Mercurial > repos > menegidio > mitoprokka
changeset 1:2c228021040a draft default tip
Deleted selected files
| author | menegidio |
|---|---|
| date | Fri, 25 Jun 2021 00:53:19 +0000 |
| parents | 8813044f72bf |
| children | |
| files | mito-prokka/.shed.yml mito-prokka/mito-prokka.xml mito-prokka/test-data/out.err mito-prokka/test-data/out.faa mito-prokka/test-data/out.ffn mito-prokka/test-data/out.fna mito-prokka/test-data/out.fsa mito-prokka/test-data/out.gbk mito-prokka/test-data/out.gff mito-prokka/test-data/out.sqn mito-prokka/test-data/out.tbl mito-prokka/test-data/out.tsv mito-prokka/test-data/out.txt mito-prokka/test-data/phiX174.fasta |
| diffstat | 14 files changed, 0 insertions(+), 1998 deletions(-) [+] |
line wrap: on
line diff
--- a/mito-prokka/.shed.yml Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -name: mito-prokka -owner: menegidio -remote_repository_url: "github.com/menegidio-lab/mitogalaxy/tree/master/tools-shed/mito-prokka" -homepage_url: "https://github.com/tseemann/prokka" -type: unrestricted -description: Mito-Prokka - Rapid annotation of bacteria, archaeal, viral and mitochondria genomes -long_description: | - 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. Mito-Prokka is a version adapted for annotation of - mitochondria and chloroplasts. -categories: -- "Sequence Analysis"
--- a/mito-prokka/mito-prokka.xml Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,249 +0,0 @@ -<tool id="prokka" name="Prokka" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> - <description>Prokaryotic genome annotation</description> - <macros> - <token name="@TOOL_VERSION@">1.14.6</token> - <token name="@VERSION_SUFFIX@">0</token> - </macros> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">prokka</requirement> - </requirements> - - <version_command>prokka --version</version_command> - <command detect_errors="exit_code"><![CDATA[ -prokka ---cpus \${GALAXY_SLOTS:-8} ---quiet ## to avoid non-error messages written to stderr ---outdir outdir --prefix prokka ## used in outputs section -#if $locustag - --locustag '$locustag' -#end if -#if str($increment) - --increment $increment -#end if ---gffver $gffver -#if $compliant.compliant_select == "no" - #if $compliant.addgenes - --addgenes - #end if - #if str($compliant.mincontig) - --mincontig $compliant.mincontig - #end if -#else - --compliant -#end if -#if $centre - --centre '$centre' -#end if -#if $genus - --genus '$genus' -#end if -#if $species - --species '$species' -#end if -#if $strain - --strain '$strain' -#end if -#if $plasmid - --plasmid '$plasmid' -#end if ---kingdom $kingdom.kingdom_select -#if str($kingdom.gcode) - --gcode $kingdom.gcode -#end if -#if $usegenus - --usegenus -#end if -#if $proteins - --proteins '$proteins' -#end if -#if $metagenome - --metagenome -#end if -#if $fast - --fast -#end if -#if str($evalue) - --evalue $evalue -#end if -#if $rfam - --rfam -#end if -#if $norrna - --norrna -#end if -#if $notrna - --notrna -#end if -$input - ]]></command> - <inputs> - <param name="input" type="data" format="fasta" label="Contigs to annotate" help="FASTA format" /> - <param argument="--locustag" type="text" value="" label="Locus tag prefix" /> - <param argument="--increment" type="integer" value="1" min="1" optional="true" label="Locus tag counter increment" /> - <param argument="--gffver" type="select" label="GFF version"> - <option value="3">3</option> - <option value="2">2</option> - <option value="1">1</option> - </param> - <conditional name="compliant"> - <param name="compliant_select" type="select" label="Force GenBank/ENA/DDJB compliance" - help="Equivalent to --addgenes --mincontiglen 200 --centre Prokka (or other centre specified below) (--compliant)"> - <option value="no">No</option> - <option value="yes">Yes</option> - </param> - <when value="no"> - <param name="addgenes" type="boolean" checked="false" label="Add 'gene' features for each 'CDS' feature (--addgenes)" /> - <param name="mincontig" type="integer" value="200" optional="true" label="Minimum contig size (--mincontiglen)" help="NCBI needs 200" /> - </when> - <when value="yes" /> - </conditional> - <param argument="--centre" type="text" value="" label="Sequencing centre ID" /> - <param argument="--genus" type="text" value="" label="Genus name" help="May be used to aid annotation, see --usegenus below" /> - <param argument="--species" type="text" value="" label="Species name" /> - <param argument="--strain" type="text" value="" label="Strain name" /> - <param argument="--plasmid" type="text" value="" label="Plasmid name or identifier" /> - <conditional name="kingdom"> - <param name="kingdom_select" type="select" label="Kingdom" help="(--kingdom)"> - <option value="Archaea">Archaea</option> - <option value="Bacteria">Bacteria</option> - <option value="Mitochondria" selected="true">Mitochondria</option> - <option value="Viruses">Viruses</option> - </param> - <when value="Archaea"> - <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> - </when> - <when value="Bacteria"> - <param argument="--gcode" type="integer" value="11" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> - <!-- <param name="gram" type="select" display="radio" label="Gram (- -gram)"> - <option selected="true" value="none">N/A</option> - <option value="pos">positive</option> - <option value="neg">negative</option> - </param> SignalP is not FOSS --> - </when> - <when value="Mitochondria"> - <param argument="--gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> - </when> - <when value="Viruses"> - <param argument="--gcode" type="integer" value="1" min="1" max="23" optional="true" label="Genetic code (transl_table)" /><!-- max should be 25, but prodigal would crash --> - </when> - </conditional> - <param argument="--usegenus" type="boolean" checked="false" label="Use genus-specific BLAST database" help="Will use the BLAST database for the genus specified above, if installed" /> - <param argument="--proteins" type="data" format="fasta" optional="true" label="Optional FASTA file of trusted proteins to first annotate from" /> - <param argument="--metagenome" type="boolean" checked="false" label="Improve gene predictions for highly fragmented genomes" help="Will set --meta option for Prodigal" /> - <param argument="--fast" type="boolean" checked="false" label="Fast mode" help="Skip CDS /product searching" /> - <param argument="--evalue" type="float" value="1e-06" min="0" optional="true" label="Similarity e-value cut-off" /> - <param argument="--rfam" type="boolean" checked="false" label="Enable searching for ncRNAs with Infernal+Rfam (SLOW!)" /> - <param argument="--norrna" type="boolean" checked="false" label="Don't run rRNA search with Barrnap" /> - <param argument="--notrna" type="boolean" checked="false" label="Don't run tRNA search with Aragorn" /> - - <param name="outputs" type="select" multiple="true" display="checkboxes" label="Additional outputs"> - <option value="gff" selected="True">Annotation in GFF3 format, containing both sequences and annotations (.gff)</option> - <option value="gbk" selected="True">Standard GenBank file. If the input was a multi-FASTA, then this will be a multi-GenBank, with one record for each sequence (.gbk)</option> - <option value="fna" selected="True">Nucleotide FASTA file of the input contig sequences (.fna)</option> - <option value="faa" selected="True">Protein FASTA file of the translated CDS sequences (.faa)</option> - <option value="ffn" selected="True">Nucleotide FASTA file of all the annotated sequences, not just CDS (.ffn)</option> - <option value="sqn" selected="True">An ASN1 format "Sequin" file for submission to GenBank. It needs to be edited to set the correct taxonomy, authors, related publication, etc. (.sqn)</option> - <option value="fsa" selected="True">Nucleotide FASTA file of the input contig sequences, with extra Sequin tags in the sequence description lines (.fsa)</option> - <option value="tbl" selected="True">Feature Table file (.tbl)</option> - <option value="tsv" selected="True">Annotations in tabular format including COGs etc.</option> - <option value="err" selected="True">Unacceptable annotations - the NCBI discrepancy report (.err)</option> - <option value="txt" selected="True">Statistics relating to the annotated features found (.txt)</option> - </param> - - </inputs> - <outputs> - <data name="out_gff" format="gff" label="${tool.name} on ${on_string}: gff" from_work_dir="outdir/prokka.gff"> - <filter>outputs and 'gff' in outputs</filter> - </data> - <data name="out_gbk" format="genbank" label="${tool.name} on ${on_string}: gbk" from_work_dir="outdir/prokka.gbk"> - <filter>outputs and 'gbk' in outputs</filter> - </data> - <data name="out_fna" format="fasta" label="${tool.name} on ${on_string}: fna" from_work_dir="outdir/prokka.fna"> - <filter>outputs and 'fna' in outputs</filter> - </data> - <data name="out_faa" format="fasta" label="${tool.name} on ${on_string}: faa" from_work_dir="outdir/prokka.faa"> - <filter>outputs and 'faa' in outputs</filter> - </data> - <data name="out_ffn" format="fasta" label="${tool.name} on ${on_string}: ffn" from_work_dir="outdir/prokka.ffn"> - <filter>outputs and 'ffn' in outputs</filter> - </data> - <data name="out_sqn" format="asn1" label="${tool.name} on ${on_string}: sqn" from_work_dir="outdir/prokka.sqn"> - <filter>outputs and 'sqn' in outputs</filter> - </data> - <data name="out_fsa" format="fasta" label="${tool.name} on ${on_string}: fsa" from_work_dir="outdir/prokka.fsa"> - <filter>outputs and 'fsa' in outputs</filter> - </data> - <data name="out_tbl" format="txt" label="${tool.name} on ${on_string}: tbl" from_work_dir="outdir/prokka.tbl"> - <filter>outputs and 'tbl' in outputs</filter> - </data> - <data name="out_tsv" format="tabular" label="${tool.name} on ${on_string}: tsv" from_work_dir="outdir/prokka.tsv"> - <filter>outputs and 'tsv' in outputs</filter> - </data> - <data name="out_err" format="txt" label="${tool.name} on ${on_string}: err" from_work_dir="outdir/prokka.err"> - <filter>outputs and 'err' in outputs</filter> - </data> - <data name="out_txt" format="txt" label="${tool.name} on ${on_string}: txt" from_work_dir="outdir/prokka.txt"> - <filter>outputs and 'txt' in outputs</filter> - </data> - <data name="out_log" format="txt" label="${tool.name} on ${on_string}: log" from_work_dir="outdir/prokka.log" /> - </outputs> - <tests> - <test> - <param name="input" ftype="fasta" value="phiX174.fasta" /> - <param name="outputs" value="gff,gbk,fna,faa,ffn,sqn,fsa,tbl,tsv,err,txt" /> - <output name="out_gff" file="out.gff" /> - <output name="out_gbk" > - <assert_contents> - <has_text_matching expression="LOCUS" /> - <has_text_matching expression="//" /> - </assert_contents> - </output> - <output name="out_fna" file="out.fna" /> - <output name="out_faa" file="out.faa" /> - <output name="out_ffn" file="out.ffn" /> - <output name="out_sqn" > - <assert_contents> - <has_text_matching expression="Seq-entry" /> - <has_text_matching expression="contig2" /> - </assert_contents> - </output> - <output name="out_fsa" file="out.fsa" /> - <output name="out_tbl" file="out.tbl" /> - <output name="out_tsv" file="out.tsv" /> - <output name="out_err" file="out.err" lines_diff="14" /> - <output name="out_txt" file="out.txt" /> - <output name="out_log"> - <assert_contents> - <has_text text="Type 'prokka --citation' for more details." /> - </assert_contents> - </output> - </test> - </tests> - <help><![CDATA[ -**What it does** - -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://github.com/tseemann/prokka - -**Output files** - -Prokka creates several output files, which are described in the **Additional outputs** section above. - -**License and citation** - -This Galaxy tool is Copyright © 2013 Lionel Guy, © 2013-2014 `CRS4 Srl.`_, © 2015-2016 `Earlham Institute`_, 2018 `Galaxy IUC` and is released under the `MIT license`_. - -.. _CRS4 Srl.: http://www.crs4.it/ -.. _Earlham Institute: http://earlham.ac.uk/ -.. _MIT license: https://opensource.org/licenses/MIT - -You can use this tool only if you agree to the license terms of: `Prokka`_. - -.. _Prokka: http://github.com/tseemann/prokka - ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btu135</citation> - <citation type="doi">10.1093/bioinformatics/btu153</citation> - </citations> -</tool>
--- a/mito-prokka/test-data/out.err Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,144 +0,0 @@ -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 HMJLFLJH_00001 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -outdir/prokka:CDS hypothetical protein contig2:498-614 HMJLFLJH_00002 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -outdir/prokka:CDS hypothetical protein contig4:21-884 HMJLFLJH_00003 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -outdir/prokka:CDS hypothetical protein contig5:275-406 HMJLFLJH_00004 - -DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist -outdir/prokka:CDS hypothetical protein contig6:6-767 HMJLFLJH_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 1.14.5 from https://github.com/tseemann/prokka -outdir/prokka:contig2:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka -outdir/prokka:contig3:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka -outdir/prokka:contig4:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka -outdir/prokka:contig5:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka -outdir/prokka:contig6:Annotated using prokka 1.14.5 from https://github.com/tseemann/prokka -outdir/prokka:contig7:Annotated using prokka 1.14.5 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/mito-prokka/test-data/out.faa Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ ->HMJLFLJH_00001 hypothetical protein -MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVY -GTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAEL -FAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM ->HMJLFLJH_00002 hypothetical protein -MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF ->HMJLFLJH_00003 hypothetical protein -MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAY -ANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQ -FSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVL -YGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDL -QERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS ->HMJLFLJH_00004 hypothetical protein -MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL ->HMJLFLJH_00005 hypothetical protein -MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRDYLAAAFPELNAWERAG -ADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIAGIQSATSRQNTKDQVYAQ -NEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQAQTAGQYFTNDQIKEMTRKV -SAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASGVVDIFHGIDKAVADTWNNFWKD -GKADGIGSNLSRK
--- a/mito-prokka/test-data/out.ffn Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ ->HMJLFLJH_00001 hypothetical protein -ATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTC -ATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAAC -AAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTAT -GGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCC -GTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGC -GCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTG -TTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAA -AACGTGCGTCAAAAATTACGTGCGGAAGGAGTGATGTAA ->HMJLFLJH_00002 hypothetical protein -ATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGT -ACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAA ->HMJLFLJH_00003 hypothetical protein -ATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGT -TTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT -GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATT -TCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGC -TCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAG -TTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAG -CATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT -CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCG -TCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCT -CCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTG -CAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG -TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACT -CGCGATTCAATCATGACTTCGTGA ->HMJLFLJH_00004 hypothetical protein -TTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGT -TTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATA -ACAATACTGTAG ->HMJLFLJH_00005 hypothetical protein -ATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTT -TCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAG -GATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGT -GCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACT -AAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAG -ATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAA -AATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAA -AACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAA -GCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTT -AGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCAT -ATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTT -GATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGAC -GGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAA
--- a/mito-prokka/test-data/out.fna Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ ->contig1 -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA -AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC -TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT -GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG -TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT -CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC ->contig2 -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA -TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG -GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC -CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA -TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT -CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT -ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT -GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC -CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG -GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA -TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC -AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA -TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA ->contig3 -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA -AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA -TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT -TGTTTCAGGGTTATTTGAATATCTATAACA ->contig4 -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC -AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC -TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA -TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC -AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC -GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG -ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC -CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA -TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG -TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT -ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG -AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT -GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG -AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA -TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC -ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT -TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC -TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC ->contig5 -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT -TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT -TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA -CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT -TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT -TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC -GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT -TTTGTTTCTG ->contig6 -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG -CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG -GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG -CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC -TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA -AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG -CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA -CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA -AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT -CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG -TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA -AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA -CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA -AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC -ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG -GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC -GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG -TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT -GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT -GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT -TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA -CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT -TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG -CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT -TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA -GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC -CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG -TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA -AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT ->contig7 -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT -GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC -GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT -TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG -CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
--- a/mito-prokka/test-data/out.fsa Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,99 +0,0 @@ ->contig1 [gcode=11] [organism=Genus species] [strain=strain] -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA -AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC -TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT -GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG -TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT -CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC ->contig2 [gcode=11] [organism=Genus species] [strain=strain] -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA -TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG -GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC -CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA -TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT -CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT -ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT -GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC -CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG -GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA -TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC -AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA -TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA ->contig3 [gcode=11] [organism=Genus species] [strain=strain] -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA -AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA -TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT -TGTTTCAGGGTTATTTGAATATCTATAACA ->contig4 [gcode=11] [organism=Genus species] [strain=strain] -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC -AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC -TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA -TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC -AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC -GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG -ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC -CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA -TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG -TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT -ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG -AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT -GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG -AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA -TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC -ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT -TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC -TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC ->contig5 [gcode=11] [organism=Genus species] [strain=strain] -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT -TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT -TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA -CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT -TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT -TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC -GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT -TTTGTTTCTG ->contig6 [gcode=11] [organism=Genus species] [strain=strain] -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG -CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG -GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG -CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC -TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA -AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG -CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA -CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA -AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT -CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG -TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA -AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA -CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA -AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC -ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG -GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC -GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG -TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT -GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT -GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT -TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA -CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT -TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG -CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT -TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA -GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC -CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG -TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA -AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT ->contig7 [gcode=11] [organism=Genus species] [strain=strain] -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT -GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC -GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT -TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG -CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
--- a/mito-prokka/test-data/out.gbk Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,257 +0,0 @@ -LOCUS contig1 350 bp DNA linear 27-MAR-2018 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.13 from - https://github.com/tseemann/prokka. -FEATURES Location/Qualifiers - source 1..350 - /organism="Genus species" - /mol_type="genomic DNA" - /strain="strain" -ORIGIN - 1 gagttttatc gcttccatga cgcagaagtt aacactttcg gatatttctg atgagtcgaa - 61 aaattatctt gataaagcag gaattactac tgcttgttta cgaattaaat cgaagtggac - 121 tgctggcgga aaatgagaaa attcgaccta tccttgcgca gctcgagaag ctcttacttt - 181 gcgacctttc gccatcaact aacgattctg tcaaaaactg acgcgttgga tgaggagaag - 241 tggcttaata tgcttggcac gttcgtcaag gactggttta gatatgagtc acattttgtt - 301 catggtagag attctcttgt tgacatttta aaagagcgtg gattactatc -// -LOCUS contig2 840 bp DNA linear 27-MAR-2018 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.13 from - https://github.com/tseemann/prokka. -FEATURES Location/Qualifiers - source 1..840 - /organism="Genus species" - /mol_type="genomic DNA" - /strain="strain" - CDS 40..498 - /locus_tag="HMJLFLJH_00001" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWI - ATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAE - FTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM" - CDS 498..614 - /locus_tag="HMJLFLJH_00002" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MSKGKKRSGARPGRPQPLRGTKGKRKGARLWYVGGQQF" -ORIGIN - 1 tgagtccgat gctgttcaac cactaatagg taagaaatca tgagtcaagt tactgaacaa - 61 tccgtacgtt tccagaccgc tttggcctct attaagctca ttcaggcttc tgccgttttg - 121 gatttaaccg aagatgattt cgattttctg acgagtaaca aagtttggat tgctactgac - 181 cgctctcgtg ctcgtcgctg cgttgaggct tgcgtttatg gtacgctgga ctttgtggga - 241 taccctcgct ttcctgctcc tgttgagttt attgctgccg tcattgctta ttatgttcat - 301 cccgtcaaca ttcaaacggc ctgtctcatc atggaaggcg ctgaatttac ggaaaacatt - 361 attaatggcg tcgagcgtcc ggttaaagcc gctgaattgt tcgcgtttac cttgcgtgta - 421 cgcgcaggaa acactgacgt tcttactgac gcagaagaaa acgtgcgtca aaaattacgt - 481 gcggaaggag tgatgtaatg tctaaaggta aaaaacgttc tggcgctcgc cctggtcgtc - 541 cgcagccgtt gcgaggtact aaaggcaagc gtaaaggcgc tcgtctttgg tatgtaggtg - 601 gtcaacaatt ttaattgcag gggcttcggc cccttacttg aggataaatt atgtctaata - 661 ttcaaactgg cgccgagcgt atgccgcatg acctttccca tcttggcttc cttgctggtc - 721 agattggtcg tcttattacc atttcaacta ctccggttat cgctggcgac tccttcgaga - 781 tggacgccgt tggcgctctc cgtctttctc cattgcgtcg tggccttgct attgactcta -// -LOCUS contig3 210 bp DNA linear 27-MAR-2018 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.13 from - https://github.com/tseemann/prokka. -FEATURES Location/Qualifiers - source 1..210 - /organism="Genus species" - /mol_type="genomic DNA" - /strain="strain" -ORIGIN - 1 ctgtagacat ttttactttt tatgtccctc atcgtcacgt ttatggtgaa cagtggatta - 61 agttcatgaa ggatggtgtt aatgccactc ctctcccgac tgttaacact actggttata - 121 ttgaccatgc cgcttttctt ggcacgatta accctgatac caataaaatc cctaagcatt - 181 tgtttcaggg ttatttgaat atctataaca -// -LOCUS contig4 1260 bp DNA linear 27-MAR-2018 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.13 from - https://github.com/tseemann/prokka. -FEATURES Location/Qualifiers - source 1..1260 - /organism="Genus species" - /mol_type="genomic DNA" - /strain="strain" - CDS 21..884 - /locus_tag="HMJLFLJH_00003" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MPDRTEANPNELNQDDARYGFRCCHLKNIWTAPLPPETELSRQM - TTSTTSIDIMGLQAAYANLHTDQERDYFMQRYHDVISSFGGKTSYDADNRPLLVMRSN - LWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEI - QYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSY - VSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRN - LPTTRDSIMTS" -ORIGIN - 1 actattttaa agcgccgtgg atgcctgacc gtaccgaggc taaccctaat gagcttaatc - 61 aagatgatgc tcgttatggt ttccgttgct gccatctcaa aaacatttgg actgctccgc - 121 ttcctcctga gactgagctt tctcgccaaa tgacgacttc taccacatct attgacatta - 181 tgggtctgca agctgcttat gctaatttgc atactgacca agaacgtgat tacttcatgc - 241 agcgttacca tgatgttatt tcttcatttg gaggtaaaac ctcttatgac gctgacaacc - 301 gtcctttact tgtcatgcgc tctaatctct gggcatctgg ctatgatgtt gatggaactg - 361 accaaacgtc gttaggccag ttttctggtc gtgttcaaca gacctataaa cattctgtgc - 421 cgcgtttctt tgttcctgag catggcacta tgtttactct tgcgcttgtt cgttttccgc - 481 ctactgcgac taaagagatt cagtacctta acgctaaagg tgctttgact tataccgata - 541 ttgctggcga ccctgttttg tatggcaact tgccgccgcg tgaaatttct atgaaggatg - 601 ttttccgttc tggtgattcg tctaagaagt ttaagattgc tgagggtcag tggtatcgtt - 661 atgcgccttc gtatgtttct cctgcttatc accttcttga aggcttccca ttcattcagg - 721 aaccgccttc tggtgatttg caagaacgcg tacttattcg ccaccatgat tatgaccagt - 781 gtttccagtc cgttcagttg ttgcagtgga atagtcaggt taaatttaat gtgaccgttt - 841 atcgcaatct gccgaccact cgcgattcaa tcatgacttc gtgataaaag attgagtgtg - 901 aggttataac gccgaagcgg taaaaatttt aatttttgcc gctgaggggt tgaccaagcg - 961 aagcgcggta ggttttctgc ttaggagttt aatcatgttt cagactttta tttctcgcca - 1021 taattcaaac tttttttctg ataagctggt tctcacttct gttactccag cttcttcggc - 1081 acctgtttta cagacaccta aagctacatc gtcaacgtta tattttgata gtttgacggt - 1141 taatgctggt aatggtggtt ttcttcattg cattcagatg gatacatctg tcaacgccgc - 1201 taatcaggtt gtttctgttg gtgctgatat tgcttttgat gccgacccta aattttttgc -// -LOCUS contig5 490 bp DNA linear 27-MAR-2018 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.13 from - https://github.com/tseemann/prokka. -FEATURES Location/Qualifiers - source 1..490 - /organism="Genus species" - /mol_type="genomic DNA" - /strain="strain" - CDS 275..406 - /locus_tag="HMJLFLJH_00004" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MVLLLAVLLLLLLVAPCLNCLEAVKKPPPVAFKVMCLLPITIL" -ORIGIN - 1 ctgtttggtt cgctttgagt cttcttcggt tccgactacc ctcccgactg cctatgatgt - 61 ttatcctttg aatggtcgcc atgatggtgg ttattatacc gtcaaggact gtgtgactat - 121 tgacgtcctt ccccgtacgc cgggcaataa cgtttatgtt ggtttcatgg tttggtctaa - 181 ctttaccgct actaaatgcc gcggattggt ttcgctgaat caggttatta aagagattat - 241 ttgtctccag ccacttaagt gaggtgattt atgtttggtg ctattgctgg cggtattgct - 301 tctgctcttg ctggtggcgc catgtctaaa ttgtttggag gcggtcaaaa agccgcctcc - 361 ggtggcattc aaggtgatgt gcttgctacc gataacaata ctgtaggcat gggtgatgct - 421 ggtattaaat ctgccattca aggctctaat gttcctaacc ctgatgaggc cgcccctagt - 481 tttgtttctg -// -LOCUS contig6 1960 bp DNA linear 27-MAR-2018 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.13 from - https://github.com/tseemann/prokka. -FEATURES Location/Qualifiers - source 1..1960 - /organism="Genus species" - /mol_type="genomic DNA" - /strain="strain" - CDS 6..767 - /locus_tag="HMJLFLJH_00005" - /inference="ab initio prediction:Prodigal:2.6" - /codon_start=1 - /transl_table=11 - /product="hypothetical protein" - /translation="MAKAGKGLLEGTLQAGTSAVSDKLLDLVGLGGKSAADKGKDTRD - YLAAAFPELNAWERAGADASSAGMVDAGFENQKELTKMQLDNQKEIAEMQNETQKEIA - GIQSATSRQNTKDQVYAQNEMLAYQQKESTARVASIMENTNLSKQQQVSEIMRQMLTQ - AQTAGQYFTNDQIKEMTRKVSAEVDLVHQQTQNQRYGSSHIGATAKDISNVVTDAASG - VVDIFHGIDKAVADTWNNFWKDGKADGIGSNLSRK" -ORIGIN - 1 gtgctatggc taaagctggt aaaggacttc ttgaaggtac gttgcaggct ggcacttctg - 61 ccgtttctga taagttgctt gatttggttg gacttggtgg caagtctgcc gctgataaag - 121 gaaaggatac tcgtgattat cttgctgctg catttcctga gcttaatgct tgggagcgtg - 181 ctggtgctga tgcttcctct gctggtatgg ttgacgccgg atttgagaat caaaaagagc - 241 ttactaaaat gcaactggac aatcagaaag agattgccga gatgcaaaat gagactcaaa - 301 aagagattgc tggcattcag tcggcgactt cacgccagaa tacgaaagac caggtatatg - 361 cacaaaatga gatgcttgct tatcaacaga aggagtctac tgctcgcgtt gcgtctatta - 421 tggaaaacac caatctttcc aagcaacagc aggtttccga gattatgcgc caaatgctta - 481 ctcaagctca aacggctggt cagtatttta ccaatgacca aatcaaagaa atgactcgca - 541 aggttagtgc tgaggttgac ttagttcatc agcaaacgca gaatcagcgg tatggctctt - 601 ctcatattgg cgctactgca aaggatattt ctaatgtcgt cactgatgct gcttctggtg - 661 tggttgatat ttttcatggt attgataaag ctgttgccga tacttggaac aatttctgga - 721 aagacggtaa agctgatggt attggctcta atttgtctag gaaataaccg tcaggattga - 781 caccctccca attgtatgtt ttcatgcctc caaatcttgg aggctttttt atggttcgtt - 841 cttattaccc ttctgaatgt cacgctgatt attttgactt tgagcgtatc gaggctctta - 901 aacctgctat tgaggcttgt ggcatttcta ctctttctca atccccaatg cttggcttcc - 961 ataagcagat ggataaccgc atcaagctct tggaagagat tctgtctttt cgtatgcagg - 1021 gcgttgagtt cgataatggt gatatgtatg ttgacggcca taaggctgct tctgacgttc - 1081 gtgatgagtt tgtatctgtt actgagaagt taatggatga attggcacaa tgctacaatg - 1141 tgctccccca acttgatatt aataacacta tagaccaccg ccccgaaggg gacgaaaaat - 1201 ggtttttaga gaacgagaag acggttacgc agttttgccg caagctggct gctgaacgcc - 1261 ctcttaagga tattcgcgat gagtataatt accccaaaaa gaaaggtatt aaggatgagt - 1321 gttcaagatt gctggaggcc tccactatga aatcgcgtag aggctttgct attcagcgtt - 1381 tgatgaatgc aatgcgacag gctcatgctg atggttggtt tatcgttttt gacactctca - 1441 cgttggctga cgaccgatta gaggcgtttt atgataatcc caatgctttg cgtgactatt - 1501 ttcgtgatat tggtcgtatg gttcttgctg ccgagggtcg caaggctaat gattcacacg - 1561 ccgactgcta tcagtatttt tgtgtgcctg agtatggtac agctaatggc cgtcttcatt - 1621 tccatgcggt gcactttatg cggacacttc ctacaggtag cgttgaccct aattttggtc - 1681 gtcgggtacg caatcgccgc cagttaaata gcttgcaaaa tacgtggcct tatggttaca - 1741 gtatgcccat cgcagttcgc tacacgcagg acgctttttc acgttctggt tggttgtggc - 1801 ctgttgatgc taaaggtgag ccgcttaaag ctaccagtta tatggctgtt ggtttctatg - 1861 tggctaaata cgttaacaaa aagtcagata tggaccttgc tgctaaaggt ctaggagcta - 1921 aagaatggaa caactcacta aaaaccaagc tgtcgctact -// -LOCUS contig7 276 bp DNA linear 27-MAR-2018 -DEFINITION Genus species strain strain. -ACCESSION -VERSION -KEYWORDS . -SOURCE Genus species - ORGANISM Genus species - Unclassified. -COMMENT Annotated using prokka 1.13 from - https://github.com/tseemann/prokka. -FEATURES Location/Qualifiers - source 1..276 - /organism="Genus species" - /mol_type="genomic DNA" - /strain="strain" -ORIGIN - 1 tcccaagaag ctgttcagaa tcagaatgag ccgcaacttc gggatgaaaa tgctcacaat - 61 gacaaatctg tccacggagt gcttaatcca acttaccaag ctgggttacg acgcgacgcc - 121 gttcaaccag atattgaagc agaacgcaaa aagagagatg agattgaggc tgggaaaagt - 181 tactgtagcc gacgttttgg cggcgcaacc tgtgacgaca aatctgctca aatttatgcg - 241 cgcttcgata aaaatgattg gcgtatccaa cctgca -//
--- a/mito-prokka/test-data/out.gff Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,113 +0,0 @@ -##gff-version 3 -##sequence-region contig1 1 350 -##sequence-region contig2 1 840 -##sequence-region contig3 1 210 -##sequence-region contig4 1 1260 -##sequence-region contig5 1 490 -##sequence-region contig6 1 1960 -##sequence-region contig7 1 276 -contig2 Prodigal:002006 CDS 40 498 . + 0 ID=HMJLFLJH_00001;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00001;product=hypothetical protein -contig2 Prodigal:002006 CDS 498 614 . + 0 ID=HMJLFLJH_00002;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00002;product=hypothetical protein -contig4 Prodigal:002006 CDS 21 884 . + 0 ID=HMJLFLJH_00003;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00003;product=hypothetical protein -contig5 Prodigal:002006 CDS 275 406 . + 0 ID=HMJLFLJH_00004;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00004;product=hypothetical protein -contig6 Prodigal:002006 CDS 6 767 . + 0 ID=HMJLFLJH_00005;inference=ab initio prediction:Prodigal:002006;locus_tag=HMJLFLJH_00005;product=hypothetical protein -##FASTA ->contig1 -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAA -AAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGAC -TGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTT -GCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAG -TGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT -CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC ->contig2 -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAA -TCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTG -GATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGAC -CGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGA -TACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT -CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATT -ATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGT -GCGGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTC -CGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG -GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATA -TTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTC -AGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGA -TGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA ->contig3 -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA -AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATA -TTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATT -TGTTTCAGGGTTATTTGAATATCTATAACA ->contig4 -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATC -AAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGC -TTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTA -TGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGC -AGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC -GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTG -ACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGC -CTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATA -TTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG -TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTT -ATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGG -AACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGT -GTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG -AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCG -AAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCA -TAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGC -ACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGT -TAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC -TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC ->contig5 -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGT -TTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTAT -TGACGTCCTTCCCCGTACGCCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAA -CTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT -TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCT -TCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCC -GGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGT -TTTGTTTCTG ->contig6 -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTG -CCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAG -GAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTG -CTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGC -TTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA -AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATG -CACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTA -CTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCA -AGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT -CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTG -TGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGA -AAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGA -CACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA -AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCC -ATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGG -GCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTC -GTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATG -TGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT -GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGT -GTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTT -TGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCA -CGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT -TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACG -CCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATT -TCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACA -GTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC -CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATG -TGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTA -AAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT ->contig7 -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAAT -GACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCC -GTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGT -TACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG -CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
--- a/mito-prokka/test-data/out.sqn Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,836 +0,0 @@ -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 1.13 from - https://github.com/tseemann/prokka" , - user { - type - str "NcbiCleanup" , - data { - { - label - str "method" , - data - str "SeriousSeqEntryCleanup" } , - { - label - str "version" , - data - int 8 } , - { - label - str "month" , - data - int 3 } , - { - label - str "day" , - data - int 27 } , - { - label - str "year" , - data - int 2018 } } } , - create-date - std { - year 2018 , - month 3 , - day 27 } } , - 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 1.13 from - https://github.com/tseemann/prokka" , - user { - type - str "NcbiCleanup" , - data { - { - label - str "method" , - data - str "SeriousSeqEntryCleanup" } , - { - label - str "version" , - data - int 8 } , - { - label - str "month" , - data - int 3 } , - { - label - str "day" , - data - int 27 } , - { - label - str "year" , - data - int 2018 } } } , - create-date - std { - year 2018 , - month 3 , - day 27 } } , - 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 HMJLFLJH_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 HMJLFLJH_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:2.6" } } , - xref { - { - data - gene { - locus-tag "HMJLFLJH_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:2.6" } } , - xref { - { - data - gene { - locus-tag "HMJLFLJH_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 1.13 from - https://github.com/tseemann/prokka" , - user { - type - str "NcbiCleanup" , - data { - { - label - str "method" , - data - str "SeriousSeqEntryCleanup" } , - { - label - str "version" , - data - int 8 } , - { - label - str "month" , - data - int 3 } , - { - label - str "day" , - data - int 27 } , - { - label - str "year" , - data - int 2018 } } } , - create-date - std { - year 2018 , - month 3 , - day 27 } } , - 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 1.13 from - https://github.com/tseemann/prokka" , - user { - type - str "NcbiCleanup" , - data { - { - label - str "method" , - data - str "SeriousSeqEntryCleanup" } , - { - label - str "version" , - data - int 8 } , - { - label - str "month" , - data - int 3 } , - { - label - str "day" , - data - int 27 } , - { - label - str "year" , - data - int 2018 } } } , - create-date - std { - year 2018 , - month 3 , - day 27 } } , - 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 HMJLFLJH_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:2.6" } } , - xref { - { - data - gene { - locus-tag "HMJLFLJH_00003" } } } } } } } } , - set { - class nuc-prot , - descr { - source { - org { - taxname "Genus species" , - orgname { - mod { - { - subtype strain , - subname "strain" } } , - gcode 11 } } } , - comment "Annotated using prokka 1.13 from - https://github.com/tseemann/prokka" , - user { - type - str "NcbiCleanup" , - data { - { - label - str "method" , - data - str "SeriousSeqEntryCleanup" } , - { - label - str "version" , - data - int 8 } , - { - label - str "month" , - data - int 3 } , - { - label - str "day" , - data - int 27 } , - { - label - str "year" , - data - int 2018 } } } , - create-date - std { - year 2018 , - month 3 , - day 27 } } , - 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 HMJLFLJH_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:2.6" } } , - xref { - { - data - gene { - locus-tag "HMJLFLJH_00004" } } } } } } } } , - set { - class nuc-prot , - descr { - source { - org { - taxname "Genus species" , - orgname { - mod { - { - subtype strain , - subname "strain" } } , - gcode 11 } } } , - comment "Annotated using prokka 1.13 from - https://github.com/tseemann/prokka" , - user { - type - str "NcbiCleanup" , - data { - { - label - str "method" , - data - str "SeriousSeqEntryCleanup" } , - { - label - str "version" , - data - int 8 } , - { - label - str "month" , - data - int 3 } , - { - label - str "day" , - data - int 27 } , - { - label - str "year" , - data - int 2018 } } } , - create-date - std { - year 2018 , - month 3 , - day 27 } } , - 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 HMJLFLJH_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:2.6" } } , - xref { - { - data - gene { - locus-tag "HMJLFLJH_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 1.13 from - https://github.com/tseemann/prokka" , - user { - type - str "NcbiCleanup" , - data { - { - label - str "method" , - data - str "SeriousSeqEntryCleanup" } , - { - label - str "version" , - data - int 8 } , - { - label - str "month" , - data - int 3 } , - { - label - str "day" , - data - int 27 } , - { - label - str "year" , - data - int 2018 } } } , - create-date - std { - year 2018 , - month 3 , - day 27 } } , - inst { - repr raw , - mol dna , - length 276 , - seq-data - iupacna "TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAA -TGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGA -AGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGA -CGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA" } } } }
--- a/mito-prokka/test-data/out.tbl Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ ->Feature contig1 ->Feature contig2 -40 498 CDS - inference ab initio prediction:Prodigal:002006 - locus_tag HMJLFLJH_00001 - product hypothetical protein -498 614 CDS - inference ab initio prediction:Prodigal:002006 - locus_tag HMJLFLJH_00002 - product hypothetical protein ->Feature contig3 ->Feature contig4 -21 884 CDS - inference ab initio prediction:Prodigal:002006 - locus_tag HMJLFLJH_00003 - product hypothetical protein ->Feature contig5 -275 406 CDS - inference ab initio prediction:Prodigal:002006 - locus_tag HMJLFLJH_00004 - product hypothetical protein ->Feature contig6 -6 767 CDS - inference ab initio prediction:Prodigal:002006 - locus_tag HMJLFLJH_00005 - product hypothetical protein ->Feature contig7
--- a/mito-prokka/test-data/out.tsv Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -locus_tag ftype length_bp gene EC_number COG product -HMJLFLJH_00001 CDS 459 hypothetical protein -HMJLFLJH_00002 CDS 117 hypothetical protein -HMJLFLJH_00003 CDS 864 hypothetical protein -HMJLFLJH_00004 CDS 132 hypothetical protein -HMJLFLJH_00005 CDS 762 hypothetical protein
--- a/mito-prokka/test-data/out.txt Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -organism: Genus species strain -contigs: 7 -bases: 5386 -CDS: 5
--- a/mito-prokka/test-data/phiX174.fasta Wed May 26 16:01:54 2021 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,85 +0,0 @@ ->contig1 -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT -GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA -ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG -TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA -GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC ->contig2 -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT -TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT -CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT -TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG -TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG -TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT -AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC -CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC -TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA ->contig3 -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA -GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT -GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA ->contig4 -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC -TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC -ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC -CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC -TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT -TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT -TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC -GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC -TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA -TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG -TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC ->contig5 -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG -AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT -TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG -CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA -AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG ->contig6 -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA -TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT -CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG -TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA -GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA -AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC -TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT -CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG -TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT -TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC -ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA -ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG -GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT -GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT -ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG -CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC -CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG -CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA -TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT ->contig7 -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG -TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC -TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA -