Mercurial > repos > crs4 > prokka
changeset 13:a17498c603ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/prokka/ commit ce8dd97ca529558ec475f5eb1f2ce40d765fe396
| author | iuc |
|---|---|
| date | Tue, 21 Mar 2017 10:13:06 -0400 |
| parents | da479161bbe4 |
| children | eaee459f3d69 |
| files | prokka.xml readme.rst test-data/out.err test-data/out.gbk test-data/out.gff test-data/out.sqn test-data/out.tbl |
| diffstat | 7 files changed, 247 insertions(+), 141 deletions(-) [+] |
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--- a/prokka.xml Fri Jan 20 03:39:08 2017 -0500 +++ b/prokka.xml Tue Mar 21 10:13:06 2017 -0400 @@ -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>
--- a/readme.rst Fri Jan 20 03:39:08 2017 -0500 +++ b/readme.rst Tue Mar 21 10:13:06 2017 -0400 @@ -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>.
--- 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 @@ -1,46 +1,144 @@ ->PROKKA_00001 hypothetical protein -ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC -ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC -AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT -GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC -GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC -GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG -TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA -AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA ->PROKKA_00002 hypothetical protein -ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT -ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA ->PROKKA_00003 hypothetical protein -ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT -TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT -GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT -TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC -TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG -TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG -CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT -CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG -TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT -CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG -CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG -TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT -CGCGATTCAATCATGACTTCGTGA ->PROKKA_00004 hypothetical protein -TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT -TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA -ACAATACTGTAG ->PROKKA_00005 hypothetical protein -ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT -TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG -GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT -GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT -AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG -ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA -AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA -AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA -GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT -AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT -ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT -GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC -GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA +Discrepancy Report Results + +Summary +DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein" +FATAL: MISSING_PROTEIN_ID:5 proteins have invalid IDs. +DISC_SOURCE_QUALS_ASNDISC:strain (all present, all same) +DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all same) +DISC_FEATURE_COUNT:CDS: 5 present +DISC_COUNT_NUCLEOTIDES:7 nucleotide Bioseqs are present +FEATURE_LOCATION_CONFLICT:5 features have inconsistent gene locations. +NO_ANNOTATION:3 bioseqs have no features +DISC_QUALITY_SCORES:Quality scores are missing on all sequences. +ONCALLER_COMMENT_PRESENT:7 comment descriptors were found (all same) +SHORT_PROT_SEQUENCES:2 protein sequences are shorter than 50 aa. +MISSING_GENOMEASSEMBLY_COMMENTS:7 bioseqs are missing GenomeAssembly structured comments +MOLTYPE_NOT_MRNA:7 molecule types are not set as mRNA. +TECHNIQUE_NOT_TSA:7 technique are not set as TSA +MISSING_STRUCTURED_COMMENT:7 sequences do not include structured comments. +MISSING_PROJECT:12 sequences do not include project. +DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same) + + +Detailed Report + +DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein" + +FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::5 proteins have invalid IDs. +outdir/prokka:contig2_1 (length 152) +outdir/prokka:contig2_2 (length 38) +outdir/prokka:contig4_1 (length 287) +outdir/prokka:contig5_1 (length 43) +outdir/prokka:contig6_1 (length 253) + +DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all same) +DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'strain' for strain +DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all same) +DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::7 sources have 'Genus species' for taxname +DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 5 present +DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::7 nucleotide Bioseqs are present +outdir/prokka:contig1 (length 350) +outdir/prokka:contig2 (length 840) +outdir/prokka:contig3 (length 210) +outdir/prokka:contig4 (length 1260) +outdir/prokka:contig5 (length 490) +outdir/prokka:contig6 (length 1960) +outdir/prokka:contig7 (length 276) + +DiscRep_ALL:FEATURE_LOCATION_CONFLICT::5 features have inconsistent gene locations. +DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist +outdir/prokka:CDS hypothetical protein contig2:40-498 PROKKA_00001 + +DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist +outdir/prokka:CDS hypothetical protein contig2:498-614 PROKKA_00002 + +DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist +outdir/prokka:CDS hypothetical protein contig4:21-884 PROKKA_00003 + +DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist +outdir/prokka:CDS hypothetical protein contig5:275-406 PROKKA_00004 + +DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist +outdir/prokka:CDS hypothetical protein contig6:6-767 PROKKA_00005 + +DiscRep_ALL:NO_ANNOTATION::3 bioseqs have no features +outdir/prokka:contig1 (length 350) +outdir/prokka:contig3 (length 210) +outdir/prokka:contig7 (length 276) + +DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences. + +DiscRep_ALL:ONCALLER_COMMENT_PRESENT::7 comment descriptors were found (all same) +outdir/prokka:contig1:Annotated using prokka 1.12 from https://github.com/tseemann/prokka +outdir/prokka:contig2:Annotated using prokka 1.12 from https://github.com/tseemann/prokka +outdir/prokka:contig3:Annotated using prokka 1.12 from https://github.com/tseemann/prokka +outdir/prokka:contig4:Annotated using prokka 1.12 from https://github.com/tseemann/prokka +outdir/prokka:contig5:Annotated using prokka 1.12 from https://github.com/tseemann/prokka +outdir/prokka:contig6:Annotated using prokka 1.12 from https://github.com/tseemann/prokka +outdir/prokka:contig7:Annotated using prokka 1.12 from https://github.com/tseemann/prokka + +DiscRep_ALL:SHORT_PROT_SEQUENCES::2 protein sequences are shorter than 50 aa. +outdir/prokka:contig2_2 (length 38) +outdir/prokka:contig5_1 (length 43) + +DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::7 bioseqs are missing GenomeAssembly structured comments +outdir/prokka:contig1 (length 350) +outdir/prokka:contig2 (length 840) +outdir/prokka:contig3 (length 210) +outdir/prokka:contig4 (length 1260) +outdir/prokka:contig5 (length 490) +outdir/prokka:contig6 (length 1960) +outdir/prokka:contig7 (length 276) + +DiscRep_ALL:MOLTYPE_NOT_MRNA::7 molecule types are not set as mRNA. +outdir/prokka:contig1 (length 350) +outdir/prokka:contig2 (length 840) +outdir/prokka:contig3 (length 210) +outdir/prokka:contig4 (length 1260) +outdir/prokka:contig5 (length 490) +outdir/prokka:contig6 (length 1960) +outdir/prokka:contig7 (length 276) + +DiscRep_ALL:TECHNIQUE_NOT_TSA::7 technique are not set as TSA +outdir/prokka:contig1 (length 350) +outdir/prokka:contig2 (length 840) +outdir/prokka:contig3 (length 210) +outdir/prokka:contig4 (length 1260) +outdir/prokka:contig5 (length 490) +outdir/prokka:contig6 (length 1960) +outdir/prokka:contig7 (length 276) + +DiscRep_ALL:MISSING_STRUCTURED_COMMENT::7 sequences do not include structured comments. +outdir/prokka:contig1 (length 350) +outdir/prokka:contig2 (length 840) +outdir/prokka:contig3 (length 210) +outdir/prokka:contig4 (length 1260) +outdir/prokka:contig5 (length 490) +outdir/prokka:contig6 (length 1960) +outdir/prokka:contig7 (length 276) + +DiscRep_ALL:MISSING_PROJECT::12 sequences do not include project. +outdir/prokka:contig1 (length 350) +outdir/prokka:contig2 (length 840) +outdir/prokka:contig2_1 (length 152) +outdir/prokka:contig2_2 (length 38) +outdir/prokka:contig3 (length 210) +outdir/prokka:contig4 (length 1260) +outdir/prokka:contig4_1 (length 287) +outdir/prokka:contig5 (length 490) +outdir/prokka:contig5_1 (length 43) +outdir/prokka:contig6 (length 1960) +outdir/prokka:contig6_1 (length 253) +outdir/prokka:contig7 (length 276) + +DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same) +DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing) +DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::7 Molinfos are missing field technique +outdir/prokka:contig1 (length 350) +outdir/prokka:contig2 (length 840) +outdir/prokka:contig3 (length 210) +outdir/prokka:contig4 (length 1260) +outdir/prokka:contig5 (length 490) +outdir/prokka:contig6 (length 1960) +outdir/prokka:contig7 (length 276) +
--- 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 @@ -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"
--- 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 @@ -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
--- 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 @@ -17,8 +17,8 @@ gcode 11 } } } , molinfo { biomol genomic } , - comment "Annotated using prokka 1.11 from - http://www.vicbioinformatics.com" , + comment "Annotated using prokka 1.12 from + https://github.com/tseemann/prokka" , user { type str "NcbiCleanup" , @@ -37,22 +37,22 @@ label str "month" , data - int 10 } , + int 3 } , { label str "day" , data - int 11 } , + int 21 } , { label str "year" , data - int 2016 } } } , + int 2017 } } } , create-date std { - year 2016 , - month 10 , - day 11 } } , + year 2017 , + month 3 , + day 21 } } , inst { repr raw , mol dna , @@ -75,8 +75,8 @@ subtype strain , subname "strain" } } , gcode 11 } } } , - comment "Annotated using prokka 1.11 from - http://www.vicbioinformatics.com" , + comment "Annotated using prokka 1.12 from + https://github.com/tseemann/prokka" , user { type str "NcbiCleanup" , @@ -95,22 +95,22 @@ label str "month" , data - int 10 } , + int 3 } , { label str "day" , data - int 11 } , + int 21 } , { label str "year" , data - int 2016 } } } , + int 2017 } } } , create-date std { - year 2016 , - month 10 , - day 11 } } , + year 2017 , + month 3 , + day 21 } } , seq-set { seq { id { @@ -234,7 +234,7 @@ qual { { qual "inference" , - val "ab initio prediction:Prodigal:2.60" } } , + val "ab initio prediction:Prodigal:2.6" } } , xref { { data @@ -264,7 +264,7 @@ qual { { qual "inference" , - val "ab initio prediction:Prodigal:2.60" } } , + val "ab initio prediction:Prodigal:2.6" } } , xref { { data @@ -286,8 +286,8 @@ gcode 11 } } } , molinfo { biomol genomic } , - comment "Annotated using prokka 1.11 from - http://www.vicbioinformatics.com" , + comment "Annotated using prokka 1.12 from + https://github.com/tseemann/prokka" , user { type str "NcbiCleanup" , @@ -306,22 +306,22 @@ label str "month" , data - int 10 } , + int 3 } , { label str "day" , data - int 11 } , + int 21 } , { label str "year" , data - int 2016 } } } , + int 2017 } } } , create-date std { - year 2016 , - month 10 , - day 11 } } , + year 2017 , + month 3 , + day 21 } } , inst { repr raw , mol dna , @@ -342,8 +342,8 @@ subtype strain , subname "strain" } } , gcode 11 } } } , - comment "Annotated using prokka 1.11 from - http://www.vicbioinformatics.com" , + comment "Annotated using prokka 1.12 from + https://github.com/tseemann/prokka" , user { type str "NcbiCleanup" , @@ -362,22 +362,22 @@ label str "month" , data - int 10 } , + int 3 } , { label str "day" , data - int 11 } , + int 21 } , { label str "year" , data - int 2016 } } } , + int 2017 } } } , create-date std { - year 2016 , - month 10 , - day 11 } } , + year 2017 , + month 3 , + day 21 } } , seq-set { seq { id { @@ -473,7 +473,7 @@ qual { { qual "inference" , - val "ab initio prediction:Prodigal:2.60" } } , + val "ab initio prediction:Prodigal:2.6" } } , xref { { data @@ -491,8 +491,8 @@ subtype strain , subname "strain" } } , gcode 11 } } } , - comment "Annotated using prokka 1.11 from - http://www.vicbioinformatics.com" , + comment "Annotated using prokka 1.12 from + https://github.com/tseemann/prokka" , user { type str "NcbiCleanup" , @@ -511,22 +511,22 @@ label str "month" , data - int 10 } , + int 3 } , { label str "day" , data - int 11 } , + int 21 } , { label str "year" , data - int 2016 } } } , + int 2017 } } } , create-date std { - year 2016 , - month 10 , - day 11 } } , + year 2017 , + month 3 , + day 21 } } , seq-set { seq { id { @@ -609,7 +609,7 @@ qual { { qual "inference" , - val "ab initio prediction:Prodigal:2.60" } } , + val "ab initio prediction:Prodigal:2.6" } } , xref { { data @@ -627,8 +627,8 @@ subtype strain , subname "strain" } } , gcode 11 } } } , - comment "Annotated using prokka 1.11 from - http://www.vicbioinformatics.com" , + comment "Annotated using prokka 1.12 from + https://github.com/tseemann/prokka" , user { type str "NcbiCleanup" , @@ -647,22 +647,22 @@ label str "month" , data - int 10 } , + int 3 } , { label str "day" , data - int 11 } , + int 21 } , { label str "year" , data - int 2016 } } } , + int 2017 } } } , create-date std { - year 2016 , - month 10 , - day 11 } } , + year 2017 , + month 3 , + day 21 } } , seq-set { seq { id { @@ -767,7 +767,7 @@ qual { { qual "inference" , - val "ab initio prediction:Prodigal:2.60" } } , + val "ab initio prediction:Prodigal:2.6" } } , xref { { data @@ -789,8 +789,8 @@ gcode 11 } } } , molinfo { biomol genomic } , - comment "Annotated using prokka 1.11 from - http://www.vicbioinformatics.com" , + comment "Annotated using prokka 1.12 from + https://github.com/tseemann/prokka" , user { type str "NcbiCleanup" , @@ -809,22 +809,22 @@ label str "month" , data - int 10 } , + int 3 } , { label str "day" , data - int 11 } , + int 21 } , { label str "year" , data - int 2016 } } } , + int 2017 } } } , create-date std { - year 2016 , - month 10 , - day 11 } } , + year 2017 , + month 3 , + day 21 } } , inst { repr raw , mol dna ,
--- 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 @@ -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