| Previous changeset 12:da479161bbe4 (2017-01-20) Next changeset 14:eaee459f3d69 (2018-03-28) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396 |
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modified:
prokka.xml readme.rst test-data/out.err test-data/out.gbk test-data/out.gff test-data/out.sqn test-data/out.tbl |
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| diff -r da479161bbe4 -r a17498c603ec prokka.xml --- a/prokka.xml Fri Jan 20 03:39:08 2017 -0500 +++ b/prokka.xml Tue Mar 21 10:13:06 2017 -0400 |
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| @@ -1,7 +1,7 @@ -<tool id="prokka" name="Prokka" version="1.11.1"> +<tool id="prokka" name="Prokka" version="1.12.0"> <description>prokaryotic genome annotation</description> <requirements> - <requirement type="package" version="1.11">prokka</requirement> + <requirement type="package" version="1.12">prokka</requirement> </requirements> <!-- Need to use stdio because prokka writes some warnings on stderr (due to the "use warnings" Perl pragma) --> <stdio> @@ -189,7 +189,7 @@ <output name="out_sqn" file="out.sqn" lines_diff="84" /> <output name="out_fsa" file="out.fsa" /> <output name="out_tbl" file="out.tbl" /> - <output name="out.err" file="out.err" /> + <output name="out_err" file="out.err" /> <output name="out_txt" file="out.txt" /> <output name="out_log"> <assert_contents> @@ -203,7 +203,7 @@ Prokka_ is a software tool to rapidly annotate bacterial, archaeal and viral genomes, and produce output files that require only minor tweaking to submit to GenBank/ENA/DDBJ. -.. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml +.. _Prokka: http://github.com/tseemann/prokka **Output files** @@ -219,7 +219,7 @@ You can use this tool only if you agree to the license terms of: `Prokka`_. -.. _Prokka: http://www.vicbioinformatics.com/software.prokka.shtml +.. _Prokka: http://github.com/tseemann/prokka ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btu135</citation> |
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| diff -r da479161bbe4 -r a17498c603ec readme.rst --- a/readme.rst Fri Jan 20 03:39:08 2017 -0500 +++ b/readme.rst Tue Mar 21 10:13:06 2017 -0400 |
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| @@ -9,6 +9,7 @@ Version history --------------- +- Release 9 (prokka 1.12.0): Support Prokka 1.12. Uses updated conda dependency 1.12 - Release 8 (prokka 1.11.1): Use Conda for installing tool dependencies, ToolShed dependencies are not supported anymore. Add a test. The tool is now maintained by the IUC. - Release 7 (prokka 1.11.0): Support Prokka 1.11. Upgrade dependencies to package_barrnap_0_7, package_blast_plus_2_2_31, package_hmmer_3_1b2, package_tbl2asn_24_3. - Release 6 (prokka 1.4.0): Use <stdio> because prokka writes some warnings on stderr. Update Orione citation. Update Prokka citation. Support Prokka 1.10. Upgrade dependencies to package_minced_0_1_6, package_barrnap_0_5 and package_tbl2asn_23_7. Added --proteins option. Add <citations>. |
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| diff -r da479161bbe4 -r a17498c603ec test-data/out.err --- a/test-data/out.err Fri Jan 20 03:39:08 2017 -0500 +++ b/test-data/out.err Tue Mar 21 10:13:06 2017 -0400 |
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| b'@@ -1,46 +1,144 @@\n->PROKKA_00001 hypothetical protein\n-ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC\n-ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC\n-AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT\n-GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC\n-GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC\n-GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG\n-TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA\n-AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA\n->PROKKA_00002 hypothetical protein\n-ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT\n-ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA\n->PROKKA_00003 hypothetical protein\n-ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT\n-TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT\n-TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT\n-GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT\n-TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC\n-TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG\n-TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG\n-CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT\n-CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG\n-TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG\n-TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT\n-CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG\n-CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG\n-TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT\n-CGCGATTCAATCATGACTTCGTGA\n->PROKKA_00004 hypothetical protein\n-TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT\n-TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA\n-ACAATACTGTAG\n->PROKKA_00005 hypothetical protein\n-ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT\n-TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG\n-GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT\n-GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT\n-AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG\n-ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA\n-AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA\n-AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA\n-GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT\n-AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT\n-ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT\n-GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC\n-GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA\n+Discrepancy Report Results\n+\n+Summary\n+DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"\n+FATAL: MISSING_PROTEIN_ID:5 proteins have invalid IDs.\n+DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same)\n+DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same)\n+DISC_FEATURE_COUNT:CDS: 5 present\n+DISC_COUNT_NUCLEOTIDES:7 nucleotide Bioseqs are present\n+FEATURE_LOCATION_CONFLICT:5 features have inconsistent gene locations.\n+NO_ANNOTATION:3 bioseqs have no features\n+DISC_QUALITY_SCORES:Quality scores are missing on all sequences.\n+ONCALLER_COMMENT_PRESENT:7 comment descriptors were found (all same)\n+SHORT_PROT_SEQUENCES:2 protein sequences are shorter than 50 aa.\n+MISSING_GENOMEASSEMBLY_COMMENTS:7 bioseqs are missing GenomeAssembly structured comments\n+MOLTYPE_NOT_MRNA:7 molecule types are not set as mRNA.\n+TECHNIQUE_NOT_TSA:7 technique are not set as TSA\n+MISSING_STRUCTURED_COMMENT:7 sequences do not include structured comments.\n+MISSING_PROJECT:12 sequences do not include project.\n+DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)\n+\n+\n+Detailed Report\n+\n+DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"\n+\n+FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::5 proteins have invalid IDs.\n+outdir/prokka:contig2_1 (length 152)\n+outdir/prokka:contig2_2 (length 38)\n+outdir/prokka:contig4_1 (length'..b'ir/prokka:CDS\thypothetical protein\tcontig2:498-614\tPROKKA_00002\n+\n+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist\n+outdir/prokka:CDS\thypothetical protein\tcontig4:21-884\tPROKKA_00003\n+\n+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist\n+outdir/prokka:CDS\thypothetical protein\tcontig5:275-406\tPROKKA_00004\n+\n+DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist\n+outdir/prokka:CDS\thypothetical protein\tcontig6:6-767\tPROKKA_00005\n+\n+DiscRep_ALL:NO_ANNOTATION::3 bioseqs have no features\n+outdir/prokka:contig1 (length 350)\n+outdir/prokka:contig3 (length 210)\n+outdir/prokka:contig7 (length 276)\n+\n+DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.\n+\n+DiscRep_ALL:ONCALLER_COMMENT_PRESENT::7 comment descriptors were found (all same)\n+outdir/prokka:contig1:Annotated using prokka 1.12 from https://github.com/tseemann/prokka\n+outdir/prokka:contig2:Annotated using prokka 1.12 from https://github.com/tseemann/prokka\n+outdir/prokka:contig3:Annotated using prokka 1.12 from https://github.com/tseemann/prokka\n+outdir/prokka:contig4:Annotated using prokka 1.12 from https://github.com/tseemann/prokka\n+outdir/prokka:contig5:Annotated using prokka 1.12 from https://github.com/tseemann/prokka\n+outdir/prokka:contig6:Annotated using prokka 1.12 from https://github.com/tseemann/prokka\n+outdir/prokka:contig7:Annotated using prokka 1.12 from https://github.com/tseemann/prokka\n+\n+DiscRep_ALL:SHORT_PROT_SEQUENCES::2 protein sequences are shorter than 50 aa.\n+outdir/prokka:contig2_2 (length 38)\n+outdir/prokka:contig5_1 (length 43)\n+\n+DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::7 bioseqs are missing GenomeAssembly structured comments\n+outdir/prokka:contig1 (length 350)\n+outdir/prokka:contig2 (length 840)\n+outdir/prokka:contig3 (length 210)\n+outdir/prokka:contig4 (length 1260)\n+outdir/prokka:contig5 (length 490)\n+outdir/prokka:contig6 (length 1960)\n+outdir/prokka:contig7 (length 276)\n+\n+DiscRep_ALL:MOLTYPE_NOT_MRNA::7 molecule types are not set as mRNA.\n+outdir/prokka:contig1 (length 350)\n+outdir/prokka:contig2 (length 840)\n+outdir/prokka:contig3 (length 210)\n+outdir/prokka:contig4 (length 1260)\n+outdir/prokka:contig5 (length 490)\n+outdir/prokka:contig6 (length 1960)\n+outdir/prokka:contig7 (length 276)\n+\n+DiscRep_ALL:TECHNIQUE_NOT_TSA::7 technique are not set as TSA\n+outdir/prokka:contig1 (length 350)\n+outdir/prokka:contig2 (length 840)\n+outdir/prokka:contig3 (length 210)\n+outdir/prokka:contig4 (length 1260)\n+outdir/prokka:contig5 (length 490)\n+outdir/prokka:contig6 (length 1960)\n+outdir/prokka:contig7 (length 276)\n+\n+DiscRep_ALL:MISSING_STRUCTURED_COMMENT::7 sequences do not include structured comments.\n+outdir/prokka:contig1 (length 350)\n+outdir/prokka:contig2 (length 840)\n+outdir/prokka:contig3 (length 210)\n+outdir/prokka:contig4 (length 1260)\n+outdir/prokka:contig5 (length 490)\n+outdir/prokka:contig6 (length 1960)\n+outdir/prokka:contig7 (length 276)\n+\n+DiscRep_ALL:MISSING_PROJECT::12 sequences do not include project.\n+outdir/prokka:contig1 (length 350)\n+outdir/prokka:contig2 (length 840)\n+outdir/prokka:contig2_1 (length 152)\n+outdir/prokka:contig2_2 (length 38)\n+outdir/prokka:contig3 (length 210)\n+outdir/prokka:contig4 (length 1260)\n+outdir/prokka:contig4_1 (length 287)\n+outdir/prokka:contig5 (length 490)\n+outdir/prokka:contig5_1 (length 43)\n+outdir/prokka:contig6 (length 1960)\n+outdir/prokka:contig6_1 (length 253)\n+outdir/prokka:contig7 (length 276)\n+\n+DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)\n+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)\n+DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::7 Molinfos are missing field technique\n+outdir/prokka:contig1 (length 350)\n+outdir/prokka:contig2 (length 840)\n+outdir/prokka:contig3 (length 210)\n+outdir/prokka:contig4 (length 1260)\n+outdir/prokka:contig5 (length 490)\n+outdir/prokka:contig6 (length 1960)\n+outdir/prokka:contig7 (length 276)\n+\n' |
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| diff -r da479161bbe4 -r a17498c603ec test-data/out.gbk --- a/test-data/out.gbk Fri Jan 20 03:39:08 2017 -0500 +++ b/test-data/out.gbk Tue Mar 21 10:13:06 2017 -0400 |
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| @@ -1,4 +1,4 @@ -LOCUS contig1 350 bp DNA linear 11-OCT-2016 +LOCUS contig1 350 bp DNA linear 21-MAR-2017 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -6,7 +6,8 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com. +COMMENT Annotated using prokka 1.12 from + https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..350 /organism="Genus species" @@ -20,7 +21,7 @@ 241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt 301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc // -LOCUS contig2 840 bp DNA linear 11-OCT-2016 +LOCUS contig2 840 bp DNA linear 21-MAR-2017 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -28,7 +29,8 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com. +COMMENT Annotated using prokka 1.12 from + https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..840 /organism="Genus species" @@ -36,7 +38,7 @@ /strain="strain" CDS 40..498 /locus_tag="PROKKA_00001" - /inference="ab initio prediction:Prodigal:2.60" + /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 /product="hypothetical protein" @@ -45,7 +47,7 @@ FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM" CDS 498..614 /locus_tag="PROKKA_00002" - /inference="ab initio prediction:Prodigal:2.60" + /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 /product="hypothetical protein" @@ -66,7 +68,7 @@ 721 agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga 781 tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta // -LOCUS contig3 210 bp DNA linear 11-OCT-2016 +LOCUS contig3 210 bp DNA linear 21-MAR-2017 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -74,7 +76,8 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com. +COMMENT Annotated using prokka 1.12 from + https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..210 /organism="Genus species" @@ -86,7 +89,7 @@ 121 ttgaccatgc cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt 181 tgtttcaggg ttatttgaat atctataaca // -LOCUS contig4 1260 bp DNA linear 11-OCT-2016 +LOCUS contig4 1260 bp DNA linear 21-MAR-2017 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -94,7 +97,8 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com. +COMMENT Annotated using prokka 1.12 from + https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..1260 /organism="Genus species" @@ -102,7 +106,7 @@ /strain="strain" CDS 21..884 /locus_tag="PROKKA_00003" - /inference="ab initio prediction:Prodigal:2.60" + /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 /product="hypothetical protein" @@ -135,7 +139,7 @@ 1141 taatgctggt aatggtggtt ttcttcattg cattcagatg gatacatctg tcaacgccgc 1201 taatcaggtt gtttctgttg gtgctgatat tgcttttgat gccgacccta aattttttgc // -LOCUS contig5 490 bp DNA linear 11-OCT-2016 +LOCUS contig5 490 bp DNA linear 21-MAR-2017 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -143,7 +147,8 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com. +COMMENT Annotated using prokka 1.12 from + https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..490 /organism="Genus species" @@ -151,7 +156,7 @@ /strain="strain" CDS 275..406 /locus_tag="PROKKA_00004" - /inference="ab initio prediction:Prodigal:2.60" + /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 /product="hypothetical protein" @@ -167,7 +172,7 @@ 421 ggtattaaat ctgccattca aggctctaat gttcctaacc ctgatgaggc cgcccctagt 481 tttgtttctg // -LOCUS contig6 1960 bp DNA linear 11-OCT-2016 +LOCUS contig6 1960 bp DNA linear 21-MAR-2017 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -175,7 +180,8 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com. +COMMENT Annotated using prokka 1.12 from + https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..1960 /organism="Genus species" @@ -183,7 +189,7 @@ /strain="strain" CDS 6..767 /locus_tag="PROKKA_00005" - /inference="ab initio prediction:Prodigal:2.60" + /inference="ab initio prediction:Prodigal:2.6" /codon_start=1 /transl_table=11 /product="hypothetical protein" @@ -227,7 +233,7 @@ 1861 tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta 1921 aagaatggaa caactcacta aaaaccaagc tgtcgctact // -LOCUS contig7 276 bp DNA linear 11-OCT-2016 +LOCUS contig7 276 bp DNA linear 21-MAR-2017 DEFINITION Genus species strain strain. ACCESSION VERSION @@ -235,7 +241,8 @@ SOURCE Genus species ORGANISM Genus species Unclassified. -COMMENT Annotated using prokka 1.11 from http://www.vicbioinformatics.com. +COMMENT Annotated using prokka 1.12 from + https://github.com/tseemann/prokka. FEATURES Location/Qualifiers source 1..276 /organism="Genus species" |
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| diff -r da479161bbe4 -r a17498c603ec test-data/out.gff --- a/test-data/out.gff Fri Jan 20 03:39:08 2017 -0500 +++ b/test-data/out.gff Tue Mar 21 10:13:06 2017 -0400 |
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| @@ -6,11 +6,11 @@ ##sequence-region contig5 1 490 ##sequence-region contig6 1 1960 ##sequence-region contig7 1 276 -contig2 Prodigal:2.60 CDS 40 498 . + 0 ID=PROKKA_00001;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00001;product=hypothetical protein -contig2 Prodigal:2.60 CDS 498 614 . + 0 ID=PROKKA_00002;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00002;product=hypothetical protein -contig4 Prodigal:2.60 CDS 21 884 . + 0 ID=PROKKA_00003;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00003;product=hypothetical protein -contig5 Prodigal:2.60 CDS 275 406 . + 0 ID=PROKKA_00004;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00004;product=hypothetical protein -contig6 Prodigal:2.60 CDS 6 767 . + 0 ID=PROKKA_00005;inference=ab initio prediction:Prodigal:2.60;locus_tag=PROKKA_00005;product=hypothetical protein +contig2 Prodigal:2.6 CDS 40 498 . + 0 ID=PROKKA_00001;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00001;product=hypothetical protein +contig2 Prodigal:2.6 CDS 498 614 . + 0 ID=PROKKA_00002;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00002;product=hypothetical protein +contig4 Prodigal:2.6 CDS 21 884 . + 0 ID=PROKKA_00003;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00003;product=hypothetical protein +contig5 Prodigal:2.6 CDS 275 406 . + 0 ID=PROKKA_00004;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00004;product=hypothetical protein +contig6 Prodigal:2.6 CDS 6 767 . + 0 ID=PROKKA_00005;inference=ab initio prediction:Prodigal:2.6;locus_tag=PROKKA_00005;product=hypothetical protein ##FASTA >contig1 GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA |
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| diff -r da479161bbe4 -r a17498c603ec test-data/out.sqn --- a/test-data/out.sqn Fri Jan 20 03:39:08 2017 -0500 +++ b/test-data/out.sqn Tue Mar 21 10:13:06 2017 -0400 |
| b |
| b'@@ -17,8 +17,8 @@\n gcode 11 } } } ,\n molinfo {\n biomol genomic } ,\n- comment "Annotated using prokka 1.11 from\n- http://www.vicbioinformatics.com" ,\n+ comment "Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka" ,\n user {\n type\n str "NcbiCleanup" ,\n@@ -37,22 +37,22 @@\n label\n str "month" ,\n data\n- int 10 } ,\n+ int 3 } ,\n {\n label\n str "day" ,\n data\n- int 11 } ,\n+ int 21 } ,\n {\n label\n str "year" ,\n data\n- int 2016 } } } ,\n+ int 2017 } } } ,\n create-date\n std {\n- year 2016 ,\n- month 10 ,\n- day 11 } } ,\n+ year 2017 ,\n+ month 3 ,\n+ day 21 } } ,\n inst {\n repr raw ,\n mol dna ,\n@@ -75,8 +75,8 @@\n subtype strain ,\n subname "strain" } } ,\n gcode 11 } } } ,\n- comment "Annotated using prokka 1.11 from\n- http://www.vicbioinformatics.com" ,\n+ comment "Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka" ,\n user {\n type\n str "NcbiCleanup" ,\n@@ -95,22 +95,22 @@\n label\n str "month" ,\n data\n- int 10 } ,\n+ int 3 } ,\n {\n label\n str "day" ,\n data\n- int 11 } ,\n+ int 21 } ,\n {\n label\n str "year" ,\n data\n- int 2016 } } } ,\n+ int 2017 } } } ,\n create-date\n std {\n- year 2016 ,\n- month 10 ,\n- day 11 } } ,\n+ year 2017 ,\n+ month 3 ,\n+ day 21 } } ,\n seq-set {\n seq {\n id {\n@@ -234,7 +234,7 @@\n qual {\n {\n qual "inference" ,\n- val "ab initio prediction:Prodigal:2.60" } } ,\n+ val "ab initio prediction:Prodigal:2.6" } } ,\n xref {\n {\n data\n@@ -264,7 +264,7 @@\n qual {\n {\n qual "inference" ,\n- val "ab initio prediction:Prodigal:2.60" } } ,\n+ val "ab initio prediction:Prodigal:2.6" } } ,\n xref {\n {\n data\n@@ -286,8 +286,8 @@\n gcode 11 } } } ,\n molinfo {\n biomol genomic } ,\n- comment "Annotated using prokka 1.11 from\n- http://www.vicbioinformatics.com" ,\n+ comment "Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka" ,\n user {\n type\n str "NcbiCleanup" ,\n@@ -306,22 +306,22 @@\n label\n str "month" ,\n data\n- int 10 } ,\n+ int 3 } ,\n {\n label\n str "day" ,\n data\n- int 11 } ,\n+ int 21 } ,\n {\n label\n str "year" ,\n data\n- int 2016 } } } ,\n+ int 2017 } } } ,\n create-date\n std {\n- year 2016 ,\n- month 10 ,\n- day 11 } } ,\n+ year 2017 ,\n+ month 3 ,\n+ day 21 } } ,\n inst {\n repr raw ,\n mol dna ,\n@@ -342,8 +342,8 @@\n subtype strain ,\n subname "strain" } } ,\n gcode 11 } } } ,\n- comment "Annotated using prokka 1.11 from\n- http://www.vicbioinformatics.com" ,\n+ comment "Annotated using prokka 1.12 from\n+'..b' qual "inference" ,\n- val "ab initio prediction:Prodigal:2.60" } } ,\n+ val "ab initio prediction:Prodigal:2.6" } } ,\n xref {\n {\n data\n@@ -491,8 +491,8 @@\n subtype strain ,\n subname "strain" } } ,\n gcode 11 } } } ,\n- comment "Annotated using prokka 1.11 from\n- http://www.vicbioinformatics.com" ,\n+ comment "Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka" ,\n user {\n type\n str "NcbiCleanup" ,\n@@ -511,22 +511,22 @@\n label\n str "month" ,\n data\n- int 10 } ,\n+ int 3 } ,\n {\n label\n str "day" ,\n data\n- int 11 } ,\n+ int 21 } ,\n {\n label\n str "year" ,\n data\n- int 2016 } } } ,\n+ int 2017 } } } ,\n create-date\n std {\n- year 2016 ,\n- month 10 ,\n- day 11 } } ,\n+ year 2017 ,\n+ month 3 ,\n+ day 21 } } ,\n seq-set {\n seq {\n id {\n@@ -609,7 +609,7 @@\n qual {\n {\n qual "inference" ,\n- val "ab initio prediction:Prodigal:2.60" } } ,\n+ val "ab initio prediction:Prodigal:2.6" } } ,\n xref {\n {\n data\n@@ -627,8 +627,8 @@\n subtype strain ,\n subname "strain" } } ,\n gcode 11 } } } ,\n- comment "Annotated using prokka 1.11 from\n- http://www.vicbioinformatics.com" ,\n+ comment "Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka" ,\n user {\n type\n str "NcbiCleanup" ,\n@@ -647,22 +647,22 @@\n label\n str "month" ,\n data\n- int 10 } ,\n+ int 3 } ,\n {\n label\n str "day" ,\n data\n- int 11 } ,\n+ int 21 } ,\n {\n label\n str "year" ,\n data\n- int 2016 } } } ,\n+ int 2017 } } } ,\n create-date\n std {\n- year 2016 ,\n- month 10 ,\n- day 11 } } ,\n+ year 2017 ,\n+ month 3 ,\n+ day 21 } } ,\n seq-set {\n seq {\n id {\n@@ -767,7 +767,7 @@\n qual {\n {\n qual "inference" ,\n- val "ab initio prediction:Prodigal:2.60" } } ,\n+ val "ab initio prediction:Prodigal:2.6" } } ,\n xref {\n {\n data\n@@ -789,8 +789,8 @@\n gcode 11 } } } ,\n molinfo {\n biomol genomic } ,\n- comment "Annotated using prokka 1.11 from\n- http://www.vicbioinformatics.com" ,\n+ comment "Annotated using prokka 1.12 from\n+ https://github.com/tseemann/prokka" ,\n user {\n type\n str "NcbiCleanup" ,\n@@ -809,22 +809,22 @@\n label\n str "month" ,\n data\n- int 10 } ,\n+ int 3 } ,\n {\n label\n str "day" ,\n data\n- int 11 } ,\n+ int 21 } ,\n {\n label\n str "year" ,\n data\n- int 2016 } } } ,\n+ int 2017 } } } ,\n create-date\n std {\n- year 2016 ,\n- month 10 ,\n- day 11 } } ,\n+ year 2017 ,\n+ month 3 ,\n+ day 21 } } ,\n inst {\n repr raw ,\n mol dna ,\n' |
| b |
| diff -r da479161bbe4 -r a17498c603ec test-data/out.tbl --- a/test-data/out.tbl Fri Jan 20 03:39:08 2017 -0500 +++ b/test-data/out.tbl Tue Mar 21 10:13:06 2017 -0400 |
| b |
| @@ -1,27 +1,27 @@ >Feature contig1 >Feature contig2 40 498 CDS - inference ab initio prediction:Prodigal:2.60 + inference ab initio prediction:Prodigal:2.6 locus_tag PROKKA_00001 product hypothetical protein 498 614 CDS - inference ab initio prediction:Prodigal:2.60 + inference ab initio prediction:Prodigal:2.6 locus_tag PROKKA_00002 product hypothetical protein >Feature contig3 >Feature contig4 21 884 CDS - inference ab initio prediction:Prodigal:2.60 + inference ab initio prediction:Prodigal:2.6 locus_tag PROKKA_00003 product hypothetical protein >Feature contig5 275 406 CDS - inference ab initio prediction:Prodigal:2.60 + inference ab initio prediction:Prodigal:2.6 locus_tag PROKKA_00004 product hypothetical protein >Feature contig6 6 767 CDS - inference ab initio prediction:Prodigal:2.60 + inference ab initio prediction:Prodigal:2.6 locus_tag PROKKA_00005 product hypothetical protein >Feature contig7 |