Mercurial > repos > iuc > mitos
changeset 4:c7553ba39670 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 5eec533bf2834c3a35cc248acd6e24635c619484
| author | iuc |
|---|---|
| date | Wed, 01 Mar 2023 22:40:00 +0000 |
| parents | f20804c311de |
| children | 8b08ea650060 |
| files | mitos.xml test-data/missing_genes.txt test-data/mitos2_NC_012920.bed test-data/mitos2_NC_012920.gff test-data/mitos2_NC_012920.mitos |
| diffstat | 5 files changed, 85 insertions(+), 94 deletions(-) [+] |
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--- a/mitos.xml Tue Jun 14 17:16:57 2022 +0000 +++ b/mitos.xml Wed Mar 01 22:40:00 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> +<tool id="mitos" name="@MITOS_NAME@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>de-novo annotation of metazoan mitochondrial genomes</description> <xrefs> <xref type='bio.tools'>mitos</xref> @@ -6,12 +6,11 @@ <macros> <import>macros.xml</import> <token name="@MITOS_NAME@">MITOS</token> - <token name="@TOOL_VERSION@">1.0.5</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">1.1.1</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> <requirements> <requirement type="package" version="@TOOL_VERSION@">mitos</requirement> - <requirement type="package">zip</requirement> </requirements> <version_command>python -c "import mitos; print(mitos.__version__)"</version_command> <command detect_errors="aggressive"><![CDATA[ @@ -37,16 +36,13 @@ --fragovl $fragovl --fragfac $advanced_prot.fragfac --ststrange $advanced_prot.ststrange - #if "raw" in str($addoutputs).split(','): - && zip -9 -y -r output.zip outdir/ > /dev/null + --zip #end if ]]></command> <inputs> <param argument="--input" label="sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence"> - <options options_filter_attribute="metadata.sequences"> - <filter type="add_value" value="1"/> - </options> + <validator type="dataset_metadata_in_range" metadata_name="sequences" min="1" max="1"/> </param> <param argument="--code" label="Genetic code" type="select"> <option value="2">Vertebrate (2)</option> @@ -122,15 +118,11 @@ <data name="ncRNA_plot_out" format="pdf" from_work_dir="outdir/plots/rna.pdf" label="${tool.name} on ${on_string}: ncRNA prediction plot"> <filter>"protein_plot" in str(addoutputs)</filter> </data> - <!--<collection name="ncRNA_structure_plot_ps_out" type="list" label="${tool.name} on ${on_string}: ncRNA postscript structure plots"> - <discover_datasets pattern="(?P<name>.+)\.ps" format="ps" directory="outdir/plots" /> - <filter>"ncRNA_structure_ps_plots" in str(addoutputs)</filter> - </collection>--> <collection name="ncRNA_structure_plot_svg_out" type="list" label="${tool.name} on ${on_string}: ncRNA svg structure plots"> <discover_datasets pattern="(?P<name>.+)\.svg" format="svg" directory="outdir/plots" /> <filter>"ncRNA_structure_svg_plots" in str(addoutputs)</filter> </collection> - <data name="rawout" format="zip" from_work_dir="output.zip" label="${tool.name} on ${on_string}: raw data"> + <data name="rawout" format="zip" from_work_dir="outdir.zip" label="${tool.name} on ${on_string}: raw data"> <filter>"raw" in str(addoutputs)</filter> </data> </outputs> @@ -167,7 +159,7 @@ <output name="faaout" file="NC_012920.faa" ftype="fasta" /> <output name="rawout" ftype="zip"> <assert_contents> - <has_archive_member path=".*/result.bed"/> + <has_archive_member path="result.bed"/> </assert_contents> </output> <output name="geneorderout" file="NC_012920.geneorder" ftype="fasta" />
--- a/test-data/missing_genes.txt Tue Jun 14 17:16:57 2022 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -missing:cox2 cox3 trnS2 cox1 trnL1 nad3 nad2 nad1 nad5 nad4 atp8 atp6 trnS1 rrnL trnP trnK trnM trnN trnA trnC trnD trnE trnF trnG cob nad4l trnQ trnR trnT trnV trnW
--- a/test-data/mitos2_NC_012920.bed Tue Jun 14 17:16:57 2022 +0000 +++ b/test-data/mitos2_NC_012920.bed Wed Mar 01 22:40:00 2023 +0000 @@ -1,6 +1,6 @@ -NC_012920 647 1601 rrnS 0.0 + -NC_012920 3229 3304 trnL2(taa) 2.10000007428e-06 + -NC_012920 4262 4331 trnI(gat) 6.00000021223e-07 + -NC_012920 5825 5891 trnY(gta) 4.20000016347e-15 - -NC_012920 12137 12206 trnH(gtg) 1.99999999495e-06 + -NC_012920 14148 14673 nad6 876137.8 - +NC_012920\t647\t1601\trrnS\t[-0-9.e]+\t\+ +NC_012920\t3229\t3304\ttrnL2\(taa\)\t[-0-9.e]+\t\+ +NC_012920\t4262\t4331\ttrnI\(gat\)\t[-0-9.e]+\t\+ +NC_012920\t5825\t5891\ttrnY\(gta\)\t[-0-9.e]+\t- +NC_012920\t12137\t12206\ttrnH\(gtg\)\t[-0-9.e]+\t\+ +NC_012920\t14148\t14673\tnad6\t[-0-9.e]+\t-
--- a/test-data/mitos2_NC_012920.gff Tue Jun 14 17:16:57 2022 +0000 +++ b/test-data/mitos2_NC_012920.gff Wed Mar 01 22:40:00 2023 +0000 @@ -1,54 +1,54 @@ -NC_012920 mitfi ncRNA_gene 577 647 . + . ID=gene_trnF;gene_id=trnF -NC_012920 mitfi tRNA 577 647 . + . ID=transcript_trnF;Parent=gene_trnF;gene_id=trnF -NC_012920 mitfi exon 577 647 9.99999974738e-06 + . Parent=transcript_trnF;Name=trnF -NC_012920 mitfi ncRNA_gene 648 1601 . + . ID=gene_rrnS;gene_id=rrnS -NC_012920 mitfi rRNA 648 1601 . + . ID=transcript_rrnS;Parent=gene_rrnS;gene_id=rrnS -NC_012920 mitfi exon 648 1601 0.0 + . Parent=transcript_rrnS;Name=rrnS -NC_012920 mitfi ncRNA_gene 3230 3304 . + . ID=gene_trnL2;gene_id=trnL2 -NC_012920 mitfi tRNA 3230 3304 . + . ID=transcript_trnL2;Parent=gene_trnL2;gene_id=trnL2 -NC_012920 mitfi exon 3230 3304 2.10000007428e-06 + . Parent=transcript_trnL2;Name=trnL2 -NC_012920 mitfi ncRNA_gene 4263 4331 . + . ID=gene_trnI;gene_id=trnI -NC_012920 mitfi tRNA 4263 4331 . + . ID=transcript_trnI;Parent=gene_trnI;gene_id=trnI -NC_012920 mitfi exon 4263 4331 6.00000021223e-07 + . Parent=transcript_trnI;Name=trnI -NC_012920 mitfi ncRNA_gene 4402 4469 . + . ID=gene_trnM;gene_id=trnM -NC_012920 mitfi tRNA 4402 4469 . + . ID=transcript_trnM;Parent=gene_trnM;gene_id=trnM -NC_012920 mitfi exon 4402 4469 0.00340000004508 + . Parent=transcript_trnM;Name=trnM -NC_012920 mitfi ncRNA_gene 5587 5655 . - . ID=gene_trnA;gene_id=trnA -NC_012920 mitfi tRNA 5587 5655 . - . ID=transcript_trnA;Parent=gene_trnA;gene_id=trnA -NC_012920 mitfi exon 5587 5655 0.00179999996908 - . Parent=transcript_trnA;Name=trnA -NC_012920 mitfi ncRNA_gene 5657 5729 . - . ID=gene_trnN;gene_id=trnN -NC_012920 mitfi tRNA 5657 5729 . - . ID=transcript_trnN;Parent=gene_trnN;gene_id=trnN -NC_012920 mitfi exon 5657 5729 0.0740000009537 - . Parent=transcript_trnN;Name=trnN -NC_012920 mitfi ncRNA_gene 5826 5891 . - . ID=gene_trnY;gene_id=trnY -NC_012920 mitfi tRNA 5826 5891 . - . ID=transcript_trnY;Parent=gene_trnY;gene_id=trnY -NC_012920 mitfi exon 5826 5891 4.20000016347e-15 - . Parent=transcript_trnY;Name=trnY -NC_012920 mitfi ncRNA_gene 7446 7514 . - . ID=gene_trnS2;gene_id=trnS2 -NC_012920 mitfi tRNA 7446 7514 . - . ID=transcript_trnS2;Parent=gene_trnS2;gene_id=trnS2 -NC_012920 mitfi exon 7446 7514 0.0399999991059 - . Parent=transcript_trnS2;Name=trnS2 -NC_012920 mitfi ncRNA_gene 7518 7585 . + . ID=gene_trnD;gene_id=trnD -NC_012920 mitfi tRNA 7518 7585 . + . ID=transcript_trnD;Parent=gene_trnD;gene_id=trnD -NC_012920 mitfi exon 7518 7585 0.000709999992978 + . Parent=transcript_trnD;Name=trnD -NC_012920 mitfi ncRNA_gene 8295 8364 . + . ID=gene_trnK;gene_id=trnK -NC_012920 mitfi tRNA 8295 8364 . + . ID=transcript_trnK;Parent=gene_trnK;gene_id=trnK -NC_012920 mitfi exon 8295 8364 0.0379999987781 + . Parent=transcript_trnK;Name=trnK -NC_012920 mitfi ncRNA_gene 10405 10469 . + . ID=gene_trnR;gene_id=trnR -NC_012920 mitfi tRNA 10405 10469 . + . ID=transcript_trnR;Parent=gene_trnR;gene_id=trnR -NC_012920 mitfi exon 10405 10469 0.00510000018403 + . Parent=transcript_trnR;Name=trnR -NC_012920 mitfi ncRNA_gene 12138 12206 . + . ID=gene_trnH;gene_id=trnH -NC_012920 mitfi tRNA 12138 12206 . + . ID=transcript_trnH;Parent=gene_trnH;gene_id=trnH -NC_012920 mitfi exon 12138 12206 1.99999999495e-06 + . Parent=transcript_trnH;Name=trnH -NC_012920 mitfi ncRNA_gene 12266 12336 . + . ID=gene_trnL1;gene_id=trnL1 -NC_012920 mitfi tRNA 12266 12336 . + . ID=transcript_trnL1;Parent=gene_trnL1;gene_id=trnL1 -NC_012920 mitfi exon 12266 12336 0.0260000005364 + . Parent=transcript_trnL1;Name=trnL1 -NC_012920 mitos gene 14149 14670 . - . ID=gene_nad6;gene_id=nad6 -NC_012920 mitos mRNA 14149 14670 . - . ID=transcript_nad6;Parent=gene_nad6;gene_id=nad6 -NC_012920 mitos exon 14149 14670 39.7 - 2.0 Parent=transcript_nad6;Name=nad6 -NC_012920 mitfi ncRNA_gene 14674 14742 . - . ID=gene_trnE;gene_id=trnE -NC_012920 mitfi tRNA 14674 14742 . - . ID=transcript_trnE;Parent=gene_trnE;gene_id=trnE -NC_012920 mitfi exon 14674 14742 0.0320000015199 - . Parent=transcript_trnE;Name=trnE -NC_012920 mitfi ncRNA_gene 15888 15953 . + . ID=gene_trnT;gene_id=trnT -NC_012920 mitfi tRNA 15888 15953 . + . ID=transcript_trnT;Parent=gene_trnT;gene_id=trnT -NC_012920 mitfi exon 15888 15953 0.001200000057 + . Parent=transcript_trnT;Name=trnT -NC_012920 mitfi ncRNA_gene 15956 16023 . - . ID=gene_trnP;gene_id=trnP -NC_012920 mitfi tRNA 15956 16023 . - . ID=transcript_trnP;Parent=gene_trnP;gene_id=trnP -NC_012920 mitfi exon 15956 16023 0.00520000001416 - . Parent=transcript_trnP;Name=trnP +NC_012920\tmitfi\tncRNA_gene\t577\t647\t\.\t\+\t\.\tID=gene_trnF;gene_id=trnF +NC_012920\tmitfi\ttRNA\t577\t647\t\.\t\+\t\.\tID=transcript_trnF;Parent=gene_trnF;gene_id=trnF +NC_012920\tmitfi\texon\t577\t647\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnF;Name=trnF +NC_012920\tmitfi\tncRNA_gene\t648\t1601\t\.\t\+\t\.\tID=gene_rrnS;gene_id=rrnS +NC_012920\tmitfi\trRNA\t648\t1601\t\.\t\+\t\.\tID=transcript_rrnS;Parent=gene_rrnS;gene_id=rrnS +NC_012920\tmitfi\texon\t648\t1601\t0\.0\t\+\t\.\tParent=transcript_rrnS;Name=rrnS +NC_012920\tmitfi\tncRNA_gene\t3230\t3304\t\.\t\+\t\.\tID=gene_trnL2;gene_id=trnL2 +NC_012920\tmitfi\ttRNA\t3230\t3304\t\.\t\+\t\.\tID=transcript_trnL2;Parent=gene_trnL2;gene_id=trnL2 +NC_012920\tmitfi\texon\t3230\t3304\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnL2;Name=trnL2 +NC_012920\tmitfi\tncRNA_gene\t4263\t4331\t\.\t\+\t\.\tID=gene_trnI;gene_id=trnI +NC_012920\tmitfi\ttRNA\t4263\t4331\t\.\t\+\t\.\tID=transcript_trnI;Parent=gene_trnI;gene_id=trnI +NC_012920\tmitfi\texon\t4263\t4331\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnI;Name=trnI +NC_012920\tmitfi\tncRNA_gene\t4402\t4469\t\.\t\+\t\.\tID=gene_trnM;gene_id=trnM +NC_012920\tmitfi\ttRNA\t4402\t4469\t\.\t\+\t\.\tID=transcript_trnM;Parent=gene_trnM;gene_id=trnM +NC_012920\tmitfi\texon\t4402\t4469\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnM;Name=trnM +NC_012920\tmitfi\tncRNA_gene\t5587\t5655\t\.\t-\t\.\tID=gene_trnA;gene_id=trnA +NC_012920\tmitfi\ttRNA\t5587\t5655\t\.\t-\t\.\tID=transcript_trnA;Parent=gene_trnA;gene_id=trnA +NC_012920\tmitfi\texon\t5587\t5655\t[-0-9.e]+\t-\t\.\tParent=transcript_trnA;Name=trnA +NC_012920\tmitfi\tncRNA_gene\t5657\t5729\t\.\t-\t\.\tID=gene_trnN;gene_id=trnN +NC_012920\tmitfi\ttRNA\t5657\t5729\t\.\t-\t\.\tID=transcript_trnN;Parent=gene_trnN;gene_id=trnN +NC_012920\tmitfi\texon\t5657\t5729\t[-0-9.e]+\t-\t\.\tParent=transcript_trnN;Name=trnN +NC_012920\tmitfi\tncRNA_gene\t5826\t5891\t\.\t-\t\.\tID=gene_trnY;gene_id=trnY +NC_012920\tmitfi\ttRNA\t5826\t5891\t\.\t-\t\.\tID=transcript_trnY;Parent=gene_trnY;gene_id=trnY +NC_012920\tmitfi\texon\t5826\t5891\t[-0-9.e]+\t-\t\.\tParent=transcript_trnY;Name=trnY +NC_012920\tmitfi\tncRNA_gene\t7446\t7514\t\.\t-\t\.\tID=gene_trnS2;gene_id=trnS2 +NC_012920\tmitfi\ttRNA\t7446\t7514\t\.\t-\t\.\tID=transcript_trnS2;Parent=gene_trnS2;gene_id=trnS2 +NC_012920\tmitfi\texon\t7446\t7514\t[-0-9.e]+\t-\t\.\tParent=transcript_trnS2;Name=trnS2 +NC_012920\tmitfi\tncRNA_gene\t7518\t7585\t\.\t\+\t\.\tID=gene_trnD;gene_id=trnD +NC_012920\tmitfi\ttRNA\t7518\t7585\t\.\t\+\t\.\tID=transcript_trnD;Parent=gene_trnD;gene_id=trnD +NC_012920\tmitfi\texon\t7518\t7585\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnD;Name=trnD +NC_012920\tmitfi\tncRNA_gene\t8295\t8364\t\.\t\+\t\.\tID=gene_trnK;gene_id=trnK +NC_012920\tmitfi\ttRNA\t8295\t8364\t\.\t\+\t\.\tID=transcript_trnK;Parent=gene_trnK;gene_id=trnK +NC_012920\tmitfi\texon\t8295\t8364\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnK;Name=trnK +NC_012920\tmitfi\tncRNA_gene\t10405\t10469\t\.\t\+\t\.\tID=gene_trnR;gene_id=trnR +NC_012920\tmitfi\ttRNA\t10405\t10469\t\.\t\+\t\.\tID=transcript_trnR;Parent=gene_trnR;gene_id=trnR +NC_012920\tmitfi\texon\t10405\t10469\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnR;Name=trnR +NC_012920\tmitfi\tncRNA_gene\t12138\t12206\t\.\t\+\t\.\tID=gene_trnH;gene_id=trnH +NC_012920\tmitfi\ttRNA\t12138\t12206\t\.\t\+\t\.\tID=transcript_trnH;Parent=gene_trnH;gene_id=trnH +NC_012920\tmitfi\texon\t12138\t12206\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnH;Name=trnH +NC_012920\tmitfi\tncRNA_gene\t12266\t12336\t\.\t\+\t\.\tID=gene_trnL1;gene_id=trnL1 +NC_012920\tmitfi\ttRNA\t12266\t12336\t\.\t\+\t\.\tID=transcript_trnL1;Parent=gene_trnL1;gene_id=trnL1 +NC_012920\tmitfi\texon\t12266\t12336\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnL1;Name=trnL1 +NC_012920\tmitos\tgene\t14149\t14670\t\.\t-\t\.\tID=gene_nad6;gene_id=nad6 +NC_012920\tmitos\tmRNA\t14149\t14670\t\.\t-\t\.\tID=transcript_nad6;Parent=gene_nad6;gene_id=nad6 +NC_012920\tmitos\texon\t14149\t14670\t[-0-9.e]+\t-\t2\.0\tParent=transcript_nad6;Name=nad6 +NC_012920\tmitfi\tncRNA_gene\t14674\t14742\t\.\t-\t\.\tID=gene_trnE;gene_id=trnE +NC_012920\tmitfi\ttRNA\t14674\t14742\t\.\t-\t\.\tID=transcript_trnE;Parent=gene_trnE;gene_id=trnE +NC_012920\tmitfi\texon\t14674\t14742\t[-0-9.e]+\t-\t\.\tParent=transcript_trnE;Name=trnE +NC_012920\tmitfi\tncRNA_gene\t15888\t15953\t\.\t\+\t\.\tID=gene_trnT;gene_id=trnT +NC_012920\tmitfi\ttRNA\t15888\t15953\t\.\t\+\t\.\tID=transcript_trnT;Parent=gene_trnT;gene_id=trnT +NC_012920\tmitfi\texon\t15888\t15953\t[-0-9.e]+\t\+\t\.\tParent=transcript_trnT;Name=trnT +NC_012920\tmitfi\tncRNA_gene\t15956\t16023\t\.\t-\t\.\tID=gene_trnP;gene_id=trnP +NC_012920\tmitfi\ttRNA\t15956\t16023\t\.\t-\t\.\tID=transcript_trnP;Parent=gene_trnP;gene_id=trnP +NC_012920\tmitfi\texon\t15956\t16023\t[-0-9.e]+\t-\t\.\tParent=transcript_trnP;Name=trnP
--- a/test-data/mitos2_NC_012920.mitos Tue Jun 14 17:16:57 2022 +0000 +++ b/test-data/mitos2_NC_012920.mitos Wed Mar 01 22:40:00 2023 +0000 @@ -1,18 +1,18 @@ -NC_012920 tRNA trnF mitfi 576 646 1 9.99999974738e-06 31.3 GAA 34 . . (((((((..((((.........)))).(.(((.......))).)....(((.........)))))))))). -NC_012920 rRNA rrnS mitfi 647 1600 1 0.0 769.2 - None . . ...(((((.......))))).((((((.(((.((((((((....(((.(((..(......)......(((.......(((.(..(((.....)))..).)))....(((.(...............)..)))...(..((...)).)...)))...((....)).....))))))........((((...(((((....))))).)))).)).)))))).....((((((((................)))..............))))).))).))))))....((((......((((.(((((...............(((((((.....(((.(((((((......)))).))).))).............((....))))))))).....))).)).))))....((((((...((...((((.........))))...))))))))..........(......................))))).((.......((((....)))).....))........((((.((((((((.......(((((..((((((((((...((((........))))........(((((((.......((.((..((((((((.(....((....(((.....)))...........)).....(((....))).....).).)))...))))))))....)))))))..)).)))))))).....((((.....))))..........(((((((.......)))))))..........))))).....(((((((.........)))))))...........)))))))))).))..............((((((................................................))))))................((((((((((....))))))))))....... -NC_012920 tRNA trnL2 mitfi 3229 3303 1 2.10000007428e-06 34.1 TAA 35 . . (((((((..((..............)).((((.........)))).....(((((.......)))))))))))). -NC_012920 tRNA trnI mitfi 4262 4330 1 6.00000021223e-07 36.3 GAT 29 . . (((((((..(((......))).(((((.......))))).....(((.(.......).)))))))))). -NC_012920 tRNA trnM mitfi 4401 4468 1 0.00340000004508 21.1 CAT 30 . . ((((.((..((((.....)))).(((((.......)))))....(..((......))..))).)))). -NC_012920 tRNA trnA mitfi 5586 5654 -1 0.00179999996908 22.2 TGC 30 . . (((((((..((((.....)))).(((((.......)))))....(((((.......)))))))))))). -NC_012920 tRNA trnN mitfi 5656 5728 -1 0.0740000009537 15.7 GTT 33 . . (((((((..(((..........))).(((((.......))))).....(((((.......)))))))))))). -NC_012920 tRNA trnY mitfi 5825 5890 -1 4.20000016347e-15 69.2 GTA 29 . . (((((((..(((......))).(((((.......)))))....(((((.....)))))))))))). -NC_012920 tRNA trnS2 mitfi 7445 7513 -1 0.0399999991059 16.8 TGA 30 . . (((((((((((.......)))).(((((.......)))))....(((((.......)))))))))))). -NC_012920 tRNA trnD mitfi 7517 7584 1 0.000709999992978 23.9 GTC 30 . . (((((((..((((.....)))).(((((.......)))))....(((((......)))))))))))). -NC_012920 tRNA trnK mitfi 8294 8363 1 0.0379999987781 16.9 TTT 28 . . (((((((..((((...)))).(((((.......))))).....(((((.........)))))))))))). -NC_012920 tRNA trnR mitfi 10404 10468 1 0.00510000018403 20.4 TCG 30 . . (((((.(..((((.....)))).(((((.......)))))....(((((...)))))).))))). -NC_012920 tRNA trnH mitfi 12137 12205 1 1.99999999495e-06 34.2 GTG 30 . . (((((((..((((.....)))).(((((.......)))))....((.((.......)).))))))))). -NC_012920 tRNA trnL1 mitfi 12265 12335 1 0.0260000005364 17.6 TAG 32 . . (((((((..((((.......)))).((((.........))))....(((((.......)))))))))))). -NC_012920 gene nad6 mitos 14148 14669 -1 39.7 . - - . . . -NC_012920 tRNA trnE mitfi 14673 14741 -1 0.0320000015199 17.2 TTC 30 . . (((((((..((((.....)))).(((((.......)))))....(((((.......)))))))))))). -NC_012920 tRNA trnT mitfi 15887 15952 1 0.001200000057 23.0 TGT 31 . . (((((((..((((......)))).((.(.........).))....(((((...)))))))))))). -NC_012920 tRNA trnP mitfi 15955 16022 -1 0.00520000001416 20.4 TGG 31 . . (((((((..((((......)))).(((((.......)))))....(((((.....)))))))))))). +NC_012920\ttRNA\ttrnF\tmitfi\t576\t646\t1\t[-0-9.e]+\t31\.3\tGAA\t34\t\.\t\.\t\(\(\(\(\(\(\(\.\.\(\(\(\(\.\.\.\.\.\.\.\.\.\)\)\)\)\.\(\.\(\(\(\.\.\.\.\.\.\.\)\)\)\.\)\.\.\.\.\(\(\(\.\.\.\.\.\.\.\.\.\)\)\)\)\)\)\)\)\)\)\. 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