTGCCCAGACGCCTCCCC\n+CGCCCCTTCAGGGGCACAAATGCGGCCCCAACGGGGCCACGTAGTGGTGCGTTTTTTGCGTTTCCACCCT\n+TTTCTTCCTTTTCCCTTTTAAACCTTTTAGGACGTCTACAGGCCACGTAATCCGTGGCCTGTAGAGTTTA\n+AAAAGGGACGGATTTGTTGCCATTAAGGGACGGATTTGTTGTTAAGAAGGGACGGATTTGTTGTTGTAAA\n+GGGACGGATTTGTTGTATTGTGGGACGCAGATACAGTGTCCCCTTATACACAAGGAATGTCGAACGTGGC\n+CTCACCCCCAATGGTTTACAAAAGCAATGCCCTGGTCGAGGCCGCGTATCGCCTCAGTGTTCAGGAACAG\n+CGGATCGTTCTGGCCTGTATTAGCCAGGTGAAGAGGAGCGAGCCTGTCACCGATGAAGTGATGTATTCAG\n+TGACGGCGGAGGACATAGCGACGATGGCGGGTGTCCCTATCGAATCTTCCTACAACCAGCTCAAAGAAGC\n+GGCCCTGCGCCTGAAACGGCGGGAAGTCCGGTTAACCCAAGAGCCCAATGGCAAGGGGAAAAGACCGAGT\n+GTGATGATTACCGGCTGGGTGCAAACAATCATCTACCGGGAGGGTGAGGGCCGTGTAGAACTCAGGTTCA\n+CCAAAGACATGCTGCCGTACCTGACGGAACTCACCAAACAGTTCACCAAATACGCCTTGGCTGACGTGGC\n+CAAGATGGACAGCACCCACGCGATCAGGCTTTACGAGCTGCTCATGCAATGGGACAGCATCGGCCAGCGC\n+GAAATAGAAATTGACCAGCTGCGAAAGTGGTTTCAACTGGAAGGCCGGTATCCCTCGATCAAGGACTTCA\n+AGTTGCGAGTGCTTGATCCAGCCGTGACGCAGATCAACGAGCACAGCCCGCTACAGGTGGAGTGGGCGCA\n+GCGAAAGACCGGGCGCAAGGTCACACATCTGTTGTTCAGTTTTGGACCGAAGAAGCCCGCCAAGGCGGTG\n+GGTAAGGCCCCAGCGAAGCGCAAGGCCGGGAAGATTTCAGATGCTGAGATCGCGAAACAGGCTCGCCCTG\n+GTGAGACATGGGAAGCGGCCCGCGCTCGACTAACCCAGATGCCGCTGGATCTGGCCTAGAGGCCGTGGCC\n+ACCACGGCCCGGCCTGCCTTTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTA\n+TTACGCCAGCTGGCGAAAGGGGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGGTTTTCCCAGT\n+CACGACGTTGTAAAACGACGGCCAGTGCCAAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGG\n+TACCGAGCTCGAATTCGTAATCATGGTCATAGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAATTCC\n+ACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTGCCTAATGAGTGAGCTAACTCACATTA\n+ATTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTCGTGCCAGCTGCATTAATGAATCGGCC\n+AACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTC\n+GGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGG\n+GATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGC\n+TGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCG\n+AAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCG\n+ACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCAC\n+GCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCA\n+GCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCA\n+CTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGT\n+GGTGGCCTAACTACGGCTACACTAGAAGGACAGTATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTT\n+CGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGC\n+AAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTTTTCTACGGGGTCTGACG\n+CTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAGGATCTTCACCTAGAT\n+CCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACAGTTAC\n+CAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCC\n+CCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGA\n+CCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGT\n+CCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAG\n+TTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGC\n+TTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTT\n+AGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAG\n+CACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCAACCAA\n+GTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCG\n+CCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCT\n+TACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTT\n+CACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGG\n+AAATGTTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGGGTTATTGTCTCATGA\n+GCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGGTTCCGCGCACATTTCCCCGAAAAGT\n+GCCACCTGACGTCTAAGAAACCATTATTATCATGACATTAACCTATAAAAATAGGCGTATCACGAGGCCC\n+TTTCGTC\n+\n'

diff -r 000000000000 -r c147914c9f02 test-data/orfipy.fa.gz

Binary file test-data/orfipy.fa.gz has changed

diff -r 000000000000 -r c147914c9f02 test-data/test1.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.bed Wed May 25 14:53:03 2022 +0000

b'@@ -0,0 +1,208 @@\n+pbr322\t60\t93\tID=pbr322_ORF.1;ORF_type=complete;ORF_len=33;ORF_frame=1;Start:TTG;Stop:TAA\t0\t+\n+pbr322\t258\t639\tID=pbr322_ORF.2;ORF_type=complete;ORF_len=381;ORF_frame=1;Start:ATG;Stop:TAA\t0\t+\n+pbr322\t780\t1071\tID=pbr322_ORF.3;ORF_type=complete;ORF_len=291;ORF_frame=1;Start:CTG;Stop:TGA\t0\t+\n+pbr322\t1179\t1515\tID=pbr322_ORF.4;ORF_type=complete;ORF_len=336;ORF_frame=1;Start:ATG;Stop:TAG\t0\t+\n+pbr322\t1626\t1737\tID=pbr322_ORF.5;ORF_type=complete;ORF_len=111;ORF_frame=1;Start:CTG;Stop:TGA\t0\t+\n+pbr322\t1881\t2103\tID=pbr322_ORF.6;ORF_type=complete;ORF_len=222;ORF_frame=1;Start:ATG;Stop:TGA\t0\t+\n+pbr322\t2109\t2142\tID=pbr322_ORF.7;ORF_type=complete;ORF_len=33;ORF_frame=1;Start:ATG;Stop:TAA\t0\t+\n+pbr322\t2214\t2283\tID=pbr322_ORF.8;ORF_type=complete;ORF_len=69;ORF_frame=1;Start:ATG;Stop:TGA\t0\t+\n+pbr322\t2370\t2430\tID=pbr322_ORF.9;ORF_type=complete;ORF_len=60;ORF_frame=1;Start:CTG;Stop:TAA\t0\t+\n+pbr322\t2553\t2856\tID=pbr322_ORF.10;ORF_type=complete;ORF_len=303;ORF_frame=1;Start:CTG;Stop:TAA\t0\t+\n+pbr322\t2889\t2919\tID=pbr322_ORF.11;ORF_type=complete;ORF_len=30;ORF_frame=1;Start:CTG;Stop:TAG\t0\t+\n+pbr322\t3027\t3132\tID=pbr322_ORF.12;ORF_type=complete;ORF_len=105;ORF_frame=1;Start:TTG;Stop:TGA\t0\t+\n+pbr322\t3150\t3195\tID=pbr322_ORF.13;ORF_type=complete;ORF_len=45;ORF_frame=1;Start:CTG;Stop:TGA\t0\t+\n+pbr322\t3270\t3303\tID=pbr322_ORF.14;ORF_type=complete;ORF_len=33;ORF_frame=1;Start:ATG;Stop:TAA\t0\t+\n+pbr322\t3507\t3561\tID=pbr322_ORF.15;ORF_type=complete;ORF_len=54;ORF_frame=1;Start:CTG;Stop:TAA\t0\t+\n+pbr322\t3594\t3819\tID=pbr322_ORF.16;ORF_type=complete;ORF_len=225;ORF_frame=1;Start:TTG;Stop:TAA\t0\t+\n+pbr322\t3837\t3942\tID=pbr322_ORF.17;ORF_type=complete;ORF_len=105;ORF_frame=1;Start:CTG;Stop:TAA\t0\t+\n+pbr322\t3957\t4005\tID=pbr322_ORF.18;ORF_type=complete;ORF_len=48;ORF_frame=1;Start:TTG;Stop:TGA\t0\t+\n+pbr322\t4077\t4122\tID=pbr322_ORF.19;ORF_type=complete;ORF_len=45;ORF_frame=1;Start:CTG;Stop:TAA\t0\t+\n+pbr322\t85\t1273\tID=pbr322_ORF.20;ORF_type=complete;ORF_len=1188;ORF_frame=2;Start:ATG;Stop:TGA\t0\t+\n+pbr322\t1276\t1351\tID=pbr322_ORF.21;ORF_type=complete;ORF_len=75;ORF_frame=2;Start:ATG;Stop:TGA\t0\t+\n+pbr322\t1354\t1459\tID=pbr322_ORF.22;ORF_type=complete;ORF_len=105;ORF_frame=2;Start:ATG;Stop:TGA\t0\t+\n+pbr322\t1510\t1720\tID=pbr322_ORF.23;ORF_type=complete;ORF_len=210;ORF_frame=2;Start:CTG;Stop:TAA\t0\t+\n+pbr322\t2008\t2215\tID=pbr322_ORF.24;ORF_type=complete;ORF_len=207;ORF_frame=2;Start:ATG;Stop:TGA\t0\t+\n+pbr322\t2320\t2371\tID=pbr322_ORF.25;ORF_type=complete;ORF_len=51;ORF_frame=2;Start:ATG;Stop:TGA\t0\t+\n+pbr322\t2782\t2830\tID=pbr322_ORF.26;ORF_type=complete;ORF_len=48;ORF_frame=2;Start:CTG;Stop:TAA\t0\t+\n+pbr322\t2989\t3031\tID=pbr322_ORF.27;ORF_type=complete;ORF_len=42;ORF_frame=2;Start:CTG;Stop:TAG\t0\t+\n+pbr322\t3082\t3151\tID=pbr322_ORF.28;ORF_type=complete;ORF_len=69;ORF_frame=2;Start:TTG;Stop:TGA\t0\t+\n+pbr322\t3331\t3538\tID=pbr322_ORF.29;ORF_type=complete;ORF_len=207;ORF_frame=2;Start:CTG;Stop:TAA\t0\t+\n+pbr322\t3685\t3715\tID=pbr322_ORF.30;ORF_type=complete;ORF_len=30;ORF_frame=2;Start:ATG;Stop:TAG\t0\t+\n+pbr322\t3862\t3916\tID=pbr322_ORF.31;ORF_type=complete;ORF_len=54;ORF_frame=2;Start:CTG;Stop:TAA\t0\t+\n+pbr322\t4042\t4219\tID=pbr322_ORF.32;ORF_type=complete;ORF_len=177;ORF_frame=2;Start:CTG;Stop:TGA\t0\t+\n+pbr322\t5\t56\tID=pbr322_ORF.33;ORF_type=complete;ORF_len=51;ORF_frame=3;Start:ATG;Stop:TAA\t0\t+\n+pbr322\t98\t140\tID=pbr322_ORF.34;ORF_type=complete;ORF_len=42;ORF_frame=3;Start:ATG;Stop:TAG\t0\t+\n+pbr322\t293\t491\tID=pbr322_ORF.35;ORF_type=complete;ORF_len=198;ORF_frame=3;Start:TTG;Stop:TGA\t0\t+\n+pbr322\t563\t623\tID=pbr322_ORF.36;ORF_type=complete;ORF_len=60;ORF_frame=3;Start:ATG;Stop:TAA\t0\t+\n+pbr322\t839\t1004\tID=pbr322_ORF.37;ORF_type=complete;ORF_len=165;ORF_frame=3;Start:TTG;Stop:TGA\t0\t+\n+pbr322\t1070\t1121\tID=pbr322_ORF.38;ORF_type=complete;ORF_len=51;ORF_frame=3;Start:ATG;Stop:TAA\t0\t+\n+pbr322\t1160\t1202\tID=pbr322_ORF.39;ORF_type=complete;ORF_len=42;ORF_frame=3;Start:ATG;Stop:TAG\t0\t+\n+pbr322\t1220\t1298\tID=pbr322_ORF.40;ORF_type=complete;ORF_len=78;ORF_frame=3;Start:TTG;Stop:TAA\t0\t+\n+pbr322\t1370\t1523\tID=pbr322_ORF.41'..b'=puc18_ORF.67;ORF_type=complete;ORF_len=198;ORF_frame=-1;Start:TTG;Stop:TGA\t0\t-\n+puc18\t1575\t1707\tID=puc18_ORF.68;ORF_type=complete;ORF_len=132;ORF_frame=-1;Start:CTG;Stop:TAG\t0\t-\n+puc18\t1452\t1572\tID=puc18_ORF.69;ORF_type=complete;ORF_len=120;ORF_frame=-1;Start:ATG;Stop:TAG\t0\t-\n+puc18\t1323\t1416\tID=puc18_ORF.70;ORF_type=complete;ORF_len=93;ORF_frame=-1;Start:ATG;Stop:TGA\t0\t-\n+puc18\t1278\t1317\tID=puc18_ORF.71;ORF_type=complete;ORF_len=39;ORF_frame=-1;Start:CTG;Stop:TAA\t0\t-\n+puc18\t990\t1143\tID=puc18_ORF.72;ORF_type=complete;ORF_len=153;ORF_frame=-1;Start:ATG;Stop:TGA\t0\t-\n+puc18\t852\t933\tID=puc18_ORF.73;ORF_type=complete;ORF_len=81;ORF_frame=-1;Start:CTG;Stop:TGA\t0\t-\n+puc18\t666\t702\tID=puc18_ORF.74;ORF_type=complete;ORF_len=36;ORF_frame=-1;Start:TTG;Stop:TAA\t0\t-\n+puc18\t624\t657\tID=puc18_ORF.75;ORF_type=complete;ORF_len=33;ORF_frame=-1;Start:TTG;Stop:TAG\t0\t-\n+puc18\t234\t423\tID=puc18_ORF.76;ORF_type=complete;ORF_len=189;ORF_frame=-1;Start:ATG;Stop:TGA\t0\t-\n+puc18\t60\t114\tID=puc18_ORF.77;ORF_type=complete;ORF_len=54;ORF_frame=-1;Start:CTG;Stop:TGA\t0\t-\n+puc18\t4256\t4448\tID=puc18_ORF.78;ORF_type=complete;ORF_len=192;ORF_frame=-2;Start:TTG;Stop:TGA\t0\t-\n+puc18\t3461\t3503\tID=puc18_ORF.79;ORF_type=complete;ORF_len=42;ORF_frame=-2;Start:TTG;Stop:TGA\t0\t-\n+puc18\t3074\t3365\tID=puc18_ORF.80;ORF_type=complete;ORF_len=291;ORF_frame=-2;Start:CTG;Stop:TAA\t0\t-\n+puc18\t2939\t3011\tID=puc18_ORF.81;ORF_type=complete;ORF_len=72;ORF_frame=-2;Start:CTG;Stop:TGA\t0\t-\n+puc18\t2816\t2933\tID=puc18_ORF.82;ORF_type=complete;ORF_len=117;ORF_frame=-2;Start:ATG;Stop:TAG\t0\t-\n+puc18\t2657\t2768\tID=puc18_ORF.83;ORF_type=complete;ORF_len=111;ORF_frame=-2;Start:ATG;Stop:TGA\t0\t-\n+puc18\t2465\t2522\tID=puc18_ORF.84;ORF_type=complete;ORF_len=57;ORF_frame=-2;Start:TTG;Stop:TGA\t0\t-\n+puc18\t2123\t2279\tID=puc18_ORF.85;ORF_type=complete;ORF_len=156;ORF_frame=-2;Start:ATG;Stop:TGA\t0\t-\n+puc18\t1928\t2039\tID=puc18_ORF.86;ORF_type=complete;ORF_len=111;ORF_frame=-2;Start:ATG;Stop:TGA\t0\t-\n+puc18\t1145\t1271\tID=puc18_ORF.87;ORF_type=complete;ORF_len=126;ORF_frame=-2;Start:TTG;Stop:TAA\t0\t-\n+puc18\t650\t743\tID=puc18_ORF.88;ORF_type=complete;ORF_len=93;ORF_frame=-2;Start:TTG;Stop:TGA\t0\t-\n+puc18\t542\t575\tID=puc18_ORF.89;ORF_type=complete;ORF_len=33;ORF_frame=-2;Start:ATG;Stop:TAA\t0\t-\n+puc18\t284\t338\tID=puc18_ORF.90;ORF_type=complete;ORF_len=54;ORF_frame=-2;Start:CTG;Stop:TAA\t0\t-\n+puc18\t158\t251\tID=puc18_ORF.91;ORF_type=complete;ORF_len=93;ORF_frame=-2;Start:TTG;Stop:TGA\t0\t-\n+puc18\t3499\t4357\tID=puc18_ORF.92;ORF_type=complete;ORF_len=858;ORF_frame=-3;Start:ATG;Stop:TAA\t0\t-\n+puc18\t3466\t3496\tID=puc18_ORF.93;ORF_type=complete;ORF_len=30;ORF_frame=-3;Start:CTG;Stop:TAG\t0\t-\n+puc18\t3169\t3310\tID=puc18_ORF.94;ORF_type=complete;ORF_len=141;ORF_frame=-3;Start:CTG;Stop:TAG\t0\t-\n+puc18\t3040\t3112\tID=puc18_ORF.95;ORF_type=complete;ORF_len=72;ORF_frame=-3;Start:CTG;Stop:TAG\t0\t-\n+puc18\t2932\t2980\tID=puc18_ORF.96;ORF_type=complete;ORF_len=48;ORF_frame=-3;Start:TTG;Stop:TGA\t0\t-\n+puc18\t2623\t2707\tID=puc18_ORF.97;ORF_type=complete;ORF_len=84;ORF_frame=-3;Start:CTG;Stop:TGA\t0\t-\n+puc18\t2365\t2404\tID=puc18_ORF.98;ORF_type=complete;ORF_len=39;ORF_frame=-3;Start:ATG;Stop:TAA\t0\t-\n+puc18\t2242\t2287\tID=puc18_ORF.99;ORF_type=complete;ORF_len=45;ORF_frame=-3;Start:CTG;Stop:TGA\t0\t-\n+puc18\t1873\t1918\tID=puc18_ORF.100;ORF_type=complete;ORF_len=45;ORF_frame=-3;Start:ATG;Stop:TAG\t0\t-\n+puc18\t1504\t1852\tID=puc18_ORF.101;ORF_type=complete;ORF_len=348;ORF_frame=-3;Start:CTG;Stop:TAA\t0\t-\n+puc18\t1399\t1459\tID=puc18_ORF.102;ORF_type=complete;ORF_len=60;ORF_frame=-3;Start:CTG;Stop:TGA\t0\t-\n+puc18\t1264\t1357\tID=puc18_ORF.103;ORF_type=complete;ORF_len=93;ORF_frame=-3;Start:CTG;Stop:TGA\t0\t-\n+puc18\t1120\t1243\tID=puc18_ORF.104;ORF_type=complete;ORF_len=123;ORF_frame=-3;Start:TTG;Stop:TAA\t0\t-\n+puc18\t694\t991\tID=puc18_ORF.105;ORF_type=complete;ORF_len=297;ORF_frame=-3;Start:CTG;Stop:TGA\t0\t-\n+puc18\t307\t514\tID=puc18_ORF.106;ORF_type=complete;ORF_len=207;ORF_frame=-3;Start:CTG;Stop:TAA\t0\t-\n+puc18\t148\t235\tID=puc18_ORF.107;ORF_type=complete;ORF_len=87;ORF_frame=-3;Start:CTG;Stop:TAG\t0\t-\n'

diff -r 000000000000 -r c147914c9f02 test-data/test2.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test2.fa Wed May 25 14:53:03 2022 +0000

[

b'@@ -0,0 +1,543 @@\n+>pbr322_ORF.1 [258-639](+) type:complete length:381 frame:1 start:ATG stop:TAA\n+ATGCGCACCCGTTCTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTT\n+CGCTACTTGGAGCCACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTC\n+TACGCCGGACGCATCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATAT\n+CGCCGACATCACCGATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCG\n+GCGTGGGTATGGTGGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCA\n+CCATTCCTTGCGGCGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCA\n+GGAGTCGCA\n+>pbr322_ORF.2 [780-1071](+) type:complete length:291 frame:1 start:CTG stop:TGA\n+CTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATCGGCCTGTCGCTTG\n+CGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCCCGCCACCAAACGT\n+TTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGGGCTACGTCTTGCT\n+GGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTCGCTTCCGGCGGCA\n+TCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCAGGTAGA\n+>pbr322_ORF.3 [1179-1515](+) type:complete length:336 frame:1 start:ATG stop:TAG\n+ATGGAACGGGTTGGCATGGATTGTAGGCGCCGCCCTATACCTTGTCTGCCTCCCCGCGTTGC\n+GTCGCGGTGCATGGAGCCGGGCCACCTCGACCTGAATGGAAGCCGGCGGCACCTCGCTAACG\n+GATTCACCACTCCAAGAATTGGAGCCAATCAATTCTTGCGGAGAACTGTGAATGCGCAAACC\n+AACCCTTGGCAGAACATATCCATCGCGTCCGCCATCTCCAGCAGCCGCACGCGGCGCATCTC\n+GGGCAGCGTTGGGTCCTGGCCACGGGTGCGCATGATCGTGCTCCTGTCGTTGAGGACCCGGC\n+TAGGCTGGCGGGGTTGCCTTACTGGT\n+>pbr322_ORF.4 [1626-1737](+) type:complete length:111 frame:1 start:CTG stop:TGA\n+CTGGAAACGCGGAAGTCAGCGCCCTGCACCATTATGTTCCGGATCTGCATCGCAGGATGCTG\n+CTGGCTACCCTGTGGAACACCTACATCTGTATTAACGAAGCGCTGGCAT\n+>pbr322_ORF.5 [1881-2103](+) type:complete length:222 frame:1 start:ATG stop:TGA\n+ATGAACAGAAATCCCCCTTACACGGAGGCATCAGTGACCAAACAGGAAAAAACCGCCCTTAA\n+CATGGCCCGCTTTATCAGAAGCCAGACATTAACGCTTCTGGAGAAACTCAACGAGCTGGACG\n+CGGATGAACAGGCAGACATCTGTGAATCGCTTCACGACCACGCTGATGAGCTTTACCGCAGC\n+TGCCTCGCGCGTTTCGGTGATGACGGTGAAAACCTC\n+>pbr322_ORF.6 [2553-2856](+) type:complete length:303 frame:1 start:CTG stop:TAA\n+CTGACGAGCATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAA\n+AGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCT\n+TACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCT\n+GTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCC\n+GTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGG\n+>pbr322_ORF.7 [3027-3132](+) type:complete length:105 frame:1 start:TTG stop:TGA\n+TTGGTAGCTCTTGATCCGGCAAACAAACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAG\n+CAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTT\n+>pbr322_ORF.8 [3594-3819](+) type:complete length:225 frame:1 start:TTG stop:TAA\n+TTGTTGCCATTGCTGCAGGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGC\n+TCCGGTTCCCAACGATCAAGGCGAGTTACATGATCCCCCATGTTGTGCAAAAAAGCGGTTAG\n+CTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTA\n+TGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCG\n+>pbr322_ORF.9 [3837-3942](+) type:complete length:105 frame:1 start:CTG stop:TAA\n+CTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGC\n+CCGGCGTCAACACGGGATAATACCGCGCCACATAGCAGAACTT\n+>pbr322_ORF.10 [85-1273](+) type:complete length:1188 frame:2 start:ATG stop:TGA\n+ATGAAATCTAACAATGCGCTCATCGTCATCCTCGGCACCGTCACCCTGGATGCTGTAGGCAT\n+AGGCTTGGTTATGCCGGTACTGCCGGGCCTCTTGCGGGATATCGTCCATTCCGACAGCATCG\n+CCAGTCACTATGGCGTGCTGCTAGCGCTATATGCGTTGATGCAATTTCTATGCGCACCCGTT\n+CTCGGAGCACTGTCCGACCGCTTTGGCCGCCGCCCAGTCCTGCTCGCTTCGCTACTTGGAGC\n+CACTATCGACTACGCGATCATGGCGACCACACCCGTCCTGTGGATCCTCTACGCCGGACGCA\n+TCGTGGCCGGCATCACCGGCGCCACAGGTGCGGTTGCTGGCGCCTATATCGCCGACATCACC\n+GATGGGGAAGATCGGGCTCGCCACTTCGGGCTCATGAGCGCTTGTTTCGGCGTGGGTATGGT\n+GGCAGGCCCCGTGGCCGGGGGACTGTTGGGCGCCATCTCCTTGCATGCACCATTCCTTGCGG\n+CGGCGGTGCTCAACGGCCTCAACCTACTACTGGGCTGCTTCCTAATGCAGGAGTCGCATAAG\n+GGAGAGCGTCGACCGATGCCCTTGAGAGCCTTCAACCCAGTCAGCTCCTTCCGGTGGGCGCG\n+GGGCATGACTATCGTCGCCGCACTTATGACTGTCTTCTTTATCATGCAACTCGTAGGACAGG\n+TGCCGGCAGCGCTCTGGGTCATTTTCGGCGAGGACCGCTTTCGCTGGAGCGCGACGATGATC\n+GGCCTGTCGCTTGCGGTATTCGGAATCTTGCACGCCCTCGCTCAAGCCTTCGTCACTGGTCC\n+CGCCACCAAACGTTTCGGCGAGAAGCAGGCCATTATCGCCGGCATGGCGGCCGACGCGCTGG\n+GCTACGTCTTGCTGGCGTTCGCGACGCGAGGCTGGATGGCCTTCCCCATTATGATTCTTCTC\n+GCTTCCGGCGGCATCGGGATGCCCGCGTTGCAGGCCATGCTGTCCAGGCA'..b'frame:-2 start:NA stop:TGA\n+TGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGT\n+TGTGTGGAATTGTGAGCGGATAACAATTTCACACAGGAAACAGCTA\n+>puc18_ORF.44 [2123-2279](-) type:complete length:156 frame:-2 start:ATG stop:TGA\n+ATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTGACTGGGAAAACCCTGGCGTTACC\n+CAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCG\n+CACCGATCGCCCTTCCCAACAGTTGCGCAGCC\n+>puc18_ORF.45 [1928-2039](-) type:complete length:111 frame:-2 start:ATG stop:TGA\n+ATGTCTCACCAGGGCGAGCCTGTTTCGCGATCTCAGCATCTGAAATCTTCCCGGCCTTGCGC\n+TTCGCTGGGGCCTTACCCACCGCCTTGGCGGGCTTCTTCGGTCCAAAAC\n+>puc18_ORF.46 [1145-1271](-) type:complete length:126 frame:-2 start:TTG stop:TAA\n+TTGGGGGTGAGGCCACGTTCGACATTCCTTGTGTATAAGGGGACACTGTATCTGCGTCCCAC\n+AATACAACAAATCCGTCCCTTTACAACAACAAATCCGTCCCTTCTTAACAACAAATCCGTCC\n+CT\n+>puc18_ORF.47 [932-1067](-) type:5-prime-partial length:135 frame:-2 start:NA stop:TGA\n+AAGGGAAAAGGAAGAAAAGGGTGGAAACGCAAAAAACGCACCACTACGTGGCCCCGTTGGGG\n+CCGCATTTGTGCCCCTGAAGGGGCGGGGGAGGCGTCTGGGCAATCCCCGTTTTACCAGTCCC\n+CTATCGCCGCC\n+>puc18_ORF.48 [3499-4357](-) type:complete length:858 frame:-3 start:ATG stop:TAA\n+ATGAGTATTCAACATTTCCGTGTCGCCCTTATTCCCTTTTTTGCGGCATTTTGCCTTCCTGT\n+TTTTGCTCACCCAGAAACGCTGGTGAAAGTAAAAGATGCTGAAGATCAGTTGGGTGCACGAG\n+TGGGTTACATCGAACTGGATCTCAACAGCGGTAAGATCCTTGAGAGTTTTCGCCCCGAAGAA\n+CGTTTTCCAATGATGAGCACTTTTAAAGTTCTGCTATGTGGCGCGGTATTATCCCGTATTGA\n+CGCCGGGCAAGAGCAACTCGGTCGCCGCATACACTATTCTCAGAATGACTTGGTTGAGTACT\n+CACCAGTCACAGAAAAGCATCTTACGGATGGCATGACAGTAAGAGAATTATGCAGTGCTGCC\n+ATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGA\n+GCTAACCGCTTTTTTGCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGG\n+AGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACA\n+ACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAGA\n+CTGGATGGAGGCGGATAAAGTTGCAGGACCACTTCTGCGCTCGGCCCTTCCGGCTGGCTGGT\n+TTATTGCTGATAAATCTGGAGCCGGTGAGCGTGGGTCTCGCGGTATCATTGCAGCACTGGGG\n+CCAGATGGTAAGCCCTCCCGTATCGTAGTTATCTACACGACGGGGAGTCAGGCAACTATGGA\n+TGAACGAAATAGACAGATCGCTGAGATAGGTGCCTCACTGATTAAGCATTGG\n+>puc18_ORF.49 [3169-3310](-) type:complete length:141 frame:-3 start:CTG stop:TAG\n+CTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGGTGGTTTGTTTGCC\n+GGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACTGGCTTCAGCAGAGCGCAGATACCAA\n+ATACTGTCCTTCTAGTG\n+>puc18_ORF.50 [2791-2929](-) type:5-prime-partial length:138 frame:-3 start:NA stop:TGA\n+GAAAGCGCCACGCTTCCCGAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGG\n+AACAGGAGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTCCTGTCG\n+GGTTTCGCCACCTC\n+>puc18_ORF.51 [2509-2620](-) type:5-prime-partial length:111 frame:-3 start:NA stop:TAA\n+GCTGATACCGCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGCGGA\n+AGAGCGCCCAATACGCAAACCGCCTCTCCCCGCGCGTTGGCCGATTCAT\n+>puc18_ORF.52 [1504-1852](-) type:complete length:348 frame:-3 start:CTG stop:TAA\n+CTGCGTCACGGCTGGATCAAGCACTCGCAACTTGAAGTCCTTGATCGAGGGATACCGGCCTT\n+CCAGTTGAAACCACTTTCGCAGCTGGTCAATTTCTATTTCGCGCTGGCCGATGCTGTCCCAT\n+TGCATGAGCAGCTCGTAAAGCCTGATCGCGTGGGTGCTGTCCATCTTGGCCACGTCAGCCAA\n+GGCGTATTTGGTGAACTGTTTGGTGAGTTCCGTCAGGTACGGCAGCATGTCTTTGGTGAACC\n+TGAGTTCTACACGGCCCTCACCCTCCCGGTAGATGATTGTTTGCACCCAGCCGGTAATCATC\n+ACACTCGGTCTTTTCCCCTTGCCATTGGGCTCTTGGGT\n+>puc18_ORF.53 [1120-1243](-) type:complete length:123 frame:-3 start:TTG stop:TAA\n+TTGTGTATAAGGGGACACTGTATCTGCGTCCCACAATACAACAAATCCGTCCCTTTACAACA\n+ACAAATCCGTCCCTTCTTAACAACAAATCCGTCCCTTAATGGCAACAAATCCGTCCCTTTT\n+>puc18_ORF.54 [694-991](-) type:complete length:297 frame:-3 start:CTG stop:TGA\n+CTGAAGGGGCGGGGGAGGCGTCTGGGCAATCCCCGTTTTACCAGTCCCCTATCGCCGCCTGA\n+GAGGGCGCAGGAAGCGAGTAATCAGGGTATCGAGGCGGATTCACCCTTGGCGTCCAACCAGC\n+GGCACCAGCGGCGCCTGAGAGGCCTACAGAGCGGTTGGACACCAAGGGGAGGGGCTAAGACC\n+GGTTTATCAGTCCCCTTTCCCTCGTTTCTTTCCAACGCGATAGCCCAGCAAGGCCGCCACCG\n+TTGCCACCGTCACCCCAGCAAGCACAGCCAGTGGCGTGTAATTGGGGTC\n+>puc18_ORF.55 [307-514](-) type:complete length:207 frame:-3 start:CTG stop:TAA\n+CTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGG\n+AGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGATCCACGCTCACCGGCTCCA\n+GATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTT\n+ATCCGCCTCCATCCAGTCTAT\n'