Mercurial > repos > crs4 > prokka
diff test-data/out.sqn @ 8:392255fa7ab9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit 9a92d439f147a5cf2370e0686854911107de1144
| author | iuc |
|---|---|
| date | Fri, 28 Oct 2016 13:03:19 -0400 |
| parents | |
| children | a17498c603ec |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.sqn Fri Oct 28 13:03:19 2016 -0400 @@ -0,0 +1,836 @@ +Seq-entry ::= set { + class genbank , + seq-set { + seq { + id { + local + str "contig1" } , + descr { + source { + org { + taxname "Genus species" , + orgname { + mod { + { + subtype strain , + subname "strain" } } , + gcode 11 } } } , + molinfo { + biomol genomic } , + comment "Annotated using prokka 1.11 from + http://www.vicbioinformatics.com" , + user { + type + str "NcbiCleanup" , + data { + { + label + str "method" , + data + str "SeriousSeqEntryCleanup" } , + { + label + str "version" , + data + int 8 } , + { + label + str "month" , + data + int 10 } , + { + label + str "day" , + data + int 11 } , + { + label + str "year" , + data + int 2016 } } } , + create-date + std { + year 2016 , + month 10 , + day 11 } } , + inst { + repr raw , + mol dna , + length 350 , + seq-data + iupacna "GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGA +AAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAG +AAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAA +AACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACA +TTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC" } } , + set { + class nuc-prot , + descr { + source { + org { + taxname "Genus species" , + orgname { + mod { + { + subtype strain , + subname "strain" } } , + gcode 11 } } } , + comment "Annotated using prokka 1.11 from + http://www.vicbioinformatics.com" , + user { + type + str "NcbiCleanup" , + data { + { + label + str "method" , + data + str "SeriousSeqEntryCleanup" } , + { + label + str "version" , + data + int 8 } , + { + label + str "month" , + data + int 10 } , + { + label + str "day" , + data + int 11 } , + { + label + str "year" , + data + int 2016 } } } , + create-date + std { + year 2016 , + month 10 , + day 11 } } , + seq-set { + seq { + id { + local + str "contig2" } , + descr { + molinfo { + biomol genomic } } , + inst { + repr raw , + mol dna , + length 840 , + seq-data + iupacna "TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTG +AACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAG +ATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT +GCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTT +ATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATG +GCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTA +CTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGG +CGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGG +TCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCG +TATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGT +TATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGA +CTCTA" } } , + seq { + id { + local + str "contig2_1" } , + descr { + title "hypothetical protein PROKKA_00001 [Genus species]" , + molinfo { + biomol peptide , + tech concept-trans } } , + inst { + repr raw , + mol aa , + length 152 , + seq-data + ncbieaa "MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCV +EACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTD +VLTDAEENVRQKLRAEGVM" } , + annot { + { + data + ftable { + { + id + local + id 3 , + data + prot { + name { + "hypothetical protein" } } , + location + int { + from 0 , + to 151 , + id + local + str "contig2_1" } } } } } } , + seq { + id { + local + str "contig2_2" } , + descr { + title "hypothetical protein PROKKA_00002 [Genus species]" , + molinfo { + biomol peptide , + tech concept-trans } } , + inst { + repr raw , + mol aa , + length 38 , + seq-data + ncbieaa "MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF" } , + annot { + { + data + ftable { + { + id + local + id 4 , + data + prot { + name { + "hypothetical protein" } } , + location + int { + from 0 , + to 37 , + id + local + str "contig2_2" } } } } } } } , + annot { + { + data + ftable { + { + id + local + id 1 , + data + cdregion { + frame one , + code { + id 11 } } , + product + whole + local + str "contig2_1" , + location + int { + from 39 , + to 497 , + strand plus , + id + local + str "contig2" } , + qual { + { + qual "inference" , + val "ab initio prediction:Prodigal:2.60" } } , + xref { + { + data + gene { + locus-tag "PROKKA_00001" } } } } , + { + id + local + id 2 , + data + cdregion { + frame one , + code { + id 11 } } , + product + whole + local + str "contig2_2" , + location + int { + from 497 , + to 613 , + strand plus , + id + local + str "contig2" } , + qual { + { + qual "inference" , + val "ab initio prediction:Prodigal:2.60" } } , + xref { + { + data + gene { + locus-tag "PROKKA_00002" } } } } } } } } , + seq { + id { + local + str "contig3" } , + descr { + source { + org { + taxname "Genus species" , + orgname { + mod { + { + subtype strain , + subname "strain" } } , + gcode 11 } } } , + molinfo { + biomol genomic } , + comment "Annotated using prokka 1.11 from + http://www.vicbioinformatics.com" , + user { + type + str "NcbiCleanup" , + data { + { + label + str "method" , + data + str "SeriousSeqEntryCleanup" } , + { + label + str "version" , + data + int 8 } , + { + label + str "month" , + data + int 10 } , + { + label + str "day" , + data + int 11 } , + { + label + str "year" , + data + int 2016 } } } , + create-date + std { + year 2016 , + month 10 , + day 11 } } , + inst { + repr raw , + mol dna , + length 210 , + seq-data + iupacna "CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATT +AAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTT +CTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA" } } , + set { + class nuc-prot , + descr { + source { + org { + taxname "Genus species" , + orgname { + mod { + { + subtype strain , + subname "strain" } } , + gcode 11 } } } , + comment "Annotated using prokka 1.11 from + http://www.vicbioinformatics.com" , + user { + type + str "NcbiCleanup" , + data { + { + label + str "method" , + data + str "SeriousSeqEntryCleanup" } , + { + label + str "version" , + data + int 8 } , + { + label + str "month" , + data + int 10 } , + { + label + str "day" , + data + int 11 } , + { + label + str "year" , + data + int 2016 } } } , + create-date + std { + year 2016 , + month 10 , + day 11 } } , + seq-set { + seq { + id { + local + str "contig4" } , + descr { + molinfo { + biomol genomic } } , + inst { + repr raw , + mol dna , + length 1260 , + seq-data + iupacna "ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCT +TAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGAC +TGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA +TACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGA +CGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAAC +GTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGG +CACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGC +TTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGT +TTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTC +TCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTAT +TCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGAC +CGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCC +GAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTA +ATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCA +GCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCT +GGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCT +GATATTGCTTTTGATGCCGACCCTAAATTTTTTGC" } } , + seq { + id { + local + str "contig4_1" } , + descr { + title "hypothetical protein PROKKA_00003 [Genus species]" , + molinfo { + biomol peptide , + tech concept-trans } } , + inst { + repr raw , + mol aa , + length 287 , + seq-data + ncbieaa "MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMG +LQAAYANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSV +PRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQW +YRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS" } , + annot { + { + data + ftable { + { + id + local + id 6 , + data + prot { + name { + "hypothetical protein" } } , + location + int { + from 0 , + to 286 , + id + local + str "contig4_1" } } } } } } } , + annot { + { + data + ftable { + { + id + local + id 5 , + data + cdregion { + frame one , + code { + id 11 } } , + product + whole + local + str "contig4_1" , + location + int { + from 20 , + to 883 , + strand plus , + id + local + str "contig4" } , + qual { + { + qual "inference" , + val "ab initio prediction:Prodigal:2.60" } } , + xref { + { + data + gene { + locus-tag "PROKKA_00003" } } } } } } } } , + set { + class nuc-prot , + descr { + source { + org { + taxname "Genus species" , + orgname { + mod { + { + subtype strain , + subname "strain" } } , + gcode 11 } } } , + comment "Annotated using prokka 1.11 from + http://www.vicbioinformatics.com" , + user { + type + str "NcbiCleanup" , + data { + { + label + str "method" , + data + str "SeriousSeqEntryCleanup" } , + { + label + str "version" , + data + int 8 } , + { + label + str "month" , + data + int 10 } , + { + label + str "day" , + data + int 11 } , + { + label + str "year" , + data + int 2016 } } } , + create-date + std { + year 2016 , + month 10 , + day 11 } } , + seq-set { + seq { + id { + local + str "contig5" } , + descr { + molinfo { + biomol genomic } } , + inst { + repr raw , + mol dna , + length 490 , + seq-data + iupacna "CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTAT +GATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCC +CGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTT +TCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTG +GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCA +TTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCT +CTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG" } } , + seq { + id { + local + str "contig5_1" } , + descr { + title "hypothetical protein PROKKA_00004 [Genus species]" , + molinfo { + biomol peptide , + tech concept-trans } } , + inst { + repr raw , + mol aa , + length 43 , + seq-data + ncbieaa "MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL" } , + annot { + { + data + ftable { + { + id + local + id 8 , + data + prot { + name { + "hypothetical protein" } } , + location + int { + from 0 , + to 42 , + id + local + str "contig5_1" } } } } } } } , + annot { + { + data + ftable { + { + id + local + id 7 , + data + cdregion { + frame one , + code { + id 11 } } , + product + whole + local + str "contig5_1" , + location + int { + from 274 , + to 405 , + strand plus , + id + local + str "contig5" } , + qual { + { + qual "inference" , + val "ab initio prediction:Prodigal:2.60" } } , + xref { + { + data + gene { + locus-tag "PROKKA_00004" } } } } } } } } , + set { + class nuc-prot , + descr { + source { + org { + taxname "Genus species" , + orgname { + mod { + { + subtype strain , + subname "strain" } } , + gcode 11 } } } , + comment "Annotated using prokka 1.11 from + http://www.vicbioinformatics.com" , + user { + type + str "NcbiCleanup" , + data { + { + label + str "method" , + data + str "SeriousSeqEntryCleanup" } , + { + label + str "version" , + data + int 8 } , + { + label + str "month" , + data + int 10 } , + { + label + str "day" , + data + int 11 } , + { + label + str "year" , + data + int 2016 } } } , + create-date + std { + year 2016 , + month 10 , + day 11 } } , + seq-set { + seq { + id { + local + str "contig6" } , + descr { + molinfo { + biomol genomic } } , + inst { + repr raw , + mol dna , + length 1960 , + seq-data + iupacna "GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCAC +TTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCG +TGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGT +TGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAA +TGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAA +TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCA +ACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAAT +CAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTC +TCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGG +TATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTC +TAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGT +TCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGA +GGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTT +GGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGC +TTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCC +CCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGT +TACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAA +AGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTT +GATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATT +AGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGG +TCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCT +TCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAA +TCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGA +CGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGT +TGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATG +GAACAACTCACTAAAAACCAAGCTGTCGCTACT" } } , + seq { + id { + local + str "contig6_1" } , + descr { + title "hypothetical protein PROKKA_00005 [Genus species]" , + molinfo { + biomol peptide , + tech concept-trans } } , + inst { + repr raw , + mol aa , + length 253 , + seq-data + ncbieaa "MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNA +WERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQNEMLAYQQKESTA +RVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNV +VTDAASGVVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK" } , + annot { + { + data + ftable { + { + id + local + id 10 , + data + prot { + name { + "hypothetical protein" } } , + location + int { + from 0 , + to 252 , + id + local + str "contig6_1" } } } } } } } , + annot { + { + data + ftable { + { + id + local + id 9 , + data + cdregion { + frame one , + code { + id 11 } } , + product + whole + local + str "contig6_1" , + location + int { + from 5 , + to 766 , + strand plus , + id + local + str "contig6" } , + qual { + { + qual "inference" , + val "ab initio prediction:Prodigal:2.60" } } , + xref { + { + data + gene { + locus-tag "PROKKA_00005" } } } } } } } } , + seq { + id { + local + str "contig7" } , + descr { + source { + org { + taxname "Genus species" , + orgname { + mod { + { + subtype strain , + subname "strain" } } , + gcode 11 } } } , + molinfo { + biomol genomic } , + comment "Annotated using prokka 1.11 from + http://www.vicbioinformatics.com" , + user { + type + str "NcbiCleanup" , + data { + { + label + str "method" , + data + str "SeriousSeqEntryCleanup" } , + { + label + str "version" , + data + int 8 } , + { + label + str "month" , + data + int 10 } , + { + label + str "day" , + data + int 11 } , + { + label + str "year" , + data + int 2016 } } } , + create-date + std { + year 2016 , + month 10 , + day 11 } } , + inst { + repr raw , + mol dna , + length 276 , + seq-data + iupacna "TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAA +TGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGA +AGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGA +CGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA" } } } }