| Next changeset 1:79e259afea34 (2020-03-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit 791f28c8a7194fdd1ecec05ad166932d461899b2" |
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added:
README gen.sh macros.xml mitos2.xml test-data/NC_012920.bed test-data/NC_012920.faa test-data/NC_012920.fas test-data/NC_012920.fasta test-data/NC_012920.geneorder test-data/NC_012920.gff test-data/NC_012920.mito test-data/NC_012920.seq test-data/NC_012920_ncrna.pdf test-data/NC_012920_prot.pdf test-data/NC_012920_trnA.svg test-data/mitos.loc test-data/mitos1-refdata/modelle-v1/12smito-1.0.cm test-data/mitos1-refdata/modelle-v1/16smito-1.0.cm test-data/mitos1-refdata/modelle-v1/Metazoa_A-1.0.cm test-data/mitos1-refdata/modelle-v1/Metazoa_Y-1.0.cm test-data/mitos1-refdata/refseq39/featureProt/nad6.fas test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.phr test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.pin test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.psd test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.psi test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.psq test-data/mitos2_NC_012920.bed test-data/mitos2_NC_012920.faa test-data/mitos2_NC_012920.fas test-data/mitos2_NC_012920.geneorder test-data/mitos2_NC_012920.gff test-data/mitos2_NC_012920.mitos test-data/mitos2_NC_012920.seq test-data/mitos2_NC_012920_ncrna.pdf test-data/mitos2_NC_012920_prot.pdf test-data/refseq63m/auxinfo.json test-data/refseq63m/featureNuc/OH.fas test-data/refseq63m/featureNuc/OH.fas.nhr test-data/refseq63m/featureNuc/OH.fas.nin test-data/refseq63m/featureNuc/OH.fas.nsq test-data/refseq63m/featureProt/nad6.fas test-data/refseq63m/featureProt/nad6.fas.phr test-data/refseq63m/featureProt/nad6.fas.pin test-data/refseq63m/featureProt/nad6.fas.psq test-data/refseq63m/featureProtHMM/nad6.db test-data/refseq63m/featureProtHMM/nad6.db.h3f test-data/refseq63m/featureProtHMM/nad6.db.h3i test-data/refseq63m/featureProtHMM/nad6.db.h3m test-data/refseq63m/featureProtHMM/nad6.db.h3p test-data/refseq63m/ncRNA/OL.cm test-data/refseq63m/ncRNA/rrnS.cm test-data/refseq63m/ncRNA/tRNA.cm test-data/refseq63m/ncRNA/trnY.cm tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r dd589aa77943 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Fri Mar 27 17:53:42 2020 -0400 |
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| @@ -0,0 +1,6 @@ +test data +========= + +Note that the test data distributed with this Galaxy tool is not for actual use. +In particular the rRNA models are just a copies of a tRNA models (name manually +edited). |
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| diff -r 000000000000 -r dd589aa77943 gen.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gen.sh Fri Mar 27 17:53:42 2020 -0400 |
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| @@ -0,0 +1,43 @@ +## Activate MITOS(1) conda env +conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=1.0.5 zip + +conda activate mitos1 + +tmp=$(mktemp -d) +runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir '/home/maze/workspace/tools-iuc/tools/mitos/test-data/mitos1-refdata/' && zip -9 -y -r $tmp/result.zip $tmp + +for i in bed faa fas geneorder gff seq +do + cp $tmp/result.$i test-data/NC_012920.$i +done +cp $tmp/result test-data/NC_012920.mito +cp $tmp/plots/trnA-*.svg test-data/NC_012920_trnA.svg +cp $tmp/plots/prot.pdf test-data/NC_012920_prot.pdf +cp $tmp/plots/rna.pdf test-data/NC_012920_ncrna.pdf +rm -rf $tmp + +conda deactivate + +## Activate MITOS2 conda env +conda create -y --quiet --override-channels --channel iuc --channel conda-forge --channel bioconda --channel defaults --name mitos2 mitos=2.0.6 zip + +conda activate mitos2 + +# data for 1st test +tmp=$(mktemp -d) +runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir './test-data/' --refseqver 'refseq63m/' --intron 0 --oril 0 --orih 0 --finovl 50 --fragovl 0.2 --fragfac 10.0 --evalue 2.0 --cutoff 0.50 --clipfac 10.0 --ncev 0.01 --maxtrnaovl 50 --maxrrnaovl 50 --noplots +cp $tmp/result.bed test-data/mitos2_NC_012920.bed +rm -rf $tmp + +# data for 3rd test +tmp=$(mktemp -d) +runmitos.py --input test-data/NC_012920.fasta --code 2 --outdir $tmp --refdir './test-data/' --refseqver 'refseq63m/' --intron 0 --oril 0 --orih 0 --evalue 3.0 --cutoff 0.49 --clipfac 9.0 --ncbicode --alarab --oldstst --ncev 0.1 --sensitive --maxtrnaovl 51 --maxrrnaovl 49 && zip -9 -y -r $tmp/result.zip $tmp +for i in faa fas geneorder gff mitos seq +do + cp $tmp/result.$i test-data/mitos2_NC_012920.$i +done +cp $tmp/plots/prot.pdf test-data/mitos2_NC_012920_prot.pdf +cp $tmp/plots/rna.pdf test-data/mitos2_NC_012920_ncrna.pdf +rm -rf $tmp + +conda deactivate |
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| diff -r 000000000000 -r dd589aa77943 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Mar 27 17:53:42 2020 -0400 |
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| @@ -0,0 +1,31 @@ +<macros> + <token name="@COMMON_HELP@"> + <![CDATA[ +@MITOS_NAME@ does a de-novo annotation of a given metazoan mitochondrial sequence. + +**Inputs** + +- A fasta formatted sequence + + - @MITOS_NAME@ processes only FASTA files containing a single sequence. If you have a FASTA file with multiple sequences you may use the tool *Split Fasta files into a collection". The resulting collection can then used as input to @MITOS_NAME@. + +- The correct genetic code needs to be selected + +- Reference data needs to be selected (can be provided by an administrator using the MITOS data manager) + +**Outputs** + +By default the annotation in BED format. Several other outputs can be enabled: + +- The annotation can be given as well in GFF, SEQ, or mito (a custom tabular format) + +- zipped raw data (all files computed during the run, e.g. BLAST and cmsearch outputs) + +- protein and ncRNA prediction plots visualize the predicted genes and their qualities + +- ncRNA structure plots (secondary structures of the predicted ncRNAs) + +See http://mitos.bioinf.uni-leipzig.de/help.py + + ]]></token> +</macros> |
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| diff -r 000000000000 -r dd589aa77943 mitos2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mitos2.xml Fri Mar 27 17:53:42 2020 -0400 |
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| b'@@ -0,0 +1,361 @@\n+<tool id="mitos2" name="@MITOS_NAME@" version="@MITOS_VERSION@">\n+ <description>de-novo annotation of metazoan mitochondrial genomes</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ <token name="@MITOS_NAME@">MITOS2</token>\n+ <token name="@MITOS_VERSION@">2.0.6</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@MITOS_VERSION@">mitos</requirement>\n+ <requirement type="package">zip</requirement>\n+ </requirements>\n+ <version_command>python -c "import mitos; print(mitos.__version__)"</version_command>\n+ <command detect_errors="aggressive"><![CDATA[\n+mkdir outdir &&\n+\n+runmitos.py\n+--input \'$input\'\n+--code $code\n+--outdir outdir\n+--refdir \'/\'\n+--refseqver \'$refseqver.fields.path\'\n+$linear\n+#for tpe in ["prot", "trna", "rrna", "intron", "oril", "orih"]\n+ #if not $tpe in str($advanced.featuretypes).split(\',\')\n+ --$tpe 0\n+ #end if\n+#end for\n+--finovl $advanced.finovl\n+$advanced.best\n+#set fragovl=float($advanced.fragovl)/100.0\n+--fragovl $fragovl\n+--fragfac $advanced.fragfac\n+\n+--evalue $advanced_prot.evalue\n+#set cutoff=float($advanced_prot.cutoff)/100.0\n+--cutoff $cutoff\n+--clipfac $advanced_prot.clipfac\n+$advanced_prot.ncbicode\n+$advanced_prot.alarab\n+$advanced_prot.oldstst\n+$advanced_ncrna.locandgloc\n+--ncev $advanced_ncrna.ncev\n+$advanced_ncrna.sensitive\n+--maxtrnaovl $advanced_ncrna.maxtrnaovl\n+--maxrrnaovl $advanced_ncrna.maxrrnaovl\n+\n+#if not ("protein_plot" in str($addoutputs).split(\',\') or "ncRNA_plot" in str($addoutputs).split(\',\')):\n+ --noplots\n+#end if\n+\n+#if "raw" in str($addoutputs).split(\',\'):\n+ && zip -9 -y -r output.zip outdir/ > /dev/null\n+#end if\n+ ]]></command>\n+ <inputs>\n+ <param argument="--input" label="Sequence" type="data" format="fasta" help="a single sequence in fasta formated sequence">\n+ <options options_filter_attribute="metadata.sequences">\n+ <filter type="add_value" value="1"/>\n+ </options>\n+ </param> \n+ <param argument="--code" label="Genetic code" type="select">\n+ <option value="2">Vertebrate (2)</option>\n+ <option value="4">Mold, Protozoan, Coelenteral (4)</option>\n+ <option value="5">Invertebrate (5)</option>\n+ <option value="9">Echinoderm, Flatworm (9)</option>\n+ <option value="13">Ascidian (13)</option>\n+ <option value="14">Alternative Flatworm (14)</option>\n+ </param>\n+ <param argument="--refseqver" label="Reference data" type="select" help="contact the administrator of this Galaxy instance if you miss reference data">\n+ <options from_data_table="mitos">\n+ <filter type="static_value" value="mitos2" column="2"/>\n+ </options>\n+ <validator message="No reference annotation is available for MITOS2" type="no_options" />\n+ </param>\n+ <param argument="--linear" checked="false" label="Treat sequence as linear" type="boolean" truevalue="--linear" falsevalue=""/>\n+ <param name="addoutputs" type="select" multiple="true" label="Outputs">\n+ <option value="bed" selected="true">BED</option>\n+ <option value="mito" selected="false">mito</option>\n+ <option value="gff" selected="false">GFF file</option>\n+ <option value="seq" selected="false">SEQ</option>\n+ <option value="fas" selected="false">nucleotide FASTA</option>\n+ <option value="faa" selected="false">protein FASTA</option>\n+ <option value="geneorder" selected="false">geneorder</option>\n+ <option value="protein_plot" selected="false">Protein prediction plot</option>\n+ <option value="ncRNA_plot" selected="false">ncRNA prediction plot</option>\n+ <!--<option value="ncRNA_structure_ps_plots" selected="false">ncRNA structure plots - postscript</option>-->\n+ <option value="ncRNA_structure_svg_plots" selected="false">ncRNA structure plots - svg</option>\n+ <option value="raw" selected="false">zipped raw results</option>\n+ </param>\n+ <section name="advanced" title="Advanced options">\n+ <param name="featuretypes" la'..b'xt="--sensitive"/>\n+ <has_text text="--maxtrnaovl 51"/>\n+ <has_text text="--maxrrnaovl 49"/>\n+ <not_has_text text="--noplots"/>\n+ </assert_command>\n+ </test>\n+ </tests>\n+ <help>@COMMON_HELP@\n+ <![CDATA[\n+\n+\n+**Advanced options**\n+\n+- Feature types\n+\n+ Select the feature types that should be annotated. By default this is protein coding genes, tRNA and rRNA which is useful for metazoan mitogenomes. In addition also the replication origins of the light (OL) and heavy (OH) strand and introns can be annotated. The annotation of the replication origins is most useful for chordate mitogenomes. Introns are usually only found in mitogenomes of non-metazoans and basal Metazoa.\n+\n+- Final overlap (nt)\n+\n+ Maximum number of nucleotides by which genes of different types may overlap. Applies to merging of the final predictions. \n+\n+- Annotate only the best copy of each feature\n+\n+ If there are copies of the same feature type only the one with the lowest e-value (for ncRNAs and OL) or highest quality score (protein coding genes and OH)\n+\n+- Fragment overlap\n+\n+ Maximum fraction (of the shorter feature) allowed that two hits overlap in the query to be counted as fragments.\n+\n+- Fragment quality factor\n+\n+ Maximum factor by which fragments may differ in their quality scores. Higher values allow that parts of a gene can differ more in their quality.\n+\n+**Advanced options for protein coding gene prediction**\n+\n+- BLAST E-value Exponent\n+\n+ The statistical significance threshold for considering matches in the BLASTX search. The value entered here is the negation of the exponent of the E-value threshold that should be used by BLAST, i.e. a value X gives an E-value of 10^(-X). \n+\n+- Quality cutoff\n+\n+ Minimum allowed quality value (in percent) of the maximum quality value per reading frame. A higher values correspond to shorter protein prediction and therefore reduced risk for conflicts with other features\n+\n+- Clipping factor\n+\n+ Clipping is started if overlapping prediction of hits with the same name differ by less than a factor X in their quality value.\n+\n+- use start/stop codons as in NCBI (default: learned start/stop codons)\n+\n+ Instead of the codon probabilities derived from the protein coding genes annotated in RefSeq the codons listed at NCBI taxonomy are used with equal probabilities (https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)\n+\n+- Use the hmmer based method of Al Arab et al. 2016. This will consider the evalue, ncbicode, fragovl, fragfac parameters\n+\n+ Note: 1) this only works for Metazoa RefSeq release 63 reference data set. 2) This will only predict the protein coding genes that are typical for metazoan mitochondrial genomes.\n+\n+- Use the old start/stop prediction method of MITOS1\n+\n+ The search for start and stop codons just takes the closest to the initial start / stop positions within 6aa (i.e. the method used in MITOS1)\n+\n+**Advanced options for ncRNA gene prediction**\n+\n+- Run mitfi in glocal and local mode (default: local only)\n+\n+ By default mitfi uses infernal\'s cmsearch in local search mode only. By enabling this option mitfi will invoke cmserach also in glocal mode if a feature is missing.\n+\n+- e-value to use for inferal fast mode\n+\n+ The e-value passed to the first pass of cmsearch in the second pass (the sensitive search) an e-value of 0.1 is used.\n+\n+- Use infernal\'s sensitive mode only\n+\n+ By default mitfi searches for ncRNAs using cmsearch\'s default fast mode first. If a ncRNA type is missing it is searched using the sensitive mode. This can be useful if low scoring copies are expected which might be missed when searching in the two stage mode. \n+\n+ - Allow tRNA/rRNA overlap of up to X nt for mitfi\n+\n+ Allow that a tRNA/rRNA overlaps with another feature by this number of nucleotides.\n+\n+]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/nar/gkz833</citation>\n+ <citation type="doi">10.1016/j.ympev.2016.09.024</citation>\n+ </citations>\n+</tool>\n+\n' |
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| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_012920.bed Fri Mar 27 17:53:42 2020 -0400 |
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| @@ -0,0 +1,25 @@ +NC_012920 576 647 trnF(gaa) 1.127e-05 + +NC_012920 1601 1670 trnV(tac) 1.671e-06 + +NC_012920 3229 3304 trnL2(taa) 0.0006685 + +NC_012920 4262 4331 trnI(gat) 5.584e-05 + +NC_012920 4328 4400 trnQ(ttg) 0.097 - +NC_012920 4401 4469 trnM(cat) 0.001232 + +NC_012920 5511 5579 trnW(tca) 0.001059 + +NC_012920 5586 5655 trnA(tgc) 1.529e-08 - +NC_012920 5658 5721 trnN(gtt) 0.1419 - +NC_012920 5760 5826 trnC(gca) 0.0006482 - +NC_012920 5760 5826 rrnS 2.104e-11 - +NC_012920 5826 5891 trnY(gta) 1.031e-09 - +NC_012920 7445 7514 trnS2(tga) 0.0475 - +NC_012920 7517 7585 trnD(gtc) 0.0005019 + +NC_012920 7517 7585 rrnL 7.886e-12 + +NC_012920 8294 8364 trnK(ttt) 0.0007967 + +NC_012920 9990 10058 trnG(tcc) 7.29e-06 + +NC_012920 10404 10469 trnR(tcg) 2.068e-06 + +NC_012920 12137 12206 trnH(gtg) 2.765e-06 + +NC_012920 12265 12336 trnL1(tag) 0.09648 + +NC_012920 12769 12817 rrnS 0.1077 - +NC_012920 14154 14673 nad6 24486974.4 - +NC_012920 14673 14742 trnE(ttc) 3.085e-06 - +NC_012920 15887 15953 trnT(tgt) 1.962e-08 + +NC_012920 15955 16023 trnP(tgg) 1.555e-06 - |
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| @@ -0,0 +1,4 @@ +>NC_012920; 14155-14673; -; nad6 +MMYALFLLSVGLVMGFVGFSSKPSPIYGGLVLIVSGVVGCVIILNFGGGYMGLMVFLIYL +GGMMVVFGYTTAMAIEEYPEAWGSGVEVLVSVLVGLAMEVGLVLWVKEYDGVVVVVNFNS +VGSWMIYEGEGSGLIREDPIGAGALYDYGRWLVVVTGWTLFVGVYIVIEIARG |
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| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_012920.fas Fri Mar 27 17:53:42 2020 -0400 |
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| @@ -0,0 +1,81 @@ +>NC_012920; 577-647; +; trnF(gaa) +GTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCA +CCCCATAAACA +>NC_012920; 1602-1670; +; trnV(tac) +CAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGA +CCGCTCTGA +>NC_012920; 3230-3304; +; trnL2(taa) +GTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAA +TTCCTCTTCTTAACA +>NC_012920; 4263-4331; +; trnI(gat) +AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCC +TTATTTCTA +>NC_012920; 4329-4400; -; trnQ(ttg) +TAGGATGGGGTGTGATAGGTGGCACGGAGAATTTTGGATTCTCAGGGATGGGTTCGATTC +TCATAGTCCTAG +>NC_012920; 4402-4469; +; trnM(cat) +AGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTC +CCGTACTA +>NC_012920; 5512-5579; +; trnW(tca) +AGAAATTTAGGTTAAATACAGACCAAGAGCCTTCAAAGCCCTCAGTAAGTTGCAATACTT +AATTTCTG +>NC_012920; 5587-5655; -; trnA(tgc) +AAGGGCTTAGCTTAATTAAAGTGGCTGATTTGCGTTCAGTTGATGCAGAGTGGGGTTTTG +CAGTCCTTA +>NC_012920; 5659-5721; -; trnN(gtt) +AGCCAGTTGATTAGGGTGCTTAGCTGTTAACTAAGTGTTTGTGGGTTTAAGTCCCATTGG +TCT +>NC_012920; 5761-5826; -; trnC(gca) +AGCTCCGAGGTGATTTTCATATTGAATTGCAAATTCGAAGAAGCAGCTTCAAACCTGCCG +GGGCTT +>NC_012920; 5761-5826; -; rrnS +AGCTCCGAGGTGATTTTCATATTGAATTGCAAATTCGAAGAAGCAGCTTCAAACCTGCCG +GGGCTT +>NC_012920; 5827-5891; -; trnY(gta) +GGTAAAATGGCTGAGTGAAGCATTGGACTGTAAATCTAAAGACAGGGGTTAGGCCTCTTT +TTACC +>NC_012920; 7446-7514; -; trnS2(tga) +GAAAAAGTCATGGAGGCCATGGGGTTGGCTTGAAACCAGCTTTGGGGGGTTCGATTCCTT +CCTTTTTTG +>NC_012920; 7518-7585; +; trnD(gtc) +AAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCTAAATCCTAT +ATATCTTA +>NC_012920; 7518-7585; +; rrnL +AAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCTAAATCCTAT +ATATCTTA +>NC_012920; 8295-8364; +; trnK(ttt) +CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTC +TTTACAGTGA +>NC_012920; 9991-10058; +; trnG(tcc) +ACTCTTTTAGTATAAATAGTACCGTTAACTTCCAATTAACTAGTTTTGACAACATTCAAA +AAAGAGTA +>NC_012920; 10405-10469; +; trnR(tcg) +TGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTATGATAATCATATTT +ACCAA +>NC_012920; 12138-12206; +; trnH(gtg) +GTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCC +TTATTTACC +>NC_012920; 12266-12336; +; trnL1(tag) +ACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCC +AAATAAAAGTA +>NC_012920; 12770-12817; -; rrnS +GGGCGTATCATCAACTGATGAGCAAGAAGGATATAATTCCTACGCCCT +>NC_012920; 14155-14673; -; nad6 +ATGATGTATGCTTTGTTTCTGTTGAGTGTGGGTTTAGTAATGGGGTTTGTGGGGTTTTCT +TCTAAGCCTTCTCCTATTTATGGGGGTTTAGTATTGATTGTTAGCGGTGTGGTCGGGTGT +GTTATTATTCTGAATTTTGGGGGAGGTTATATGGGTTTAATAGTTTTTTTAATTTATTTA +GGGGGAATGATGGTTGTCTTTGGATATACTACAGCGATGGCTATTGAGGAGTATCCTGAG +GCATGGGGGTCAGGGGTTGAGGTCTTGGTGAGTGTTTTAGTGGGGTTAGCGATGGAGGTA +GGATTGGTGCTGTGGGTGAAAGAGTATGATGGGGTGGTGGTTGTGGTAAACTTTAATAGT +GTAGGAAGCTGAATAATTTATGAAGGAGAGGGGTCAGGGTTGATTCGGGAGGATCCTATT +GGTGCGGGGGCTTTGTATGATTATGGGCGTTGATTAGTAGTAGTTACTGGTTGAACATTG +TTTGTTGGTGTATATATTGTAATTGAGATTGCTCGGGGG +>NC_012920; 14674-14742; -; trnE(ttc) +GTTCTTGTAGTTGAAATACAACGATGGTTTTTCATATCATTGGTCGTGGTTGTAGTCCGT +GCGAGAATA +>NC_012920; 15888-15953; +; trnT(tgt) +GTCCTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCA +AGGACA +>NC_012920; 15956-16023; -; trnP(tgg) +CAGAGAATAGTTTAAATTAGAATCTTAGCTTTGGGTGCTAATGGTGGAGTTAAAGACTTT +TTCTCTGA |
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| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_012920.fasta Fri Mar 27 17:53:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,3 @@\n+> NC_012920\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATCATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAAAGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAATTCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGCTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGGCCATAATATGATTTATCTCCACACTAGCAGAGACCAACCGAACCCCCTTCGACCTTGCCGAAGGGGAGTCCGAACTAGTCTCAGGCTTCAACATCGAATACGCCGCAGGCCCCTTCGCC'..b'TTCAAACTAGACTACTTCTCCATAATATTCATCCCTGTAGCATTGTTCGTTACATGGTCCATCATAGAATTCTCACTGTGATATATAAACTCAGACCCAAACATTAATCAGTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAACAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTTTCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAACTCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAACCACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTCACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACCAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGACCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTACTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGCAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACTCCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCCTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGAGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCAACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920.geneorder --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_012920.geneorder Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>NC_012920 +trnF trnV trnL2 trnI -trnQ trnM trnW -trnA -trnN -trnC -rrnS -trnY -trnS2 trnD rrnL trnK trnG trnR trnH trnL1 -rrnS -nad6 -trnE trnT -trnP |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_012920.gff Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,25 @@ +NC_012920 mitfi tRNA 577 647 1.127e-05 + . Name=trnF(gaa) ; model Y; evalue 0.000011; pvalue 0.000000; qstart 1; qstop 68 +NC_012920 mitfi tRNA 1602 1670 1.671e-06 + . Name=trnV(tac) ; model A; evalue 0.000002; pvalue 0.000000; qstart 1; qstop 65 +NC_012920 mitfi tRNA 3230 3304 0.0006685 + . Name=trnL2(taa) ; model Y; evalue 0.000669; pvalue 0.000001; qstart 1; qstop 68 +NC_012920 mitfi tRNA 4263 4331 5.584e-05 + . Name=trnI(gat) ; model Y; evalue 0.000056; pvalue 0.000000; qstart 1; qstop 68 +NC_012920 mitfi tRNA 4329 4400 0.097 - . Name=trnQ(ttg) ; model Y; evalue 0.097000; pvalue 0.000096; qstart 1; qstop 68 +NC_012920 mitfi tRNA 4402 4469 0.001232 + . Name=trnM(cat) ; model A; evalue 0.001232; pvalue 0.000001; qstart 1; qstop 65 +NC_012920 mitfi tRNA 5512 5579 0.001059 + . Name=trnW(tca) ; model Y; evalue 0.001059; pvalue 0.000001; qstart 1; qstop 68 +NC_012920 mitfi tRNA 5587 5655 1.529e-08 - . Name=trnA(tgc) ; model A; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 65 +NC_012920 mitfi tRNA 5659 5721 0.1419 - . Name=trnN(gtt) ; model Y; evalue 0.141900; pvalue 0.000140; qstart 1; qstop 68 +NC_012920 mitfi tRNA 5761 5826 0.0006482 - . Name=trnC(gca) ; model Y; evalue 0.000648; pvalue 0.000001; qstart 1; qstop 68 +NC_012920 mitfi rRNA 5761 5826 2.104e-11 - . Name=rrnS ; model rrnS; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 66 +NC_012920 mitfi tRNA 5827 5891 1.031e-09 - . Name=trnY(gta) ; model Y; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 68 +NC_012920 mitfi tRNA 7446 7514 0.0475 - . Name=trnS2(tga) ; model Y; evalue 0.047500; pvalue 0.000047; qstart 1; qstop 68 +NC_012920 mitfi tRNA 7518 7585 0.0005019 + . Name=trnD(gtc) ; model A; evalue 0.000502; pvalue 0.000000; qstart 1; qstop 65 +NC_012920 mitfi rRNA 7518 7585 7.886e-12 + . Name=rrnL ; model rrnL; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 67 +NC_012920 mitfi tRNA 8295 8364 0.0007967 + . Name=trnK(ttt) ; model Y; evalue 0.000797; pvalue 0.000001; qstart 1; qstop 68 +NC_012920 mitfi tRNA 9991 10058 7.29e-06 + . Name=trnG(tcc) ; model A; evalue 0.000007; pvalue 0.000000; qstart 1; qstop 65 +NC_012920 mitfi tRNA 10405 10469 2.068e-06 + . Name=trnR(tcg) ; model A; evalue 0.000002; pvalue 0.000000; qstart 1; qstop 65 +NC_012920 mitfi tRNA 12138 12206 2.765e-06 + . Name=trnH(gtg) ; model Y; evalue 0.000003; pvalue 0.000000; qstart 1; qstop 68 +NC_012920 mitfi tRNA 12266 12336 0.09648 + . Name=trnL1(tag) ; model A; evalue 0.096480; pvalue 0.000093; qstart 1; qstop 65 +NC_012920 mitfi rRNA 12770 12817 0.1077 - . Name=rrnS ; model rrnS; evalue 0.107700; pvalue 0.000099; qstart 1; qstop 66 +NC_012920 mitos gene 14155 14673 24486974.4 - . Name=nad6 +NC_012920 mitfi tRNA 14674 14742 3.085e-06 - . Name=trnE(ttc) ; model A; evalue 0.000003; pvalue 0.000000; qstart 1; qstop 65 +NC_012920 mitfi tRNA 15888 15953 1.962e-08 + . Name=trnT(tgt) ; model A; evalue 0.000000; pvalue 0.000000; qstart 1; qstop 65 +NC_012920 mitfi tRNA 15956 16023 1.555e-06 - . Name=trnP(tgg) ; model A; evalue 0.000002; pvalue 0.000000; qstart 1; qstop 65 |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920.mito --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_012920.mito Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,25 @@ +NC_012920 tRNA trnF mitfi 576 646 1 1.127e-05 TTC . . (((((((..((((.........)))).(.(((.......))).)....(((.........)))))))))). 34 +NC_012920 tRNA trnV mitfi 1601 1669 1 1.671e-06 GTA . . (((((((..((((......)))).((.((.......)).)).....((((......)))).))))))). 31 +NC_012920 tRNA trnL2 mitfi 3229 3303 1 0.0006685 TTA . . (((((((..((.(..........).)).((((.........)))).....(((((.......)))))))))))). 35 +NC_012920 tRNA trnI mitfi 4262 4330 1 5.584e-05 ATC . . (((((((..(((......))).(((((.......))))).....(((.(.......).)))))))))). 29 +NC_012920 tRNA trnQ mitfi 4328 4399 -1 0.097 CAA . . ((((((...((((........)))).(((((.......)))))....(((((.......))))).)))))). 33 +NC_012920 tRNA trnM mitfi 4401 4468 1 0.001232 ATG . . ((((.((..((((.....)))).(((((.......)))))....(..((......))..))).)))). 30 +NC_012920 tRNA trnW mitfi 5511 5578 1 0.001059 TGA . . (((((((..((((.......)))).((.((.......)).))....((((......))))))))))). 32 +NC_012920 tRNA trnA mitfi 5586 5654 -1 1.529e-08 GCA . . (((((((..((((.....)))).(((((.......)))))....(((((.......)))))))))))). 30 +NC_012920 tRNA trnN mitfi 5658 5720 -1 0.1419 AAC . . .((((((..(((..))).(((((.......))))).......(((.(...).))))))))).. 25 +NC_012920 tRNA trnC mitfi 5760 5825 -1 0.0006482 TGC . . (((((((..((((...)))).(((((.......)))))....((((........))))))))))). 28 +NC_012920 rRNA rrnS mitfi 5760 5825 -1 2.104e-11 - . . (((((((..((((...)))).(((((.......)))))....((((........))))))))))). None +NC_012920 tRNA trnY mitfi 5826 5890 -1 1.031e-09 TAC . . (((((((..(((......))).(((((.......)))))....(((((.....)))))))))))) 29 +NC_012920 tRNA trnS2 mitfi 7445 7513 -1 0.0475 TCA . . (((((((((((.......)))).(((((.......)))))....(((((.......)))))))))))). 30 +NC_012920 tRNA trnD mitfi 7517 7584 1 0.0005019 GAC . . (((((((..((((.....)))).(((((.......)))))....(((((......)))))))))))). 30 +NC_012920 rRNA rrnL mitfi 7517 7584 1 7.886e-12 - . . (((((((..((((.....)))).(((((.......)))))....(((((......)))))))))))). None +NC_012920 tRNA trnK mitfi 8294 8363 1 0.0007967 AAA . . (((((((..((((...)))).(((((.......))))).....(((((.........)))))))))))). 28 +NC_012920 tRNA trnG mitfi 9990 10057 1 7.29e-06 GGA . . (((((((..((((.....)))).(((((.......)))))....(((((......)))))))))))). 30 +NC_012920 tRNA trnR mitfi 10404 10468 1 2.068e-06 CGA . . (((((.(..((((.....)))).(((((.......)))))....(((((...)))))).))))). 30 +NC_012920 tRNA trnH mitfi 12137 12205 1 2.765e-06 CAC . . (((((((..((((.....)))).(((((.......)))))....((.((.......)).))))))))). 30 +NC_012920 tRNA trnL1 mitfi 12265 12335 1 0.09648 CTA . . (((((((..((((.......)))).((((.........))))....(((((.......)))))))))))). 32 +NC_012920 rRNA rrnS mitfi 12769 12816 -1 0.1077 - . . (((((((...(((.....))).......(((......)))))))))). None +NC_012920 gene nad6 mitos 14154 14672 -1 24486974.4 - . . . . +NC_012920 tRNA trnE mitfi 14673 14741 -1 3.085e-06 GAA . . (((((((..((((.....)))).(((((.......)))))....(((((.......)))))))))))). 30 +NC_012920 tRNA trnT mitfi 15887 15952 1 1.962e-08 ACA . . (((((((..((((......)))).((.((.......)).))....(((((...)))))))))))). 31 +NC_012920 tRNA trnP mitfi 15955 16022 -1 1.555e-06 CCA . . (((((((..((((......)))).(((((.......)))))....(((((.....)))))))))))). 31 |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920.seq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_012920.seq Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,98 @@ +>Feature NC_012920 +577 647 gene + gene trnF(gaa) +577 647 tRNA + product tRNA-PHE +1602 1670 gene + gene trnV(tac) +1602 1670 tRNA + product tRNA-VAL +3230 3304 gene + gene trnL2(taa) +3230 3304 tRNA + product tRNA-LEU2 +4263 4331 gene + gene trnI(gat) +4263 4331 tRNA + product tRNA-ILE +4400 4329 gene + gene trnQ(ttg) +4400 4329 tRNA + product tRNA-GLN +4402 4469 gene + gene trnM(cat) +4402 4469 tRNA + product tRNA-MET +5512 5579 gene + gene trnW(tca) +5512 5579 tRNA + product tRNA-TRP +5655 5587 gene + gene trnA(tgc) +5655 5587 tRNA + product tRNA-ALA +5721 5659 gene + gene trnN(gtt) +5721 5659 tRNA + product tRNA-ASN +5826 5761 gene + gene trnC(gca) +5826 5761 tRNA + product tRNA-CYS +5826 5761 gene +5826 5761 rRNA + product s-rRNA +5891 5827 gene + gene trnY(gta) +5891 5827 tRNA + product tRNA-TYR +7514 7446 gene + gene trnS2(tga) +7514 7446 tRNA + product tRNA-SER2 +7518 7585 gene + gene trnD(gtc) +7518 7585 tRNA + product tRNA-ASP +7518 7585 gene +7518 7585 rRNA + product l-rRNA +8295 8364 gene + gene trnK(ttt) +8295 8364 tRNA + product tRNA-LYS +9991 10058 gene + gene trnG(tcc) +9991 10058 tRNA + product tRNA-GLY +10405 10469 gene + gene trnR(tcg) +10405 10469 tRNA + product tRNA-ARG +12138 12206 gene + gene trnH(gtg) +12138 12206 tRNA + product tRNA-HIS +12266 12336 gene + gene trnL1(tag) +12266 12336 tRNA + product tRNA-LEU1 +12817 12770 gene +12817 12770 rRNA + product s-rRNA +14673 14155 gene + gene nad6 +14673 14155 CDS + product NADH dehydrogenase subunit 6 +14742 14674 gene + gene trnE(ttc) +14742 14674 tRNA + product tRNA-GLU +15888 15953 gene + gene trnT(tgt) +15888 15953 tRNA + product tRNA-THR +16023 15956 gene + gene trnP(tgg) +16023 15956 tRNA + product tRNA-PRO |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920_ncrna.pdf |
| b |
| Binary file test-data/NC_012920_ncrna.pdf has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920_prot.pdf |
| b |
| Binary file test-data/NC_012920_prot.pdf has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/NC_012920_trnA.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/NC_012920_trnA.svg Fri Mar 27 17:53:42 2020 -0400 |
| [ |
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| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos.loc Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +mitos1-refdata RefSeq39 + MiTFi tRNA models mitos ${__HERE__}/mitos1-refdata/ +mitos2-refdata RefSeq63 Metazoa mitos2 ${__HERE__}/refseq63m/ +wrong-refdata wrong mitos2 ${__HERE__}/dir_does_no_exist/ |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/modelle-v1/12smito-1.0.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos1-refdata/modelle-v1/12smito-1.0.cm Fri Mar 27 17:53:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,305 @@\n+INFERNAL-1 [1.0]\n+NAME 12snew_curated.47-1\n+STATES 212\n+NODES 55\n+ALPHABET 1\n+ELSELF -0.08926734\n+WBETA 1e-07\n+NSEQ 47\n+EFFNSEQ 11.611\n+CLEN 66\n+BCOM cmbuild C/C.seed25.cm C/C.seed25.stk\n+BDATE Thu Jun 4 14:45:27 2009\n+CCOM cmcalibrate -s 1244119536 C/C.seed25.cm\n+CDATE Thu Jun 4 14:45:36 2009\n+NULL 0.000 0.000 0.000 0.000 \n+PART 1 0 100 \n+E-LC 0 0.65673 -5.70339 2.98940 1500000 339214 0.003316\n+E-GC 0 0.39796 -13.07110 -0.72649 1500000 51002 0.007353\n+E-LI 0 0.63673 -4.29715 4.43509 1500000 292326 0.003848\n+E-GI 0 0.46967 -8.81201 1.57644 1500000 49319 0.007604\n+E-LV 0 0.50239 -2.62964 6.62253 15000000 117446 0.009579\n+E-GV 0 0.49685 -2.94017 8.62509 15000000 117373 0.003195\n+E-LF 0 0.57063 1.31989 9.46473 15000000 117387 0.009584\n+E-GF 0 0.51158 -0.74538 10.48538 15000000 117284 0.003197\n+FT-LC 37 0.99500 10000 1500000 0\n+ 0.114238 0.0534917 0.0372024 0.0173179 0.00938652 0.00582693 0.00429825 0.00169531 0.00115056 0.000917325 0.000524477 0.000473457 0.000384218 0.00016314 0.000132037 9.97359e-05 5.05392e-05 3.24666e-05 2.44679e-05 1.74477e-05 1.51905e-05 1.36302e-05 9.76953e-06 8.04158e-06 5.716e-06 4.20028e-06 3.057e-06 2.15474e-06 1.62487e-06 1.38562e-06 6.09062e-07 4.85161e-07 3.88424e-09 2.3704e-09 9.52993e-10 4.93218e-10 2.15012e-10 \n+ 5470.38 4863.69 4272.78 3807.6 3418.32 3018.47 2662.36 2313.68 2036.06 1787.67 1508.98 1240.03 1065.4 958.664 823.656 719.058 636.037 536.271 472.463 418.39 362.973 323.271 285.62 246.66 221.19 197.897 177.462 150.826 132.502 117.538 104.086 94.9182 64.2663 49.7975 26.8268 12.7325 9.49182 \n+FT-LI 39 0.99500 10000 1500000 0\n+ 0.112495 0.0855816 0.0479943 0.0250423 0.0146537 0.00616079 0.00410784 0.00239204 0.00209704 0.00158267 0.00115322 0.00093405 0.000768088 0.000599968 0.000392597 0.000270291 0.000202036 0.000107056 6.77495e-05 5.49263e-05 4.41381e-05 3.52187e-05 3.17897e-05 2.27152e-05 1.67326e-05 1.28462e-05 9.43281e-06 6.79172e-06 6.02734e-06 4.75098e-06 3.46767e-06 1.90864e-06 1.43162e-06 2.01454e-08 1.16477e-08 4.06632e-09 2.78202e-09 1.97877e-09 1.22513e-09 \n+ 5603.07 5027.36 4378.92 3873.34 3465.46 3105.84 2662.36 2313.68 2036.06 1787.67 1508.98 1354.71 1213.44 1065.4 958.664 823.656 719.058 636.037 536.271 472.463 418.39 362.973 323.271 285.62 246.66 221.19 197.897 177.462 150.826 132.502 117.538 104.086 94.9182 64.2663 49.7975 26.8268 19.8142 12.7325 9.49182 \n+FT-GC 40 0.99500 10000 1500000 0\n+ 0.236968 0.182336 0.142656 0.117178 0.105024 0.0913937 0.0700434 0.0376304 0.0299993 0.0205879 0.0169735 0.0134252 0.0102879 0.00986336 0.00972611 0.00818675 0.00653405 0.00541541 0.00431035 0.00328958 0.00301993 0.0024308 0.00220526 0.00170212 0.00144377 0.00109165 0.000876031 0.000718488 0.000663082 0.000546616 0.000487909 0.000452359 0.000401237 0.000361841 0.00032084 0.000273285 8.55325e-06 5.93502e-06 1.92697e-06 1.25614e-06 \n+ 5616.01 5033.64 4484.05 3939.67 3511.32 2961.32 2624.53 2335.59 2094.46 1859.11 1614.3 1435.84 1283 1110.64 988.365 888.597 784.722 696.188 592.572 515.068 458.362 405.818 350.043 303.173 268.968 239.847 213.769 190.721 168.34 151.502 134.41 115.109 100.259 89.1753 79.6016 74.5852 56.5887 13.0142 9.51581 7.45852 \n+FT-GI 41 0.99500 10000 1500000 0\n+ 0.106967 0.0801574 0.0609988 0.0560595 0.0527505 0'..b'34 0.000 0.000 0.000 0.000 \n+ IR 177 177 6 177 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATP 30 ]\n+ MP 178 177 6 182 6 -10.143 -10.082 -0.010 -8.858 -9.138 -9.533 -4.447 -3.437 -5.376 2.502 -6.036 -5.230 -0.445 -4.853 -4.562 2.817 -4.271 -1.006 0.452 -4.601 -2.049 -3.764 \n+ ML 179 177 6 182 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076 \n+ MR 180 177 6 182 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076 \n+ D 181 177 6 182 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n+ IL 182 182 5 182 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 \n+ IR 183 183 6 183 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATP 31 ]\n+ MP 184 183 6 188 4 -8.855 -9.062 -0.014 -7.476 -3.866 -1.094 -4.569 3.008 -2.532 -4.593 -0.058 -3.903 -4.191 1.901 -4.375 -1.107 0.535 -4.183 -2.153 -3.270 \n+ ML 185 183 6 188 4 -3.758 -3.940 -0.507 -2.670 0.660 -0.612 -0.293 -0.076 \n+ MR 186 183 6 188 4 -4.809 -3.838 -1.706 -0.766 0.660 -0.612 -0.293 -0.076 \n+ D 187 183 6 188 4 -4.568 -4.250 -2.265 -0.520 \n+ IL 188 188 5 188 4 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 \n+ IR 189 189 6 189 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 32 ]\n+ ML 190 189 6 192 3 -9.793 -0.006 -8.447 -1.410 -0.044 -2.059 1.271 \n+ D 191 189 6 192 3 -6.174 -1.687 -0.566 \n+ IL 192 192 3 192 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 33 ]\n+ ML 193 192 3 195 3 -9.793 -0.006 -8.447 -3.257 -3.018 -3.929 1.890 \n+ D 194 192 3 195 3 -6.174 -1.687 -0.566 \n+ IL 195 195 3 195 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 34 ]\n+ ML 196 195 3 198 3 -9.793 -0.006 -8.447 -2.956 -4.405 1.905 -3.687 \n+ D 197 195 3 198 3 -6.174 -1.687 -0.566 \n+ IL 198 198 3 198 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 35 ]\n+ ML 199 198 3 201 3 -9.793 -0.006 -8.447 -3.788 1.924 -4.717 -3.403 \n+ D 200 198 3 201 3 -6.174 -1.687 -0.566 \n+ IL 201 201 3 201 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 36 ]\n+ ML 202 201 3 204 3 -9.793 -0.006 -8.447 1.950 -4.780 -4.471 -4.223 \n+ D 203 201 3 204 3 -6.174 -1.687 -0.566 \n+ IL 204 204 3 204 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 37 ]\n+ ML 205 204 3 207 3 -9.793 -0.033 -5.539 1.900 -4.002 -3.127 -3.461 \n+ D 206 204 3 207 3 -6.174 -1.687 -0.566 \n+ IL 207 207 3 207 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 38 ]\n+ ML 208 207 3 210 2 * 0.000 1.403 -1.298 -1.053 -1.099 \n+ D 209 207 3 210 2 * 0.000 \n+ IL 210 210 3 210 2 -1.823 -0.479 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ END 39 ]\n+ E 211 210 3 -1 0 \n+//\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/modelle-v1/16smito-1.0.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos1-refdata/modelle-v1/16smito-1.0.cm Fri Mar 27 17:53:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,309 @@\n+INFERNAL-1 [1.0]\n+NAME 16snew_curated.81-1\n+STATES 215\n+NODES 56\n+ALPHABET 1\n+ELSELF -0.08926734\n+WBETA 1e-07\n+NSEQ 51\n+EFFNSEQ 10.038\n+CLEN 67\n+BCOM cmbuild D/D.seed25.cm D/D.seed25.stk\n+BDATE Thu Jun 4 15:07:51 2009\n+CCOM cmcalibrate -s 1244120884 D/D.seed25.cm\n+CDATE Thu Jun 4 15:08:04 2009\n+NULL 0.000 0.000 0.000 0.000 \n+PART 1 0 100 \n+E-LC 0 0.68594 -5.17883 3.04982 1500000 318026 0.003537\n+E-GC 0 0.38394 -13.73686 -1.30381 1500000 44375 0.008451\n+E-LI 0 0.61145 -4.69543 4.25021 1500000 267097 0.004212\n+E-GI 0 0.46024 -9.16275 1.13368 1500000 42864 0.008749\n+E-LV 0 0.51714 -1.83750 6.92800 15620000 108996 0.010748\n+E-GV 0 0.53259 -1.48562 9.08436 15620000 108760 0.003590\n+E-LF 0 0.60480 2.35802 9.85054 15620000 108825 0.010765\n+E-GF 0 0.58273 1.25623 10.91597 15620000 108710 0.003592\n+FT-LC 37 0.99500 10000 1500000 0\n+ 0.000398308 0.000205928 0.000180008 0.000120025 6.63133e-05 5.10891e-05 4.03485e-05 2.84008e-05 2.61925e-05 2.31052e-05 1.54629e-05 1.106e-05 5.43483e-06 3.59326e-06 3.28494e-06 2.55351e-06 1.55459e-06 1.1765e-06 9.34155e-07 7.25322e-07 5.70234e-07 4.72759e-07 3.14698e-07 2.47129e-07 1.65727e-07 1.23094e-07 9.2509e-08 7.61319e-08 7.23964e-08 6.99345e-08 6.39683e-08 3.33696e-08 2.39203e-08 2.06776e-08 1.22945e-10 1.17664e-10 2.90558e-11 \n+ 4689.63 4002.41 3572.25 3129.1 2764.23 2485.11 2179.46 1916.03 1714.24 1530.93 1372.19 1211.45 1072.13 960.962 861.32 765.501 664.482 583.46 511.698 440.161 383.928 337.115 297.626 261.177 212.762 186.706 162.755 145 128.324 110.652 98.7592 88.1983 79.1966 71.0903 26.1209 20.8961 7.10903 \n+FT-LI 37 0.99500 10000 1500000 0\n+ 0.0025769 0.00138199 0.00103861 0.000927636 0.000414727 0.000360445 0.000310064 0.000229884 0.000229611 0.000176742 0.000152247 9.68217e-05 6.06755e-05 4.13034e-05 3.9188e-05 2.8934e-05 1.55132e-05 1.30691e-05 1.20101e-05 8.2844e-06 6.60663e-06 6.27933e-06 5.02321e-06 3.75917e-06 2.57366e-06 1.98091e-06 1.45943e-06 1.31442e-06 1.28104e-06 1.23856e-06 1.04271e-06 8.37252e-07 5.89354e-07 4.65796e-07 5.67097e-09 5.37732e-09 1.45973e-09 \n+ 4749.58 4002.41 3572.25 3129.1 2764.23 2485.11 2179.46 1916.03 1721.51 1530.93 1372.19 1211.45 1072.13 960.962 861.32 765.501 664.482 583.46 511.698 440.161 383.928 344.744 297.626 261.177 212.762 186.706 162.755 145 128.324 113.019 98.7592 88.1983 79.1966 71.0903 26.1209 20.8961 7.10903 \n+FT-GC 36 0.99500 10000 1500000 0\n+ 0.00784903 0.00692477 0.00525712 0.00498237 0.00446475 0.00401959 0.00380679 0.00326094 0.00258073 0.00211996 0.00165836 0.00128251 0.00125434 0.000984245 0.000769829 0.000518773 0.000409513 0.000363838 0.000350492 0.00030655 0.000290155 0.000273504 0.000259097 0.000242375 0.000232343 0.000208837 0.000190833 0.000134851 0.000124369 0.000103661 9.39919e-05 8.86414e-05 3.05921e-06 1.64901e-06 8.57754e-07 7.53072e-07 \n+ 4735.16 3863.77 3143.57 2794.48 2471.17 2219.91 1774.82 1563.09 1405.8 1140.43 996.803 838.878 740.095 652.564 529.381 467.86 407.509 363.102 323.345 289.793 258.665 228.872 195.21 170.823 150.532 127.201 106.055 92.2132 77.1078 68.4654 61.1112 55.7531 33.6489 11.5297 7.80744 5.57531 \n+FT-GI 38 0.99500 10000 1500000 0\n+ 0.00208246 0.0016148 0.0012342 0.00117602 0.000980422 0.0008853 0.000773834 0.000716028 0.000600315 0.000398051 0.000332846 0.000283764 0.000191342 0.000190078 0.0'..b'34 0.000 0.000 0.000 0.000 \n+ IR 180 180 6 180 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATP 31 ]\n+ MP 181 180 6 185 6 -10.017 -9.956 -0.011 -8.733 -9.013 -9.408 -2.271 -1.779 -3.684 1.546 -2.415 -3.856 0.860 -3.481 -3.505 2.520 -3.440 0.001 1.393 -3.250 -1.318 -1.776 \n+ ML 182 180 6 185 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076 \n+ MR 183 180 6 185 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076 \n+ D 184 180 6 185 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n+ IL 185 185 5 185 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 \n+ IR 186 186 6 186 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATP 32 ]\n+ MP 187 186 6 191 4 -8.672 -8.879 -0.016 -7.293 -1.443 -3.624 -3.642 0.706 -2.565 -4.092 2.256 -3.618 -3.863 0.764 -3.896 -0.646 2.214 -1.807 -0.050 -1.361 \n+ ML 188 186 6 191 4 -3.758 -3.940 -0.507 -2.670 0.660 -0.612 -0.293 -0.076 \n+ MR 189 186 6 191 4 -4.809 -3.838 -1.706 -0.766 0.660 -0.612 -0.293 -0.076 \n+ D 190 186 6 191 4 -4.568 -4.250 -2.265 -0.520 \n+ IL 191 191 5 191 4 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 \n+ IR 192 192 6 192 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 33 ]\n+ ML 193 192 6 195 3 -9.614 -0.007 -8.268 -1.755 -0.952 -2.533 1.592 \n+ D 194 192 6 195 3 -6.174 -1.687 -0.566 \n+ IL 195 195 3 195 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 34 ]\n+ ML 196 195 3 198 3 -9.614 -0.007 -8.268 -3.497 -3.276 -4.223 1.909 \n+ D 197 195 3 198 3 -6.174 -1.687 -0.566 \n+ IL 198 198 3 198 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 35 ]\n+ ML 199 198 3 201 3 -9.614 -0.007 -8.268 -2.797 -4.243 1.894 -3.522 \n+ D 200 198 3 201 3 -6.174 -1.687 -0.566 \n+ IL 201 201 3 201 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 36 ]\n+ ML 202 201 3 204 3 -9.614 -0.007 -8.268 -3.497 -3.276 -4.223 1.909 \n+ D 203 201 3 204 3 -6.174 -1.687 -0.566 \n+ IL 204 204 3 204 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 37 ]\n+ ML 205 204 3 207 3 -9.614 -0.007 -8.268 -3.645 1.916 -4.572 -3.268 \n+ D 206 204 3 207 3 -6.174 -1.687 -0.566 \n+ IL 207 207 3 207 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 38 ]\n+ ML 208 207 3 210 3 -9.614 -0.007 -8.268 1.627 -2.607 -1.426 -1.419 \n+ D 209 207 3 210 3 -6.174 -1.687 -0.566 \n+ IL 210 210 3 210 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 39 ]\n+ ML 211 210 3 213 2 * 0.000 1.011 -1.692 -0.564 -0.002 \n+ D 212 210 3 213 2 * 0.000 \n+ IL 213 213 3 213 2 -1.823 -0.479 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ END 40 ]\n+ E 214 213 3 -1 0 \n+//\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/modelle-v1/Metazoa_A-1.0.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos1-refdata/modelle-v1/Metazoa_A-1.0.cm Fri Mar 27 17:53:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,301 @@\n+INFERNAL-1 [1.0]\n+NAME A.seed25-1\n+STATES 209\n+NODES 54\n+ALPHABET 1\n+ELSELF -0.08926734\n+WBETA 1e-07\n+NSEQ 36\n+EFFNSEQ 7.662\n+CLEN 65\n+BCOM cmbuild A/A.seed25.cm A/A.seed25.stk\n+BDATE Thu Jun 4 14:35:09 2009\n+CCOM cmcalibrate -s 1244119372 A/A.seed25.cm\n+CDATE Thu Jun 4 14:42:52 2009\n+NULL 0.000 0.000 0.000 0.000 \n+PART 1 0 100 \n+E-LC 0 0.70691 -4.92486 3.07253 1500000 320917 0.003506\n+E-GC 0 0.40832 -13.02576 -1.06871 1500000 49475 0.007580\n+E-LI 0 0.60214 -4.78922 4.30346 1500000 268505 0.004190\n+E-GI 0 0.43261 -9.86686 1.29887 1500000 46973 0.007983\n+E-LV 0 0.53075 -1.85653 6.96169 15000000 121275 0.009276\n+E-GV 0 0.52786 -1.99317 8.94975 15000000 120971 0.003100\n+E-LF 0 0.62383 2.38719 9.88734 15000000 121100 0.009290\n+E-GF 0 0.60533 1.34816 10.89140 15000000 121026 0.003099\n+FT-LC 36 0.99500 10000 1500000 0\n+ 0.000397367 0.000307642 0.000160963 0.000135713 6.63715e-05 4.08061e-05 2.88535e-05 2.51404e-05 2.37261e-05 1.39981e-05 1.1269e-05 7.893e-06 6.53184e-06 4.01054e-06 3.18169e-06 2.91534e-06 2.3745e-06 2.01141e-06 1.36658e-06 1.12477e-06 8.86235e-07 7.07117e-07 6.0043e-07 4.09309e-07 2.75978e-07 1.83657e-07 1.30492e-07 1.13799e-07 7.94193e-08 6.78567e-08 4.61576e-08 3.57222e-08 6.22131e-11 6.12339e-11 1.99109e-11 1.1657e-11 \n+ 5804.62 5142.97 4596.71 3932.92 3506.43 3110.62 2761.21 2288.5 2033.97 1774.24 1562.22 1385.88 1247.21 1102.29 970.569 873.453 756.705 673.805 600.736 518.495 431.88 368.364 331.299 287.913 258.781 231.295 208.021 171.443 150.299 134.167 117.987 102.529 58.5213 23.2892 12.5116 10.2529 \n+FT-LI 35 0.99500 10000 1500000 0\n+ 0.00352852 0.00267436 0.00204402 0.0017517 0.000860686 0.000630462 0.000547295 0.000464883 0.000355195 0.000259171 0.000199899 0.000164851 0.000110223 8.56413e-05 6.36128e-05 5.40474e-05 4.42238e-05 3.75421e-05 3.2727e-05 2.88192e-05 2.20172e-05 1.77789e-05 1.45705e-05 1.03897e-05 8.49051e-06 6.01041e-06 5.8105e-06 4.13986e-06 3.63819e-06 2.39777e-06 2.23853e-06 1.11012e-08 1.10951e-08 3.78079e-09 2.79696e-09 \n+ 5626.36 4932.44 4427.83 3932.92 3506.43 3110.62 2761.21 2288.5 2033.97 1774.24 1562.22 1317.59 1185.75 1052.56 873.453 756.705 669.197 600.736 518.495 431.88 364.251 320.324 287.913 258.781 231.295 194.347 171.443 150.299 134.167 117.987 102.529 58.5213 23.2892 12.5116 10.2529 \n+FT-GC 35 0.99500 10000 1500000 0\n+ 0.00740361 0.00728891 0.00495415 0.00401927 0.00273442 0.00250156 0.00236076 0.00173471 0.00137509 0.00117735 0.00110087 0.000992604 0.000773165 0.000639702 0.000481849 0.000399606 0.00035118 0.000316204 0.000275863 0.000267596 0.000228318 0.000167619 0.000146911 0.000133742 0.000110975 0.000102249 8.95882e-05 7.82678e-05 7.43273e-05 6.49988e-05 5.91295e-05 5.60077e-05 5.17943e-05 7.67417e-07 3.59113e-07 \n+ 5362.21 4690.78 4158.43 3677.58 3207.36 2778.71 2490.34 1959.54 1714.17 1464.54 1298.34 1160.78 1042.85 937.456 837.631 741.222 658.296 583.234 485.497 421.121 375.368 335.6 294.467 264.388 232.405 189.978 168.928 150.393 131.561 117.98 103.645 87.5918 80.6215 24.3323 8.06215 \n+FT-GI 35 0.99500 10000 1500000 0\n+ 0.00712675 0.00653563 0.00471224 0.00443875 0.00290512 0.00248511 0.00227069 0.0018916 0.00161396 0.00127756 0.00112119 0.000895945 0.000709995 0.000564245 0.000498563 0.00039569 0.000332146 0.000315273 0.000296305 0.000269458 0.000204182 0.00016014 0.000141608 0.000'..b'34 0.000 0.000 0.000 0.000 \n+ IR 174 174 6 174 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATP 30 ]\n+ MP 175 174 6 179 6 -9.805 -9.744 -0.013 -8.520 -8.800 -9.195 -3.951 -2.976 -4.851 2.162 -5.531 -4.714 0.173 -4.372 -4.075 2.726 -3.792 0.812 -0.118 -4.091 -1.714 -1.883 \n+ ML 176 174 6 179 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076 \n+ MR 177 174 6 179 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076 \n+ D 178 174 6 179 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n+ IL 179 179 5 179 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 \n+ IR 180 180 6 180 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATP 31 ]\n+ MP 181 180 6 185 4 -8.342 -8.549 -0.020 -6.963 -3.828 -3.004 -4.534 2.801 -4.561 -4.563 0.948 -3.965 -4.099 1.889 -4.097 -0.155 0.425 -4.066 -1.697 -1.808 \n+ ML 182 180 6 185 4 -3.758 -3.940 -0.507 -2.670 0.660 -0.612 -0.293 -0.076 \n+ MR 183 180 6 185 4 -4.809 -3.838 -1.706 -0.766 0.660 -0.612 -0.293 -0.076 \n+ D 184 180 6 185 4 -4.568 -4.250 -2.265 -0.520 \n+ IL 185 185 5 185 4 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 \n+ IR 186 186 6 186 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 32 ]\n+ ML 187 186 6 189 3 -9.293 -0.008 -7.947 -1.325 -0.398 -1.340 1.291 \n+ D 188 186 6 189 3 -6.174 -1.687 -0.566 \n+ IL 189 189 3 189 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 33 ]\n+ ML 190 189 3 192 3 -9.293 -0.008 -7.947 -2.553 -1.556 -3.344 1.762 \n+ D 191 189 3 192 3 -6.174 -1.687 -0.566 \n+ IL 192 192 3 192 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 34 ]\n+ ML 193 192 3 195 3 -9.293 -0.008 -7.947 -3.166 -3.024 -3.902 1.887 \n+ D 194 192 3 195 3 -6.174 -1.687 -0.566 \n+ IL 195 195 3 195 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 35 ]\n+ ML 196 195 3 198 3 -9.293 -0.008 -7.947 -2.537 -3.967 1.871 -3.248 \n+ D 197 195 3 198 3 -6.174 -1.687 -0.566 \n+ IL 198 198 3 198 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 36 ]\n+ ML 199 198 3 201 3 -9.293 -0.008 -7.947 -3.371 1.899 -4.286 -3.020 \n+ D 200 198 3 201 3 -6.174 -1.687 -0.566 \n+ IL 201 201 3 201 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 37 ]\n+ ML 202 201 3 204 3 -9.293 -0.008 -7.947 1.846 -3.376 -2.550 -2.848 \n+ D 203 201 3 204 3 -6.174 -1.687 -0.566 \n+ IL 204 204 3 204 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 38 ]\n+ ML 205 204 3 207 2 * 0.000 0.214 -0.284 -0.967 0.592 \n+ D 206 204 3 207 2 * 0.000 \n+ IL 207 207 3 207 2 -1.823 -0.479 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ END 39 ]\n+ E 208 207 3 -1 0 \n+//\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/modelle-v1/Metazoa_Y-1.0.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos1-refdata/modelle-v1/Metazoa_Y-1.0.cm Fri Mar 27 17:53:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,313 @@\n+INFERNAL-1 [1.0]\n+NAME Y.seed25-1\n+STATES 218\n+NODES 57\n+ALPHABET 1\n+ELSELF -0.08926734\n+WBETA 1e-07\n+NSEQ 41\n+EFFNSEQ 9.204\n+CLEN 68\n+BCOM cmbuild Y/Y.seed25.cm Y/Y.seed25.stk\n+BDATE Fri Jun 5 16:44:25 2009\n+CCOM cmcalibrate --mpi -s 1244213078 Y/Y.seed25.cm\n+CDATE Fri Jun 5 16:44:38 2009\n+NULL 0.000 0.000 0.000 0.000 \n+PART 1 0 100 \n+E-LC 0 0.69366 -5.39590 2.90570 1500000 356473 0.003156\n+E-GC 0 0.39344 -14.01120 -1.58783 1500000 49753 0.007537\n+E-LI 0 0.59933 -5.11205 4.16736 1500000 292705 0.003843\n+E-GI 0 0.42638 -10.27778 0.99910 1500000 45944 0.008162\n+E-LV 0 0.50762 -3.27736 5.69133 16240000 115576 0.010539\n+E-GV 0 0.48259 -4.00052 7.63704 16240000 111589 0.003638\n+E-LF 0 0.56925 1.25800 9.23037 16240000 113914 0.010692\n+E-GF 0 0.54340 -0.00437 10.33139 16240000 111616 0.003637\n+FT-LC 42 0.99500 10000 1500000 0\n+ 0.0129247 0.0101162 0.00913756 0.00630848 0.00341654 0.00303756 0.000843618 0.000433025 0.000345623 0.000218532 0.000191617 0.000105544 7.5533e-05 5.24113e-05 4.24162e-05 3.07348e-05 1.88156e-05 1.39799e-05 1.06514e-05 6.64865e-06 6.1536e-06 4.26767e-06 3.58691e-06 2.79324e-06 2.41767e-06 2.18626e-06 1.68404e-06 1.27892e-06 1.10906e-06 1.0225e-06 8.88663e-07 5.76515e-07 5.30667e-07 3.46196e-07 3.0048e-07 1.01763e-09 3.79688e-10 3.25843e-10 1.45442e-10 1.23902e-10 7.484e-11 2.4042e-11 \n+ 4322.09 3852.61 3298.1 2936.51 2598.24 2313.38 2065.62 1839.15 1652.49 1448.05 1294.44 1055.19 930.452 819.062 726.776 625.722 562.858 494.629 441.906 395.253 349.722 307.854 275.196 247.407 212.765 185.595 160.062 143.654 124.315 106.483 92.2529 82.3727 73.0084 65.375 65.0059 49.6315 25.1236 18.496 14.4966 8.8648 7.54581 6.50059 \n+FT-LI 43 0.99500 10000 1500000 0\n+ 0.0610105 0.0395336 0.033597 0.0232697 0.0132173 0.010154 0.00410853 0.00316628 0.00249503 0.00144903 0.00116555 0.000771968 0.000699245 0.000597934 0.000393493 0.000343528 0.000270905 0.000225104 0.000182602 0.000120402 9.84194e-05 7.14266e-05 5.13937e-05 4.86763e-05 4.13451e-05 3.93083e-05 3.58968e-05 2.94296e-05 2.177e-05 1.86732e-05 1.71581e-05 1.50061e-05 1.19604e-05 1.03263e-05 7.05503e-06 6.78426e-06 6.2151e-08 1.63124e-08 1.28785e-08 1.11741e-08 7.87894e-09 7.81643e-09 3.06508e-09 \n+ 4439.29 3852.61 3298.1 2936.51 2598.24 2313.38 2065.62 1839.15 1652.49 1448.05 1294.44 1159.1 1013.97 906.92 813.023 726.776 625.722 562.858 494.629 441.906 395.253 349.722 307.854 274.258 236.797 212.765 185.595 160.062 143.654 124.315 106.483 92.2529 82.3727 73.0084 65.375 65.0059 54.1479 18.496 16.1525 14.4966 8.8648 7.54581 6.50059 \n+FT-GC 41 0.99500 10000 1500000 0\n+ 0.0604139 0.0450242 0.0427577 0.0398523 0.033994 0.0218763 0.0191067 0.0175132 0.0140107 0.0103011 0.00987201 0.00932771 0.00794648 0.00462524 0.00366473 0.00275189 0.00267195 0.00235196 0.00203125 0.00179929 0.00170893 0.00158861 0.0013491 0.0011709 0.000999815 0.000804956 0.000728541 0.000624115 0.000537218 0.000401063 0.000344412 0.000307848 0.000281361 0.000242445 0.000222978 0.000207493 0.00018781 1.10574e-05 6.7514e-06 1.31824e-06 8.43334e-07 \n+ 4651.91 4141.21 3712.72 3334 2924.76 2622.13 2340.62 2057.79 1820.96 1575.89 1356.41 1186.04 1061.59 951.231 854.663 700.139 628.378 559.09 496.902 443.073 392.082 349.608 304.536 250.835 225.125 199.217 161.171 144.103 129.614 115.51 '..b'34 0.000 0.000 0.000 0.000 \n+ IR 183 183 6 183 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATP 31 ]\n+ MP 184 183 6 188 6 -9.946 -9.885 -0.012 -8.662 -8.942 -9.337 -4.247 -3.224 -5.181 2.236 -5.843 -4.978 0.655 -4.676 -4.349 2.883 -4.041 -0.537 -0.237 -4.369 -1.829 -3.565 \n+ ML 185 183 6 188 6 -6.250 -6.596 -1.310 -1.005 -6.446 -3.975 0.660 -0.612 -0.293 -0.076 \n+ MR 186 183 6 188 6 -6.988 -5.717 -1.625 -5.695 -0.829 -3.908 0.660 -0.612 -0.293 -0.076 \n+ D 187 183 6 188 6 -9.049 -7.747 -3.544 -4.226 -4.244 -0.319 \n+ IL 188 188 5 188 6 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 \n+ IR 189 189 6 189 5 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATP 32 ]\n+ MP 190 189 6 194 4 -8.564 -8.771 -0.017 -7.186 -3.880 -1.395 -4.673 2.953 -5.128 -4.631 -0.147 -3.992 -4.160 1.955 -4.202 -0.376 0.653 -4.187 -2.030 -3.261 \n+ ML 191 189 6 194 4 -3.758 -3.940 -0.507 -2.670 0.660 -0.612 -0.293 -0.076 \n+ MR 192 189 6 194 4 -4.809 -3.838 -1.706 -0.766 0.660 -0.612 -0.293 -0.076 \n+ D 193 189 6 194 4 -4.568 -4.250 -2.265 -0.520 \n+ IL 194 194 5 194 4 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 \n+ IR 195 195 6 195 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 33 ]\n+ ML 196 195 6 198 3 -9.509 -0.007 -8.163 -1.625 0.173 -2.443 1.241 \n+ D 197 195 6 198 3 -6.174 -1.687 -0.566 \n+ IL 198 198 3 198 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 34 ]\n+ ML 199 198 3 201 3 -9.509 -0.007 -8.163 -3.395 -3.196 -4.124 1.902 \n+ D 200 198 3 201 3 -6.174 -1.687 -0.566 \n+ IL 201 201 3 201 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 35 ]\n+ ML 202 201 3 204 3 -9.509 -0.007 -8.163 -1.999 -3.854 1.833 -3.100 \n+ D 203 201 3 204 3 -6.174 -1.687 -0.566 \n+ IL 204 204 3 204 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 36 ]\n+ ML 205 204 3 207 3 -9.509 -0.007 -8.163 -3.395 -3.196 -4.124 1.902 \n+ D 206 204 3 207 3 -6.174 -1.687 -0.566 \n+ IL 207 207 3 207 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 37 ]\n+ ML 208 207 3 210 3 -9.509 -0.007 -8.163 1.939 -4.472 -4.197 -3.928 \n+ D 209 207 3 210 3 -6.174 -1.687 -0.566 \n+ IL 210 210 3 210 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 38 ]\n+ ML 211 210 3 213 3 -9.509 -0.007 -8.163 1.695 -2.843 -1.240 -2.326 \n+ D 212 210 3 213 3 -6.174 -1.687 -0.566 \n+ IL 213 213 3 213 3 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ MATL 39 ]\n+ ML 214 213 3 216 2 * 0.000 1.639 -1.236 -2.206 -2.037 \n+ D 215 213 3 216 2 * 0.000 \n+ IL 216 216 3 216 2 -1.823 -0.479 0.000 0.000 0.000 0.000 \n+\t\t\t\t[ END 40 ]\n+ E 217 216 3 -1 0 \n+//\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/refseq39/featureProt/nad6.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos1-refdata/refseq39/featureProt/nad6.fas Fri Mar 27 17:53:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,3752 @@\n+>NC_007102:9873-10397 Haematobia irritans irritans\n+MMQWILLTIMFIFNLVFMNIKHPLAMGLILLIQTILVSMTTGLMSKSFWFSYILFLVFLGGMLVLFIYVTSLASNEMFSFSIKLMLISFTIFMLMILSLYFMDKNLLMQYFSIETQSISNLNSYIMENSLSLNKLYNYPTNLLTILLMNYLLITLIAVVKITNLFKGPLRPMFN\n+>NC_006546:13838-14359 Anguilla reinhardtii\n+MSYFVFLFLVMLVLGFLGVASNPAPYFAALGLVLAAAGGCGVLAGYGGSFISLVLFLIYLGGMLVVFAYSAALAAEPYPESWGDWSVLGYVVGYFLLCVLGISVFYVEWFDCYCGIVDEYRDFSVVRGDFSGVSFIYYLGGGMLIICGWALLLTLFVVLELTRGRSRGALRAI\n+>NC_011006:13782-14303 Leptochilichthys agassizii\n+MTYLVSLFLLGLIVGLVAVASNPAPYFAAFGLVVAAGVGCGVLVGHGGAFLSLVLFLIYLGGMLVVFAYSAALAAEPFPETWGDRSVIGYVVVYLVGVGLAAGWFWGGWYEGSWVVVDEFKEFFVLRGDSSGVALMYSYGGGMLVVCAWVLLLTLFVVLELTRGLSRGTLRAV\n+>NC_002619:13580-14107 Pteropus scapulatus\n+MMTYIVFILSTVFVVGFVGFSSKPSPVYGGVGLIVSGGVGCGIIMNFSGSFLGLMVFLIYLGGMMVVFGYTAAMATELYPEVWVSNKVVFGAFVFGLFMEMLLVLYVLKEGSVGIAFEFSNLGDWVVYGVEDSGYFSKEAVGISSLYSYGMWLVVVTGWSLFIAVVVVMEVTRGG\n+>NC_012841:9781-10264 Gerris sp. NKMT033\n+MKILLAIMLTTSTLMMMMKHPLSMGFNLIIQTIIISLTMNMMMKYSWYSYILVLVMLGGMLVLFMYMASIASNEIMKFNFKMTIMMIISTTLFYLILENEMFMNQQEMIMLIENKQNMSMMKLFNSKTSIMTIMLALYLLITMIYVIFITNTFEGPMRKKN\n+>NC_004321:2990-3463 Roboastra europaea\n+MGFLYWLCVSLIFCFPLFKNPISMAAMVVVISLAVVSMLSLFSSFWFSYVLFLVYVGGLLVMFIYICLVSSNYPFKFSTIGFVLTLLGSCIVSMKMNGVVSSKFLGSGSWVNGESLLETSNISIFLFLAVLLLMMLLVVVRISGAGCFTVGSSGEKS\n+>NC_013605:13839-14360 Simenchelys parasitica\n+MSFFIFLFLVMMVLGFLGVASNPAPYFAALGLVVAAAGGCGVLASYGGSFVSLVLFLIYLGGMLVVFAYSAALAAEPYPESWGDWSVLGYVLGYVLLSVLGVITFYSGWLNYYCGIVDEYQDFSVLRGDFSGVSFMYYLGGEMLIVCGWALLLTLFVVLELTRGRSRGALRAI\n+>NC_008231:10525-10944 Agamermis sp. BH-2006\n+MKIKMLIGTMIFMLLMNHPSYMCMCLAIFCLFLGFFMKSLVPNIFIYSMLIIFIGGILLLLFYLTMINTNKTSWQNMLYLTIFMAPDFYEIHNLKFSCSTIFIEMFNLKTLMIFMMGVLMVMLMIMNTFLLKVSFMRQF\n+>NC_005925:7859-8287 Ornithoctonus huwena\n+MWLKMIVLMSLIFMISTHPMSLVMAMMVIVLMYSLEMYWSSGTFLYSMVLMLIILSGVMVIFTYMASMNPNEKFEFFFVGMMIMLLFSFYWGNEWKIMVTFEMLDMWNSSIMVVSEYLVSFLLVIMFMTIWISGWWYGPLRV\n+>NC_010217:4236-4829 Plakortis angulospiculatus\n+MKELFYAITLAILVSGIMVISALNPIHSVFWLIAVFLGASALFILLNIDFIALIFLIVYVGAIAILFLFVIMMLNLTDLEGVGDMSNYIPIGSVMGVFLLFEIFIIGREAIVYSNEDTDYTNLTDLLDSWDISIEIIKFSNIEALGRILYTDYFYSFILASFILLVAMIGAIVLTHELGIELKRQDLFIQTSRNLLQ\n+>NC_004397:13759-14280 Zenion japonicum\n+MTYIMYVLLLGLVLGLVGVASNPSPYYAALGLVMVAGAGCGVLVVCGGGFLSLVLFLIYLGGMLVVFAYSAALAAEPYPEAWGGEAVFESVVVYGMLVLGAFLWAGGDWYEGSWVPVYELKAFSVVPGDLGGVALMFSFGGVMLNLGAWVLLLTLFVVLELIRGLSRGTLCAV\n+>NC_013485:14663-15184 Rastrelliger brachysoma\n+MTYALCVLLICLVLGLVAVASNPSPYFAALGLVAVAGMGCCVLAAHGGSFLSLVLFLIYLGGMLVVFAYSAALAAEPYPETWGSPAVVMYILVYLVGVVLGCAVFWGGWYETSWVPVDDMETFSMFRGDVGGVALMYSMGGGMLVISAWALLLTLFVVLELTRGLSRGTVRAV\n+>NC_002391:13583-14110 Talpa europaea\n+MMTYIVFILSTILVVSFVGFSSKPSPIYGGLGLIVSGGVGCGIVLNYGGSFLGLMVFLIYLGGMLVVFGYTTAMAMEEYPEVWVSNKIVLSLFVLGMFSELLFVGYCVMDEKLEIVLNFNGQGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVIVTGWSLVIGVLVVMEITRGN\n+>NC_009577:13778-14299 Clupea harengus\n+MVYFAFMLLVGLVLGLVGVACNPAPYFAAFGLVVAAGMGCAVLAVSGAPFLALVLFLIYLGGMLVVFAYSSALAADPFPEGWTEVTVFEQLAFYLLGVVAAGLYFGKHWYTLFVGMVDSCSKFFTIRADMGGVVAMYGSGGFMLVFCAWVLLLTLFVVLELVRGLSRGPLRAV\n+>NC_010203:3782-4354 Aplysina fulva\n+MEGLFFLFGVNVLFSGIMVISALNPVHSVLWLIVAFTNASALFILLNVEFIALIFLIIYVGAIAILFLFVIMMLNLADLGGSEDMSNYLLAGLIIGIVFLFEIWIWQNHQETPPMAFIYSAGINYWDYTAAYTNIEIIGRILYTELYYLFIVASFVLLVAMIGAIVLTHDMGTEIKRQDIFIQTSRQLWL\n+>NC_012775:13526-14059 Saimiri sciureus\n+MTYALFSLSVTLVMGFVGFCSKPSPIYGGLVLIFSGAVGCAITLYFGGSYMGLMVFLIYLGGMMVVFGYTAAMAIDEHPESWVSSVDILGMFVLGMMMETMMLMVLGGDYKQTVEVTMNYKTVASWMIHEGEGPGLIREDPTGAGALYNYGVWVVLVTCWALFMGMHIAIELTRGGG\n+>NC_005805:13845-14366 Synaphobranchus kaupii\n+MSFFIFLFLVTMVLGFLGVASNPAPYFAALGLVVAAAGGCGVLVGYGGSFVSLVLFLIYLGGMLVVFAYSAALAAEPYPESWGDWSVLGYVVGYILLSVLGVVTFCGGWLNYHCGLVDEYRDFSALRGDFSGVSFMYNLGGEMLIVCGWALLLALFVVLELTRGRSRGALRAI\n+>NC_008132:16139-16660 Nipponia nippon\n+MTYFVVFLGVGFILGGLAVASNPSPYYGVVGLVLASVVGCGWLLSLGVSFVSLVLFMVYLGGMLVVFVYSVALAADLFPETWGDWRVVGYGVGFVSVLWVGAVVGGLAEGWKLGVVTVDSGGVFSVRLDFSGVAMFYAEGAGMFLVAGWGLLLTLFVALELVRGLSRGAIRAV\n+>NC_012455:1977-2438 Paracyclopina nana\n+MYMFSISGLLIFLGLLLVANQSPFVIALMLTVYSMFIG'..b'SFLSLILFLIYLGGMMVVFAYSAALAAEPYPETWGAWSVLVYVIVSVIGVLGAGYWFVGEWDKFMWVAEEFMELGVLRGDFSGVALVYDLGGGMLIVCGWVLLLTLFVVLELIRGMGRGCLRAI\n+>NC_013137:13797-14318 Girella punctata\n+MSFIMFLFLFCFILGVVAVASNPSPYFAALALVLVATMGCGVLVGHGGPFLSLVLLLIYLGGMLVVFAYSAALAAEPYPESWISLSIGAYMMGYVVVVLLVGGLFWDGWYESSWVPVDELDYYSVLRGDAEGVAWMYLPGGCMLIISAWVLLLTLFVVLELTRGLSRGALRAV\n+>NC_010091:14931-15449 Rhynochetos jubatus\n+MASLVLFLGGWFVLGALAVASNPSPYYGVVGLVVASIAGCGWLLSLGVSFVSLVLFMVYLGGMLVVFVYSVSLAAEPFPEAWGDWGVIGYGAGLVGVIVVGVVAWGVADVGFGVVTVDGGGLFSVRLDFSGVSMFYSHGAGMFLVAGWGLLLTLFVVLELVRGLSRGTIRAV\n+>NC_009834:2621-3100 Phallusia fumigata\n+MLFFSELSVLGWLGVMVSLYMVLGGSVVLMVALVVFFALGFMWSLLVVDLFLWGVMMGLLYLGGMMVLFSYSSMLMGGVDEGVGGGKAPLSGGELLYGAFVGAVCGCGLVGGLGTWGGWGCGGVGQLWLYGSGYFLAAVVILVVVLLVCLHLCVEGWVC\n+>NC_006299:13615-14115 Monodelphis domestica\n+MTMMMIFIISLLLIFGFVAFSSKPSPVYGGLSLVASGGLGCVMVVNFEDSFLGLVVFLVYLGGMLVVFGYTAAMATEEYPETWVGNILAFCMLLFVLLMEIMWYFIFGNTYVDSNIELIDFTVMSCIGQDFSGVPLLYWCGGWALALLGWILFITIYVVLEVVRGH\n+>NC_012897:16107-16628 Pavo muticus\n+MTYFVIFLGICFMLGVLAVASNPSPYYGVVGLVLASVVGCGWLMSLGVSFVSLALFMIYLGGMLVVFVYSVSLAADPYPEAWGSWRVVGYGLGFVLVVCVGVVLGGFVDFWKVGVSTVDSGGASLIRLDFGGVAVFYSWGVGLFLVAGWGLLLVLFVVLELVRGLSRGAIRAV\n+>NC_006132:13635-14159 Pelodiscus sinensis\n+MVFFMFLFEVCFVFWIISVASGPSPYYGVVGLVFGAVFGCLMLVGVGGSFISLVLFLIYLGGMLVVFAYSVALTGDPYPSAWRGYGDLFCMVGYVLFVVGAVMYCFDKWSLEGYGDVVMDASGLFSVRMDYIGVSWFYSYGCVMFLIAGWGLLLTLFVVLDLVRGLAWGTIRSI\n+>NC_008668:13775-14296 Acheilognathus typus\n+MTYFAFLLLVGLILGLIAVASNPTPYFAALGLVVAAGVGCGILISSGGSFLSLVLFLIYLGGMLVVFAYSAALAAEPFPEAWGSRSVVMYVLIYFVGVALVAGLFWGGWYEGSWVLVDGLKEFSLLRGDVGGVAMMYSFGGSMLVICAWVLLLTLLVVLELTRGLTRGSLRAV\n+>NC_011633:13750-14271 Takifugu chinensis\n+MFYALVFLLLGMLVVMIVLSTNPAPFYGVFNLVLVALLCCGASVLHGGTFLSLVLLMIYMGGMLVVFIYSSALSADKDPKAPTGWQVVLFFFGYFFFVFGILYTNMVLDEEVWWGVSGEMDWDAVFRGDMDGVSLMYSSGGGVLLLGAWVLLLTLLVVLELVRGLGRGALRAV\n+>NC_012456:9720-10208 Hydaropsis longirostris\n+MKMLIMTLLTLSMNFLWLKHPISMGVLIIIQTISIAMLSGMMSSTFWFSYIITITMLSGMLVLFIYMASVASNEMISVSIKMIIMTIVILSLGLILQNMDNYEDIFINKTNQEKIKTISLNPLFNMKHKFITMMMITYLLFSMITISFIVNITEGPLRINKK\n+>NC_011579:13562-14095 Martes zibellina\n+MMTYIVFILSVIFVVSFVGFSSKPSPIYGGLVLIVSGAVGCGIVLSFGGSFLGLMVFLIYLGGMLVVFGYTTAMATEQYPEVWASNKAVLGAFIVGLLSELLTACYILKGDDVEVEVVLKFNGAGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVIVTGWSLFIGVLVIMEVTRGN\n+>NC_011625:13748-14269 Takifugu niphobles\n+MFYALVFLLLGMLVVMIVLSTNPAPFYGVFNLVLVALLCCGASVLHGGTFLSLVLLMIYMGGMLVVFIYSSALSADKDPKAPTGWQVVLFFFGYFFFVFGILYTNMVLDEEVWWGVSGEMDWDAVFRGDMDGVSLMYSSGGGVLLLGAWVLLLTLLVVLELVRGLGRGALRAV\n+>NC_004383:13895-14416 Caulophryne pelagica\n+MSYFMFMLLLGLVGGLVAVASNPSPYFAALGLVVVAGVGCGILLGFGGSFLSLVLFLIYLGGMLVVFAYSAALAAEPYPESFGSSLVAPTVGAYLLGVGFISSFFWEGWYEASWVPVGELFEFCIQRADTSGVAMMYCWGGEMLVASAWVLLLTLFVVLELTRGLARGAVRAV\n+>NC_007627:13563-14072 Gekko gecko\n+MAYLFFLLALFLWVGVAGVTANPSAVFGVGALILGAVSGCGILVGLGGSFVGLVLLLVYIGGMLVVFAYSIALVVESHLESWLEYAVLVYFVGYLVVTAVLWYCFGESVVGPGADSYGVFGLRSDMVGVALLFSEGGPFLLFAGWGLLLVLFVVLELVRGQSRGCLSVP\n+>NC_002504:13549-14076 Lama pacos\n+MMTYIVFILSIMFVIGFISFSSKPSPIYGGLGLIVSGGVGCMIVLSYGGSFLGLMVFLIYLGGMMVVFGYTTAMPTEQYPDVWVSNKTVLGAFTFGLVVEMLMVVYVLKGEEVDFIFKFNGMGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVIITGWSLLIGVVVIMEITRGN\n+>NC_010961:12846-13352 Metaperipatus inae\n+MLFSLMYFLMLYLGALFLSQAHPLMMSIMIIMQTIIVCLIIGTQYMDFWYSYILFLIFIGGLLVLFIYISSLAENETFSFKKSWYMKYIGMSFIFLFLYFYVYILLKLYNKDSNMFLMVIKGLNVYQSYIYSENLIKIILFLTLYLLFCLIVVTSICQIIKGPLRQKF\n+>NC_011379:13911-14432 Xiphophorus maculatus\n+MSYLMYILLFGLVLGLVAVASNPSPYFAALGLVVVAGVGCGVLVGSGGCFLSLILFLIYLGGMLVVFAYSAAMAAEPFPEGWGSWPTLRLMVGYVAGVGVAWGLMGKFWYEEDWLGFDGVVELSVLRGDVGGVSLMYSSGGWLLIGGGWVLLLTLFVVLELTRGLSRGALRAV\n+>NC_011576:14347-14850 Achalinus meiguensis\n+MDYVFCLILLLMVVGVVVLGVTPVSYYGVVALMWVAFFCCVLMVFMGRVFTALVTYIVYLGGLVVVFGYCVSLEKDVDVVFKIVSLKFALFILVGLVVCFWALKTGAGGLLVSFDQGSYVNLEVNGYGVFYCSGGVGLMVCLWGLMITLFSVLIILGWCRKGGFRTF\n+>NC_011113:13821-14342 Epinephelus akaara\n+MCFTVICFLICWIVGAIAVASNPSPFFGALGLVMVAGVGCGFFVEFGSPFLALILFLIYLGGMLVVFAYSAALAAEPYPESWVNPTVVAYMCCYMAVVVGVASKFWHEWVGGFSGSADEWGPFYIFRADNGGVAVMYSEGGWMLVVSAGVLLLTLFVVLELTRGLSRGTLRAV\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.phr |
| b |
| Binary file test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.phr has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.pin |
| b |
| Binary file test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.pin has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.psd --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.psd Fri Mar 27 17:53:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,3752 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7:7180-7680\x02785\n+nc_013188:13368-13898\x02670\n+nc_013189:14706-15227\x0259\n+nc_013238:10548-11087\x021756\n+nc_013239:7321-7821\x021826\n+nc_013240:9889-10410\x02996\n+nc_013241:8562-9059\x021365\n+nc_013242:7260-7760\x021132\n+nc_013243:7364-7864\x02369\n+nc_013244:14978-15499\x021291\n+nc_013245:7226-7726\x02938\n+nc_013246:8480-8985\x02793\n+nc_013247:7244-7744\x02101\n+nc_013248:7237-7737\x02893\n+nc_013249:9903-10427\x021694\n+nc_013250:7296-7796\x021347\n+nc_013251:9708-10223\x021085\n+nc_013252:9802-10305\x021574\n+nc_013253:7751-8167\x0248\n+nc_013254:9711-10211\x02810\n+nc_013256:9862-10383\x021068\n+nc_013257:9986-10501\x021004\n+nc_013270:13768-14265\x02683\n+nc_013271:5674-6159\x021704\n+nc_013272:9821-10300\x02474\n+nc_013274:10025-10558\x02232\n+nc_013275:6188-6670\x021118\n+nc_013276:13526-14050\x02453\n+nc_013360:13735-14253\x02330\n+nc_013430:14701-15222\x02386\n+nc_013431:14701-15222\x02554\n+nc_013432:8110-8598\x02725\n+nc_013433:14701-15222\x02835\n+nc_013434:13765-14286\x02372\n+nc_013435:13841-14362\x021823\n+nc_013436:13818-14339\x021643\n+nc_013445:13583-14110\x021399\n+nc_013474:9334-9780\x021536\n+nc_013479:14443-14949\x02720\n+nc_013480:4856-5371\x02834\n+nc_013481:14509-15000\x021011\n+nc_013483:16108-16626\x021075\n+nc_013485:14663-15184\x0211\n+nc_013554:10461-10958\x021412\n+nc_013555:13777-14298\x021795\n+nc_013556:1525-1963\x02921\n+nc_013557:13768-14289\x02110\n+nc_013558:13558-14085\x021189\n+nc_013559:13772-14293\x02971\n+nc_013560:13773-14294\x02766\n+nc_013561:3989-4426\x02652\n+nc_013562:13770-14291\x021594\n+nc_013563:13517-14041\x02329\n+nc_013564:13775-14296\x021524\n+nc_013565:5077-5526\x02840\n+nc_013566:13775-14296\x02636\n+nc_013567:13770-14291\x02870\n+nc_013568:2472-2861\x02517\n+nc_013569:3491-3947\x021720\n+nc_013570:13773-14294\x02782\n+nc_013571:13526-14050\x02613\n+nc_013572:13775-14296\x02566\n+nc_013573:5065-5622\x02298\n+nc_013574:13780-14301\x02606\n+nc_013575:13771-14292\x02533\n+nc_013576:9699-10193\x02378\n+nc_013577:13774-14295\x0251\n+nc_013578:10139-10543\x021290\n+nc_013579:13772-14293\x021279\n+nc_013580:9803-10309\x02184\n+nc_013581:13773-14294\x021418\n+nc_013582:9734-10222\x021101\n+nc_013583:13771-14289\x021098\n+nc_013584:2683-3141\x02622\n+nc_013601:13802-14323\x02669\n+nc_013602:13814-14335\x02917\n+nc_013603:13334-13837\x021489\n+nc_013604:9861-10388\x021639\n+nc_013605:13839-14360\x026\n+nc_013606:16128-16646\x02176\n+nc_013607:13825-14343\x021325\n+nc_013608:16149-16667\x02638\n+nc_013609:14035-14562\x021117\n+nc_013610:13771-14286\x02749\n+nc_013611:16080-16598\x021572\n+nc_013612:21535-22056\x02552\n+nc_013613:13776-14294\x02106\n+nc_013614:16040-16555\x021680\n+nc_013615:16406-16924\x021657\n+nc_013616:13809-14330\x02337\n+nc_013617:16178-16693\x02278\n+nc_013618:16052-16570\x02354\n+nc_013619:16135-16656\x021767\n+nc_013620:13787-14308\x0230\n+nc_013621:16158-16676\x021130\n+nc_013622:13792-14313\x021181\n+nc_013623:16192-16710\x021509\n+nc_013624:13846-14367\x02626\n+nc_013625:16079-16597\x02440\n+nc_013626:13848-14369\x021162\n+nc_013627:13881-14402\x02468\n+nc_013628:14244-14765\x02954\n+nc_013629:16121-16639\x02899\n+nc_013630:16106-16624\x02567\n+nc_013631:13824-14345\x02389\n+nc_013632:15286-15801\x021042\n+nc_013633:13793-14311\x02310\n+nc_013634:13844-14365\x021422\n+nc_013635:16221-16739\x021049\n+nc_013658:12028-12525\x02472\n+nc_013659:12114-12569\x0221\n+nc_013661:11862-12350\x02475\n+nc_013662:7911-8420\x021515\n+nc_013663:13825-14346\x021759\n+nc_013700:13591-14118\x021716\n+nc_013701:9870-10391\x02824\n+nc_013702:13773-14294\x021081\n+nc_013704:13771-14292\x021801\n+nc_013705:13773-14294\x021113\n+nc_013706:9636-10146\x021124\n+nc_013708:11553-12059\x021356\n+nc_013709:13944-14465\x02292\n+nc_013711:13773-14294\x02513\n+nc_013712:13773-14294\x02151\n+nc_013713:8512-9018\x0273\n+nc_013723:13827-14348\x02190\n+nc_013724:13828-14349\x02424\n+nc_013725:13828-14349\x021410\n+nc_013750:13818-14339\x0238\n+nc_013751:13540-14067\x02845\n+nc_013752:10709-11155\x02702\n+nc_013753:13547-14074\x021722\n+nc_013754:13794-14312\x021056\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.psi |
| b |
| Binary file test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.psi has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.psq |
| b |
| Binary file test-data/mitos1-refdata/refseq39/featureProt/nad6.fas.psq has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos2_NC_012920.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos2_NC_012920.bed Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +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 - |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos2_NC_012920.faa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos2_NC_012920.faa Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>NC_012920; 14149-14670; -; nad6 +MYALFLLSVGLVMGFVGFSSKPSPIYGGLVLIVSGVVGCVIILNFGGGYMGLMVFLIYLG +GMMVVFGYTTAMAIEEYPEAWGSGVEVLVSVLVGLAMEVGLVLWVKEYDGVVVVVNFNSV +GSWMIYEGEGSGLIREDPIGAGALYDYGRWLVVVTGWTLFVGVYIVIEIARGN* |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos2_NC_012920.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos2_NC_012920.fas Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,75 @@ +>NC_012920; 577-647; +; trnF(gaa) +GTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCA +CCCCATAAACA +>NC_012920; 648-1601; +; rrnS +AATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCC +CGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGC +AGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAA +CCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCG +TGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTT +TTAGATCACCCCCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTG +ACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCA +AACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAA +CTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCAT +ATCCCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTG +CTCAGCCTATATACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAG +TACCCACGTAAAGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACA +TTTTCTACCCCAGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTA +GCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCC +CGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATAT +AGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAAC +>NC_012920; 3230-3304; +; trnL2(taa) +GTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAA +TTCCTCTTCTTAACA +>NC_012920; 4263-4331; +; trnI(gat) +AGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGTAAATAATAGGAGCTTAAACCCCC +TTATTTCTA +>NC_012920; 4402-4469; +; trnM(cat) +AGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTGGTTATACCCTTC +CCGTACTA +>NC_012920; 5587-5655; -; trnA(tgc) +AAGGGCTTAGCTTAATTAAAGTGGCTGATTTGCGTTCAGTTGATGCAGAGTGGGGTTTTG +CAGTCCTTA +>NC_012920; 5657-5729; -; trnN(gtt) +TAGATTGAAGCCAGTTGATTAGGGTGCTTAGCTGTTAACTAAGTGTTTGTGGGTTTAAGT +CCCATTGGTCTAG +>NC_012920; 5826-5891; -; trnY(gta) +GGTAAAATGGCTGAGTGAAGCATTGGACTGTAAATCTAAAGACAGGGGTTAGGCCTCTTT +TTACCA +>NC_012920; 7446-7514; -; trnS2(tga) +GAAAAAGTCATGGAGGCCATGGGGTTGGCTTGAAACCAGCTTTGGGGGGTTCGATTCCTT +CCTTTTTTG +>NC_012920; 7518-7585; +; trnD(gtc) +AAGGTATTAGAAAAACCATTTCATAACTTTGTCAAAGTTAAATTATAGGCTAAATCCTAT +ATATCTTA +>NC_012920; 8295-8364; +; trnK(ttt) +CACTGTAAAGCTAACTTAGCATTAACCTTTTAAGTTAAAGATTAAGAGAACCAACACCTC +TTTACAGTGA +>NC_012920; 10405-10469; +; trnR(tcg) +TGGTATATAGTTTAAACAAAACGAATGATTTCGACTCATTAAATTATGATAATCATATTT +ACCAA +>NC_012920; 12138-12206; +; trnH(gtg) +GTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTACGACCCC +TTATTTACC +>NC_012920; 12266-12336; +; trnL1(tag) +ACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCC +AAATAAAAGTA +>NC_012920; 14149-14670; -; nad6 +ATGTATGCTTTGTTTCTGTTGAGTGTGGGTTTAGTAATGGGGTTTGTGGGGTTTTCTTCT +AAGCCTTCTCCTATTTATGGGGGTTTAGTATTGATTGTTAGCGGTGTGGTCGGGTGTGTT +ATTATTCTGAATTTTGGGGGAGGTTATATGGGTTTAATAGTTTTTTTAATTTATTTAGGG +GGAATGATGGTTGTCTTTGGATATACTACAGCGATGGCTATTGAGGAGTATCCTGAGGCA +TGGGGGTCAGGGGTTGAGGTCTTGGTGAGTGTTTTAGTGGGGTTAGCGATGGAGGTAGGA +TTGGTGCTGTGGGTGAAAGAGTATGATGGGGTGGTGGTTGTGGTAAACTTTAATAGTGTA +GGAAGCTGAATAATTTATGAAGGAGAGGGGTCAGGGTTGATTCGGGAGGATCCTATTGGT +GCGGGGGCTTTGTATGATTATGGGCGTTGATTAGTAGTAGTTACTGGTTGAACATTGTTT +GTTGGTGTATATATTGTAATTGAGATTGCTCGGGGGAATAGG +>NC_012920; 14674-14742; -; trnE(ttc) +GTTCTTGTAGTTGAAATACAACGATGGTTTTTCATATCATTGGTCGTGGTTGTAGTCCGT +GCGAGAATA +>NC_012920; 15888-15953; +; trnT(tgt) +GTCCTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCA +AGGACA +>NC_012920; 15956-16023; -; trnP(tgg) +CAGAGAATAGTTTAAATTAGAATCTTAGCTTTGGGTGCTAATGGTGGAGTTAAAGACTTT +TTCTCTGA |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos2_NC_012920.geneorder --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos2_NC_012920.geneorder Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>NC_012920 +trnF rrnS trnL2 trnI trnM -trnA -trnN -trnY -trnS2 trnD trnK trnR trnH trnL1 -nad6 -trnE trnT -trnP |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos2_NC_012920.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos2_NC_012920.gff Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +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 |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos2_NC_012920.mitos --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos2_NC_012920.mitos Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +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 . . (((((((..((((......)))).(((((.......)))))....(((((.....)))))))))))). |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos2_NC_012920.seq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mitos2_NC_012920.seq Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,72 @@ +>Feature NC_012920 +576 646 gene + gene trnF(gaa) +576 646 tRNA + product tRNA-PHE +647 1600 gene +647 1600 rRNA + product s-rRNA +3229 3303 gene + gene trnL2(taa) +3229 3303 tRNA + product tRNA-LEU2 +4262 4330 gene + gene trnI(gat) +4262 4330 tRNA + product tRNA-ILE +4401 4468 gene + gene trnM(cat) +4401 4468 tRNA + product tRNA-MET +5654 5586 gene + gene trnA(tgc) +5654 5586 tRNA + product tRNA-ALA +5728 5656 gene + gene trnN(gtt) +5728 5656 tRNA + product tRNA-ASN +5890 5825 gene + gene trnY(gta) +5890 5825 tRNA + product tRNA-TYR +7513 7445 gene + gene trnS2(tga) +7513 7445 tRNA + product tRNA-SER2 +7517 7584 gene + gene trnD(gtc) +7517 7584 tRNA + product tRNA-ASP +8294 8363 gene + gene trnK(ttt) +8294 8363 tRNA + product tRNA-LYS +10404 10468 gene + gene trnR(tcg) +10404 10468 tRNA + product tRNA-ARG +12137 12205 gene + gene trnH(gtg) +12137 12205 tRNA + product tRNA-HIS +12265 12335 gene + gene trnL1(tag) +12265 12335 tRNA + product tRNA-LEU1 +14669 14148 gene + gene nad6 +14669 14148 CDS + product NADH dehydrogenase subunit 6 +14741 14673 gene + gene trnE(ttc) +14741 14673 tRNA + product tRNA-GLU +15887 15952 gene + gene trnT(tgt) +15887 15952 tRNA + product tRNA-THR +16022 15955 gene + gene trnP(tgg) +16022 15955 tRNA + product tRNA-PRO |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos2_NC_012920_ncrna.pdf |
| b |
| Binary file test-data/mitos2_NC_012920_ncrna.pdf has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/mitos2_NC_012920_prot.pdf |
| b |
| Binary file test-data/mitos2_NC_012920_prot.pdf has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/auxinfo.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq63m/auxinfo.json Fri Mar 27 17:53:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,13029 @@\n+{\n+ "fas2len": {\n+ "OH": {\n+ "NC_001566:OH-1-15516-16342": 827, \n+ "NC_003167:OH-1-15733-15986": 254, \n+ "NC_004025:OH-1-15453-17035": 1583, \n+ "NC_004405:OH-1-15691-16555": 865, \n+ "NC_004406:OH-1-15700-16592": 893, \n+ "NC_005963:OH_0-1-14371-14677": 307, \n+ "NC_005963:OH_1-1-8766-9072": 307, \n+ "NC_006304:OH-1-15357-15972": 616, \n+ "NC_006380:OH-1-0-892": 893, \n+ "NC_006403:OH-1-15416-18179": 2764, \n+ "NC_007689:OH-1-1873-2045": 173, \n+ "NC_007888:OH_0-1-11024-13297": 2274, \n+ "NC_007888:OH_1-1-0-4703": 4704, \n+ "NC_007911:OH-1-15461-16201": 741, \n+ "NC_008093:OH-1-15459-16723": 1265, \n+ "NC_008126:OH-1-16099-16119": 21, \n+ "NC_008410:OH-1-15405-17276": 1872, \n+ "NC_008643:OH-1-15656-16705": 1050, \n+ "NC_008668:OH-1-15653-16777": 1125, \n+ "NC_008683:OH-1-15684-16621": 938, \n+ "NC_008776:OH-1-15360-16845": 1486, \n+ "NC_009422:OH-1-15396-16729": 1334, \n+ "NC_009583:OH-1-15672-16978": 1307, \n+ "NC_009770:OH-1-14965-15914": 950, \n+ "NC_010245:OH-1-7499-8493": 995, \n+ "NC_011137:OH-a--1-16018-571": 1119, \n+ "NC_011171:OH-1-15704-16975": 1272, \n+ "NC_011198:OH-1-15506-16630": 1125, \n+ "NC_011321:OH-1-15658-16517": 860, \n+ "NC_011719:OH-1-15681-16795": 1115, \n+ "NC_011955:OH-1-15809-16581": 773, \n+ "NC_012309:OH-1-5584-5855": 272, \n+ "NC_012762:OH-1-15487-16826": 1340, \n+ "NC_013032:OH-1-14037-14112": 76, \n+ "NC_013068:OH-1-10096-11188": 1093, \n+ "NC_013072:OH-1-15695-16629": 935, \n+ "NC_013274:OH-1-15155-15489": 335, \n+ "NC_013759:OH-1-15682-16608": 927, \n+ "NC_013841:OH-1-15507-17242": 1736, \n+ "NC_013885:OH-1-16222-17204": 983, \n+ "NC_013976:OH-1-7824-8224": 401, \n+ "NC_014101:OH-1-15662-16526": 865, \n+ "NC_014401:OH-1-15520-16921": 1402, \n+ "NC_014882:OH-1-15658-16568": 911, \n+ "NC_015244:OH-1-15723-16647": 925, \n+ "NC_015654:OH-1-13153-14456": 1304, \n+ "NC_015801:OH-1-15653-16868": 1216, \n+ "NC_015825:OH-1-15505-17498": 1994, \n+ "NC_016015:OH-1-13521-14258": 738, \n+ "NC_016196:OH-1-14807-15182": 376, \n+ "NC_016702:OH-1-15646-16728": 1083, \n+ "NC_017752:OH-1-13451-14367": 917, \n+ "NC_017758:OH_0-1-14274-14559": 286, \n+ "NC_017758:OH_1-1-8700-9007": 308, \n+ "NC_018342:OH-1-0-1008": 1009, \n+ "NC_018361:OH-1-13177-13563": 387, \n+ "NC_018802:OH-1-15562-16767": 1206, \n+ "NC_018814:OH-1-15696-16587": 892, \n+ "NC_018823:OH-1-15671-16521": 851, \n+ "NC_019606:OH-1-13668-14431": 764, \n+ "NC_020154:OH-1-15593-16586": 994, \n+ "NC_020329:OH-1-14910-15656": 747, \n+ "NC_020335:OH_0-1-14473-14790": 318, \n+ "NC_020335:OH_1--1-8885-9204": 320, \n+ "NC_020623:OH-1-15427-16539": 1113, \n+ "NC_020639:OH-1-15436-16511": 1076, \n+ "NC_020683:OH-1-15446-16405": 960, \n+ "NC_020730:OH-1-15432-16133": 702, \n+ "NC_020750:OH-1-15430-16230": 801, \n+ "NC_021133:OH-1-15700-16523": 824, \n+ "NC_021428:OH--1-14822-15872": 1051, \n+ "NC_021445:OH-1-15581-16795": 1215, \n+ "NC_021934:OH-1-13712-14077": 366, \n+ "NC_022102:OH-1-15664-16674": 1011, \n+ "NC_022186:OH-1-15648-16476": 829, \n+ "NC_022690:OH-1-15873-16773": 901, \n+ "NC_022721:OH-1-15662-16676": 1015, \n+ "NC_022941:OH-1-15585-16439": 855, \n+ "NC_022944:OH-1-15587-16450": 864, \n+ "NC_023210:OH-1-15435-16551": 1117\n+ }, \n+ "OL": {\n+ "NC_001325:OL-1-6106-6141": 36, \n+ "NC_004025:OL-1-5165-5203": 39, \n+ "NC_006380:OL-1-6051-6081": 31, \n+ "NC_006403:OL--1-5371-5398": 28, \n+ "NC_007888:OL-1-14685-14713": 29, \n+ '..b' }, \n+ "cox2": {\n+ "TAA": 0.5483870967741935, \n+ "TAG": 0.03225806451612903, \n+ "TAN": 0.06451612903225806, \n+ "TNN": 0.3548387096774194\n+ }, \n+ "cox3": {\n+ "TAA": 0.45161290322580644, \n+ "TAG": 0.03225806451612903, \n+ "TAN": 0.0967741935483871, \n+ "TNN": 0.41935483870967744\n+ }, \n+ "nad1": {\n+ "TAA": 0.5161290322580645, \n+ "TAG": 0.2903225806451613, \n+ "TAN": 0.03225806451612903, \n+ "TNN": 0.16129032258064516\n+ }, \n+ "nad2": {\n+ "TAA": 0.6129032258064516, \n+ "TAG": 0.0967741935483871, \n+ "TAN": 0.03225806451612903, \n+ "TNN": 0.25806451612903225\n+ }, \n+ "nad3": {\n+ "TAA": 0.3870967741935484, \n+ "TAG": 0.3548387096774194, \n+ "TAN": 0.03225806451612903, \n+ "TNN": 0.22580645161290322\n+ }, \n+ "nad4": {\n+ "TAA": 0.2903225806451613, \n+ "TAG": 0.16129032258064516, \n+ "TAN": 0.16129032258064516, \n+ "TNN": 0.3870967741935484\n+ }, \n+ "nad4l": {\n+ "TAA": 0.7419354838709677, \n+ "TAG": 0.12903225806451613, \n+ "TNN": 0.12903225806451613\n+ }, \n+ "nad5": {\n+ "TAA": 0.25806451612903225, \n+ "TAG": 0.16129032258064516, \n+ "TAN": 0.06451612903225806, \n+ "TNN": 0.5161290322580645\n+ }, \n+ "nad6": {\n+ "TAA": 0.7096774193548387, \n+ "TAG": 0.12903225806451613, \n+ "TNN": 0.16129032258064516\n+ }\n+ }, \n+ "9": {\n+ "atp6": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "atp8": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "cob": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "cox1": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "cox2": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "cox3": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "nad1": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "nad2": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "nad3": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "nad4": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "nad4l": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "nad5": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "nad6": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }\n+ }, \n+ "9*": {\n+ "atp6": {\n+ "TAA": 0.25, \n+ "TAG": 0.75\n+ }, \n+ "atp8": {\n+ "TAA": 1.0\n+ }, \n+ "cob": {\n+ "TAA": 0.5, \n+ "TAG": 0.25, \n+ "TNN": 0.25\n+ }, \n+ "cox1": {\n+ "TAA": 0.5, \n+ "TAG": 0.25, \n+ "TNN": 0.25\n+ }, \n+ "cox2": {\n+ "TAA": 0.25, \n+ "TAG": 0.75\n+ }, \n+ "cox3": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "nad1": {\n+ "TAA": 0.5, \n+ "TAG": 0.25, \n+ "TNN": 0.25\n+ }, \n+ "nad2": {\n+ "TAA": 0.75, \n+ "TAG": 0.25\n+ }, \n+ "nad3": {\n+ "TAA": 1.0\n+ }, \n+ "nad4": {\n+ "TAA": 0.5, \n+ "TAG": 0.5\n+ }, \n+ "nad4l": {\n+ "TAA": 0.75, \n+ "TAG": 0.25\n+ }, \n+ "nad5": {\n+ "TAA": 1.0\n+ }, \n+ "nad6": {\n+ "TAA": 0.75, \n+ "TAG": 0.25\n+ }\n+ }\n+ }\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureNuc/OH.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq63m/featureNuc/OH.fas Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,18 @@ +>NC_011198:OH-1-15506-16630 Chelydra serpentina +ACGTAGGGATAAAACGTCTTGGCGCCTGTCGCCATATTTTGTTCTTTTTTCTTCTCCCGCGCCCGGTAGAGAAGTACCTGTTATACCCCCCTATGTATATCGTGCATCCGTTTATTTACCCCTAGCATATATCTAGTAATATTACCGCTTAATTTGACTAATGACATAATTCTATTGGTTATACATACCATGATATACTTATATGACTATTATTCAGGTAATATTTATATAATGATCTATGGACATAGCATTAAATAATTATTCTACACCATGACTGTGGCCACAGTATTGGGTTATTTCTTAATCTACCTAATCACGAGAGATAAGCAATCCTTGTCTGTAAGATACAACATCACTAGTTTCAAGTCCATTGTGTTATGGCGTCCATTCATCTCTTTTTAAAAGGCCTCTGGTTGTTTTTTCAGGCACATTACATTATTAAAGGTCATTCATCTCTTTTTAAAAGGCCTCTGGTTAAATGAGTTCTATACATTATATTTATAATCTGGCATAAGGTGGTTTTACTTGCATATAGTAGTTCTCTTTTTCTCTTTCTGTTCTCAGGCCCGCATAATTGATACCTGCCGACTCAATGAAACTGGACTTACGTTCAAATTGATTGGTCTTGCATAATTGACATGGTATTATTTAATTAATGCTTGTTGGACATATATTTTTATAAAAATCCGCGACAGTAAATATAAACCTAAACAACTAAATAAACAACTAAATATAATATTATTTTAAGGTAAACCCCCCTACCCCCCGTTAAACTAACTATTAGCCCGAATGGTCACTTGCTTCTCGTCAAACCCCTAAATCCGAGAATGACCAAACTGACATAAACGCTAGTCGTACAAATACTAAAAAAAATTAAAGCATTCATACTAATACTAAAAAGTACTAAACAATTCTAAAAACATACACCAAATTAGCCCTGACCCTCCCATCGTACGACATCGTACTTACTTCTATATACCTTATTATCTTCTACTATATTGTATTGTATTGTATTATATTATATTATTATATATATATATATATATATATATATATATATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATTATATAAT +>NC_004025:OH-1-15453-17035 Lemur catta +ACACACGAATATAAAATACTATTTTTATGTATATCGTGCATTATGTGCCCTTCCACATTAACATGTATTAGTACCATATATGTTTAATACTACATAGGACATATATGTATAATCGTACATACAATTCCAGTCCTCATGCATATAAGCAAGTACATAAACCTATACCCGTACATAAAACATACAAATATTCCAGTTCATAAAACTTCAATCCACCAGCATATAAGCCAGTACATAAACTTCATATCGTACATAGCACATTCCTCAATTGATCGGACAATTGCACATATCATTTCATAAGTCCTTGTCAACACGGATATCCCCTTCCACCAGATCGTAGCTTAATCTACCATCCTCCGTGAAACCAGCAACCCGCCCGTAGAATGCTCCTCTTCTTGCTCTGAGCCCATTAAACTTGGGGGTGTCTATAATGAAACTATATCTGACATCTGGTTCTTACCTCAGGGCCATAACAACATAACCGCTCACCTCGTTCCTCTTAAATGAGACATCTCGATGGATTAGTAGACTAATCAGCCCATGACATGTCACTAACTAGTGCTGTCAGGCAGATGGTATTTTTTAATTTTCGGGTATGCAGGGACTCAACATGGCCTGCGCCGACACGGCTCGGCCCGCGCCCGGCACATCAATTGTAGCTGAACATAGCATGTACATTCTTTACCCTCATAATTATCATAGATGGCTGTTTAATTCATGCTTAGAGGACATGGAAATAATTACTACAGGTGACTATTTAATTCATGCTCGAAAGACATAAGAAAACTTTTGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCACATGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCATACGCACACGCTAAATTAAATACCCAATTATCTTACGCAAACCCCCCTACCCCCCATTCTAGATTTATTCAGATTTTGGTATACTCTTGCCAAACCCCAAAAACAAAAGCTCCGCACTGATTTTAACTAAAAACTAGAACCTTATTTGTAGCCTTACGCAAATTTTAACTGTCACGTCCCTATTAATTTATTAGCCCCATAAAATTTCTGAACCCAATAATTACTAGTAAATTATCTCAAAAATCCCGTCCACTTAAGGAGGTACCCCTTATATAATTATTTACTAACCTAAGCAAATATATCTGCAACTAAAATTTCCACTATTACTCCTAAACCCACTATTACCAGTAATACTATCTTTCAATTCTAAGCCATATAAACTCTACTTACAAGATCTTAAAAATCAAAACCATAACACTAAAACAGCACTCAAATATTCTCCATAATAATCACAAATCCCAA +>NC_018361:OH-1-13177-13563 Sphaerotheriidae sp. HYS-2012 +CTAATGTATGATGTTTTCTTCTTTTTTTTTTTTATGAAGAAGAAAACATCATACATCCCGTAGGGTTAATACTGAGATATATGTATTTAATGGTCCATTGAAGAGAGGAAGAGCTATTGAACCAACATCACGGTAAGATTGACCCGAAGGTGCTTGATCTCATCATTGTAGGTCTTCACTAAGTAACTATCTGACGATTTATTGCCATAACGATTGATTATATTGCTCCGTCCCTTGCTCTCCCTTACGGGAATCTAGAACAGAGTATATATCTTAACCTATACACACTGAAGCTTTTTATAGAAGCTAAATTATAAGATAATTTATTTATTAATGTAAGCATTTATATTAATGAATCTCTCGTAAAATTGACATTTTTAGCCGAAA +>NC_004406:OH-1-15700-16592 Caranx melampygus +CTCAAAACATATACAATACTTCAGCAATTACATAAATGCATTTTACACCACTTACCCATACAAATGCATAATTAGATTACAATGTTGCAATAACATATATGTATTATCACCATATATAATTATAGTTACAAATACCTGACTTGCCATCTCCTAAGCATAGTTAGACATAAGACATTAATTTTATGTATGGTTAAACATGCCTTCTGAACATTTCATTGTGCAATATTTGATTGAGCAACATAAAAGTTTTACTCAGATTAGTTGGACATATATCTCAAATATCACCACTATTGTTGTCACTAGGGCAAGTTTGGCTGTGAGAACCTACCATAAATATTAACTCTGTCGTGATACCGTTTATTGATGGTCAAGGACAAAAATTGTGAGGGTTTCACTGAGTGAACTATTCCTGGCATTTGGCTCCTACTTCAAGGACTAACCGTTCTAAGCTTCCCCACAATTTTATTGACGCTTGCATAAGTTATTGGTGTAAATCCATACTTCTTAATCACCCACCATGCAAGCATCCTCTCCAGCGGGTCAGGGGTTATTCTTTTTGTCTTCCTTTCACCTGACATTTCAGAGTGCAATCGAACAACGAAATAATCAAGGTAGAACATTTAATCTTTTTATTCAAAATGGAATAGTATTTTCATGGCAGCAAGATATATTATTCCAATAACCACATATTATTTTATCAAGAGCATAAGTTATATCTTTATTTCTCTGACTATTAAAGATTTACCCCCGGCTTTTTTGCGCGTAAACCCCCCTACCCCCCAAAACTCCTAAAATCGCTATTTCTCCTGAAAACCCCCCGGAAACAGGAAAGCCTCTAGAAAGCTTTTTCCACCCTAATATACATATTTAAACACTATTATAATATTTCACAT +>NC_020730:OH-1-15432-16133 Okapia johnstoni +AGGCGCTATTAATATAGCTCCACAAAAGTCAAGAGCCTCACCAGTATTAATTTTCCTAAAAACCCACAACAACCAACACAAACTCCGCACCCCACAGCCTTAACGCAGCAAACTAAACTTACACATAGCAATATGTAAATTATTATCCCATGCAGGCACGTACATAAAATTAATGTAATAAGACATATTAATGTATAATAGTACATTATATTATATGCCCCATGCATATAAGCATGTCCATCAGGTCATTAATAGTACATAGTACATGCAGTTATTAATTGGACATAGCACATTGAGTCAAATCCACCCTCGTCAACATGCGTATCCCGTCCACTAGATCACGAGCTTGTTCACCATGCCGCGTGAAACCAGCAACCCGCTTGGCAAGGATCCCTCTTCTCGCTCCGGGCCCATTTTGCCGTGGGGGTAGCTATTTAATGAATTTTATCAGACATCTGGTTCTTTCTTCAGGGCCATCTCATCTAAAATCGCCCACTCTTTCCTCTTAAATAAGACATCTCGATGGACTAATGGCTAATCAGCCCATGCTCACACATAACTGTGGTGTCATGCATTTGGTATTTTTTTATTTTCGGGGATGCTTGGACTCAGCTATGGCCGTCAAAGGCCCCGACCCGGAGCATGAATTGTAGCTGGACTTAACTGCATCTTGAGCATCACCATAATGGTAAGCATGAGCAT +>NC_007911:OH-1-15461-16201 Siphonops annulatus +ATAACATTCCCCCTTTAATTTATCCAGGCACCCCCATTCATCATGATATAAAAAAAATATAAAAAAAATATTTTTTTTTTATCAAAAATCACCATTTTTATAAAATTTTTTTCCAAAAAAAAAGTCAGTCATGTCCCTACTATTTTTTATACTATGTATAAATGTGCATTCATCTATCTGCACTACGAATATTGCGTCGGTACGGTTAGAAGAATAGTGATACATGGGTGCGAGAAACCATCAACCCGCCCATTTTAGATTATTAGTGCGAAATTTAAGGACACTACTACTCGTAAAATTTCATTTCATTGCATACCAACAGATGGTAAATGCTTGAATTATTTTATATCCATATAGAAACATAATTCTCCTTCAGGCCCCTACATTATTTTTTTTTTCTTCACCTTTCACCCACATCTCAGAGTGCTTGTCAACTAACACGCTCAGAGTAGGACATGTCAAGTGAATCATTCTTAATCCCTCCGGCAATTATTAATGTTGTTAATAATGAATGATTTATGGACATAGTATTGTAAACGATACTGGTTCATCACACATCCTACCCTATTATTCCCCCCCCCCTGCAAAATAAAAAATTTTTTTGCAGCTAAACCCCCCCTACCCCCCCATCATGCTGTCTACGTCTTGTCAAACCCCAAAATACAAGTTTCAACAACATAACACTACGAGAGGTATTTCATAACCAACCAACCCAACAAATTTTCTTTTGTATATATATAT +>NC_021934:OH-1-13712-14077 Brachycybe lecontii +ACTCTATTATTTTTCTTCTATTAAATTATTAATACAGACTTGTATGTCATTTTTAGAAATTTGATCTTGGGGAAGTCTTATTCTCTTTTAAGTGTGTAATCATCGTATTAGATCGTTAACTTCCTGAGATGCCAACCCCGATTACTTCGTTCTCTAAAGGTTCGCTTAACATAAAATAAGATATACTTCGTGTTTTAAAATAAAGGCAACCTGAGATCAATGTCCTATATTGTATAGATAATATAGTATTAATGAATTTAACCCCCAAGAAGTTCTGGAAAAGTAAGATATATTATTATTAATATGAAGAAACATATTATTATACATTATGAATAAATAAATTAAAATAAACATAAAATTAAAACT +>NC_011955:OH-1-15809-16581 Pseudalutarius nasicornis +TCCCTTACATTTTTGGTATGGTGTAAATACATAATATGTATAAACATCCATCTTGTATTTAAACCAAGTTTCATGGAATATTAATGAAGAGTTGTTAAAACCATTAAACTTATATATCCAAAGTTTTTTAATGTCAACCAGGAAATTGAATCTTCAGCATACTTGCTAGTCAAATTATACACCAAGTACTTGACACATCTGAGGTATGGACTATTGAGCCCAATAAGAACCGACCAACCTATGTATATAAGGCTAACTCTTAATGATGGTGAGGGACAATTATTGTGGGGGTCGCTCAACTGAATTATTCCTGGCATTTGGTTCCTATTTCAGGAACAAATAGACTCCAGACTCCCCCAGTAGTCCTTGCGCTGGCATAAGTTAATGGTGGAGTACTATGATGGGACACTCCCCATGCCTAGCATTCTTTCCATAGGGCTACTGGTTTTCTTTTTTGTCCTCCTTTCAAGCTCATTTCAGAGTGCACACGGTATTAGTTGACAAGGGTGTACATTTTTCTTGAACAAGGTAAAACTTGTGAAGTTTTACGTTAAGCATTCCATAAGAATCACATTAATAATTTCAAGGGCATAAAGAAAAAATAAAACCACGAATATTATTATATTCTTAAACCTTGCTTTTAAGTGATATTGGTAGACCCCCCCTACCCCCCCAAAATCTGATGCGCTGCGTTCTTTAAAGACTCTATATCAAAAACATCAGACAACTGAGTGGAAGCTAAAAGCAAGTTGCATTATTATAGTAGTACTGAT +>NC_016196:OH-1-14807-15182 Kallima inachus +ATATATGAAAAAATATTACATAGAATTTTTTTTTTTTTTTTTTATATATTATATATTTAATATAAATTAATAAATTTTTATTATTTTTCCTTATTTTTTTTTATAATATTAATATTAAAAATTAATATCAATATAATCCGAATACAGATCATTTAAATAAAAATATATTATTAAATATAATAATTATATAAATTAAAAATTAAATAATTATTTTAATAATATATTAATAAATTTATATATATATATATATTATATAATTAATTAAATATATTTATATACTTAAAATAATTTTTTCATAACCATTCTTAATAATTTTTTTAATAAATAAAAAAAATTAAAAATAAGCTAAAGCAAGCTTTTGGCCAATTACCCAAAA |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureNuc/OH.fas.nhr |
| b |
| Binary file test-data/refseq63m/featureNuc/OH.fas.nhr has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureNuc/OH.fas.nin |
| b |
| Binary file test-data/refseq63m/featureNuc/OH.fas.nin has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureNuc/OH.fas.nsq |
| b |
| Binary file test-data/refseq63m/featureNuc/OH.fas.nsq has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureProt/nad6.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq63m/featureProt/nad6.fas Fri Mar 27 17:53:42 2020 -0400 |
| b |
| b'@@ -0,0 +1,200 @@\n+>NC_011198:nad6--1-13625-14149 Chelydra serpentina\n+MMYFMFLFGFFFVFWMVGVSCQPSPYYGVLSLVLGAASGCAVLVIMGGSFVSLVLFLIYLGGMLVLFAYSTALVAESGHIGWNYWESAFYVVIYVLCIVFAGVYYYWAWSVEGFGCATVDGDGPFTIRFDFSGVSWFYCFGSMMFVIVGWGLLLTLFVVLALVHGLSRGVVRAI\n+>NC_010221:nad6-1-5885-6374 Antrokoreana gracilipes\n+MNLPWKVEGNISFLIVPLILALCFPQMLHPIAMAISLIAVTLFLAFAISILLTTSWLAYILFLIMLGGLLVLFVYITSLAPNGKMFSISKFSTLGILTLGLVYLESWMSDSFLISEDSLLNIKKMFLPVAISTTLMLALFLLFTLLMAVMITKFNQGPMRILT\n+>NC_004025:nad6--1-13583-14098 Lemur catta\n+MYVMFLLSILLVLGFVSISSKPSPIYGGVGLIVSGAVGCGIIMGFGGSFMGLMVFLIYLGGMLVVFGYTTAMATEEYPETWGSNVVIWGVVLLGVGMELFMVAWMVEYGGFGVGDVFGGVENWMIFESKEGGVIREDSLGVASLYNKASWFAAIAGWSLFISVLIVIEIIR\n+>NC_018361:nad6-1-8296-8769 Sphaerotheriidae sp. HYS-2012\n+LTKTMLIPMIYTSLMIFTINHPLFFGLMILVFILLMIIESSTLLSSFWFSYILVLVYLGGLLILFLYIASLAPNEKFPKTQKSIIILLPLLLLLVMYMSFNSSSQIPLLNNIKSSLMKLYSLSSFSMTILMATYLLITLLIIVYLTNLNMGPLRTLN\n+>NC_004406:nad6--1-13822-14343 Caranx melampygus\n+MTFIMYLFLFCFVFGLIAVASNPSPYFAALGLVVVAGMGCGVLVGHGGPFLSLVLFLIYLGGMLVVFAYSAALAAEPYPETWGSRPVTMYMIAYVLIVVVVSGLFWGGWYESSWGSADELAEFSVFRGDMAGVALMYSLGGWMLIISAWVLLLTLFVVLELTRGLSRGALRAV\n+>NC_020730:nad6--1-13553-14080 Okapia johnstoni\n+MMTYLVFILSVVFVIGFVGFSSKPSPIYGGLGLIVSGGVGCGIVLNFGGSFLGLMVFLIYLGGMMVVFGYTTAMATEQYPEIWASNKTVLGAFVVGLLMEFLMVFYVLKDEEVEVVFKFNGMGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVVVTGWSLLIGVVVIMEITRGN\n+>NC_007911:nad6--1-13584-14087 Siphonops annulatus\n+MTYVIFLGLIGLVLGMVGVASNPSPYFAAFGLVLSSACGCLILVSFGMSFLSLVLFLIYLGGMLVVFAYSAAMAAEPYPEAWGSLSVVFYVLIYCVVLIVGWNLMGEVDVMFKAQECLMMGVDWGGVSLLYWFGGGLLLSLGWVLLLTLFVVFEVTRVIGFGAVCAV\n+>NC_021934:nad6-1-6022-6501 Brachycybe lecontii\n+MLIYYFLLNMIFFLSILFLMNTHPMLLGLITILVSFFMTMSIGLMMSSFWISYILFLIYLGAIMVLFIYMISLSPNEIFTKLNLSIIMMMFMMSIIIYLISSNLFSLNLSYAITMKFTKLFSMSMFLITLMMMIFLLFSLFAIMKITKFYQGPMRPSFS\n+>NC_011955:nad6--1-13932-14453 Pseudalutarius nasicornis\n+MTYVMVLLLGGVILGLLAVASHPSPYFGALGLVVVGGFGCGALLEHGGSFLSLVLFLIYLGGMLVVFAYTAALAAEPYPESWGSESVLLSVLWYVFVVAVACVFWGGGWYEFCWSAVGESGGFLMVGGDMSGAALMFSFGGGMLVIGAWVLLLTLLGVLELTRGLSRGALRVV\n+>NC_016196:nad6-1-9858-10385 Kallima inachus\n+MMKMFLSSSLILTSIFMFFLNHPFSMGLMILIQTLFMCMLSSMLINTYWFSYILFLIFLGGLLVLFIYVSSVASNELFKISPFNKSFIFYMFLLMIFSFFFKNNLFWMNFSFNDEMNNFFNLFLFFNNEFNFNLSKLYNEQTYLLTLMMIIYLFIALVVVVKITNIFFGPLRSNF\n+>NC_013841:nad6--1-13605-14132 Palea steindachneri\n+MMVFFMFLFEVCFVLWVISVASGPSSYYGVVGLVFGAVSGCLMLAGIGGSFISLVLFLIYLGGMLVVFAYSVALTGDPYPSAWRDYGSLFCMAGYVLLVVGAVMFCFDVWSFEGYGDVVVDANGLFSVRVDYIGVSWFYYYGCVVFLVIGWGLLLTLFVVLDLVRGLAWGTVRSI\n+>NC_016702:nad6--1-13769-14290 Clupeichthys aesarnensis\n+MLFFGCVYLVGFVLGMVGVASSPSPYYGALGLVLCSGSACAFLAITGSGFLALALFLIYLGGMVVVFGYTASLAADPHPDPWGDASVFEHFMFFFIAVVVGLMYALPPLVEFGAGVLSSWKEFFMVRAEAGGVAMLYSSAGPVLLICAWALLLTLFVVLELTRGLDRGALRAV\n+>NC_003167:nad6--1-13859-14380 Zu cristatus\n+MTYIMVMLLLGLVLGMVGVASNPSPYFAALGLVVVAGLGCGVLMHYGGSFLSLVLFLIYLGGMLVVFAYSAALAAEPYPEAWGGWAVLGYVLLYLGGVLVAGLYCWGGWFESTWVPEVELKGFTVTRGDTSGVALMYSSGGGVLVLAAWVLLLTLGVVLELTRGLSRGALRAV\n+>NC_009462:nad6-1-13284-13739 Echinococcus vogeli\n+MLLEIFVVMYFCVLMVFCYTSHCVYHCVLLVINALLASCICYVVYGFSWYSLLFCLVYVGGVYVLFIFVSVFSPNSNFVLYSGSLEIGALVCGGFWLLVCGFIFYSLVGGEFSGVLCSVSEGWLYLCLCMTLVFGFLVLSVVVSSKVNFYR\n+>NC_013759:nad6--1-13805-14326 Pseudogobio esocinus\n+MTYFMFMLLVALIVGLIAVASNPTPYFAALGLVVAAGVGCGVLVGCGGSFLSLVLFLIYLGGMLVVFAYSAALAAEPFPEAWGSRSVAGYVLVYLLGVIVMAGMFWGGWYEGSWVIIDGLKEFSMLRGDVGGVAVMYSFGGGMLVICAWVLLLTLLVVLELTRGLSRGTLRAV\n+>NC_008643:nad6--1-13778-14299 Cyprinella lutrensis\n+MTYFVSLLLMALIMGLIAVASNPTPYFAALGLMVAAGVGCGVLIGSGGPFLSLVLFLIYLGGMLVVFAYSAALAAEPFPEAWGSRSVMGYVLVYLLGVVFAGGLFWGGWQEGSWVAVDELKDFSILRGDVGGVAMMYSFGGAMLVICAWVLLLTLLVVLELTRGLSRGTLRAV\n+>NC_011137:nad6--1-14143-14667 Homo sapiens neanderthalensis\n+MMYALFLLSVGLVMGFVGFSSKPSPIYGGLVLIVSGVVGCVIILNFGGGYMGLMVFLIYLGGMMVVFGYTTAMAIEEYPEAWGSGVEVLVSVLVGLAMEVGLVLWVKEYDGVVVVVNFNSVGSWMIYEGEGSGLIREDPIGAGALYDYGRWLVVVTGWTLFVGVYVVIEIARGN\n+>NC_010245:nad6-1-6258-6821 Seriatopora caliendrum\n+MEFFSFFFILGIIGSGVMVVSALNPVLSIFWLVLVFINSAVFFLLLGIDFLALMFLLIYVGAIAILFLFVIMLLNLTDYPPVLKREVDMTNYIPIGFIIGIFFFSEIASSGLFLGSFQIENWDLSFPWFL'..b'NSMEMFMFTPENSLFTENEISLIKLYNNPTMNITVLMINYLLLTLIVVVKITNINYGSLRQTFN\n+>NC_020623:nad6--1-13548-14075 Capra ibex\n+MMMYIVFILSVIFVMGFVGFSSKPSPIYGGLGLIVSGGAGCGIVLNFGGSFLGLMVFLIYLGGMMVVFGYTTAMATEQYPEVWVSSKVVLGAFITGLLMEFLMVYYVLKDKEVEVVFKFNGMGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVIVTGWSLLIGVVVIMEITRGN\n+>NC_017758:nad6-1-12624-13058 Amblyomma elaphense\n+MKFLIFFSTSMIFMSHPLLMLLSVMLLTLFLSMIFYYYTTLSILSLMMIILILGGMMIIFMYMVSLIPNQKIHFNKKMTMIISLVIIMISININFQLKININFFMKMYFNTYVNIMIMMMLYLIITLTVIMSNSNSFNCPMSLK\n+>NC_005781:nad6-1-10027-10551 Drosophila simulans\n+MIQLMLYSLIITTSIIFLNMIHPLALGLTLLIQTIFVCMLTGLMTKSFWYSYILFLIFLGGMLVLFIYVTSLASNEMFNLSIKLTVFSSLILLFMMILSLVIDKTSFSLFLMNNDMQSIINMNSYFMENSLSLNKLYNFPTNFITILLMNYLLITLIVVVKITKLFKGPIRMMS\n+>NC_013274:nad6-1-10025-10558 Diatraea saccharalis\n+MTKMFLSMIMMLISIMMLFLKHPLSMGLMILIKTLLLCLLSGMLIKTYWFSYILFLTFLGGLLVLFIYVSSIASNEMFLPSIKIKLLMFNSFIMIMLISYLSMYNMNWMNLNINNYEMNNLFNMFLFFNNENKINLSKLYNNQTFMMIMMMMIYLFITLVVVVKITNIFYGPLRMSQ\n+>NC_012309:nad6-1-5991-6425 Ancylostoma caninum\n+MFSFFLVVSLVGGVMSYMNMDPMKSSFFLILSMLMCMPMLSFSGYVWFSYFICLLFLSGIFVILVYFSSLSKINMVKSYLVVLSLIFSFFVISLNYNMVLSNVSLSVFYYKVFWMIILYILFILLFFMNFTSFFLNFSGALRKV\n+>NC_013032:nad6-1-10736-11242 Metacrangonyx longipes\n+MNIYIYFIFSFLSYMLIIIFFYSWHPLFMGVMIALQSILVAIIIYIFNSTPWFSYLLFMIFLSGMMIILIYVSSLASNLTMKYFFLEFSSMAMFSVLFLFFTNFYIDKNYFYDNSLNFSNLPNLIVFSGSVYSKYMYLFTVLLIFYLLMILILVVKNSLFTKGPLRSN\n+>NC_010209:nad6-1-9284-9841 Ptilocaulis walpersi\n+MEGIFYLFAFNIIISGIMVVSALNPVYSVFWLIIAFINASILFILLDVDFIALIFLIVYVGAIAILFLFVIMMLNLIDYERGKDMSNYLPAGFVIGVIFFITCRIILLSNQFSTFYVNKFDFIENFSNITGFGRVLYTDYYYLFLIASLILLIAMIGAIVLTHEIKKEKKNQDIFIQISRKFWDF\n+>NC_008683:nad6--1-13807-14328 Chanodichthys mongolicus\n+MTYFMFLLLVALVVGLIAVASNPTPYFAALGLVVAAGVGCGILVGYGGSFLSLVLFLIYLGGMLVVFAYSAALAAEPFPEAWGSRSVAGYVLVYLLGVVLAAGLFWGGWYEGSWVVVDGLKEFSMLRGDVSGVAVMYSFGGVMLVICAWVLLLTLLVVLELTRGLSRGTLRAV\n+>NC_012762:nad6--1-13604-14131 Otolemur crassicaudatus\n+MMYMVYLLSVLFVLGFVGFSSKPSPIYGGLGLIISGGVGCGIVMSLGGSFMGLMVFLVYLGGMLVVFGYTTAMATEEYPESWGSSVVIWGALLLGAVLEVILILFVGEYGDGVEVVMNFDGMGDWEMYDVGGIGPFRVQSAGTGALYSYGNWFLVMAGWSLFVSIFIVIEITRGD\n+>NC_014401:nad6--1-13636-14160 Cuora pani\n+MMYFMFLFGFCFVFWMVGVSCNPSPYYGVVSLIFGALSGCGVLVSMGGSFVSLVLFLIYLGGMLVIFAYSSALMAEPFPVGWVSLEGVFYGLYYLFIIMVFMQMGCHLWSIEGIGADTVDAGGLYAVRLDFSGVSWLYCLGSGLLLVAGWGLLLTLFVVLELVRGLSRGVLRAI\n+>NC_023210:nad6--1-13555-14088 Mustela kathiah\n+MMTYIVFILSVIFVVSFVGFSSKPSPIYGGLVLIISGAIGCGIVLSFGGSFLGLMVFLIYLGGMLVVFGYTTAMATEQYPEVWASNKAVLGAFIVGLLSELLTACYILKGDDVEVEVVLKFNGAGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVIVTGWSLFIGVLVIMEVTRGN\n+>NC_012383:nad6-1-2862-3320 Siphonaria pectinata\n+MFLLMVVCSFLLLTFPMYKNPASQGGVLVVISFYLVALMSLTSSVWFSYVLFLVYIGGLLVMFIYVCLVSSNYPFKLSSVQVISGLSMSLIVAEWMPEVAPSYFLGSSTWVSGAGLIQEVNVGLFLSLVVLLLFMLLVVVRSTGVGAVVVGT\n+>NC_016015:nad6-1-8452-8967 Panulirus homarus\n+MIIFFMPIIFFLSILFTRLVHPLAAGIILLIQTSLISLSTGLVSSSFWFSYILFLVFLGGMLVLFIYVASLASNESFKTSFFYAGFISGVSLLPSTIFFFSDTLFSFQPVSMQHSSQFTKNTWNYSSDLTLLIYNFPVMKMTIVVILYLLFTLIVVVEVTSVFLGALRLSK\n+>NC_020335:nad6-1-12833-13261 Haemaphysalis parva\n+MKTIMFMSIILMMMSHPMMMLMSIMLLTLFLSLMFYYSSQLSIISMIMILLILGGMLIIFMYMVSLCPNKKIIMNKSSMIMGLIILMTSSNFILMKFEISNFIKMYSNNSMNLLLLMMMYLIVSLMVVMKISNSNQAPMKMI\n+>NC_006380:nad6--1-14444-14971 Bos grunniens\n+MMLYIVFILSVIFVIGFVGFSSKPSPIYGGLGLIVSGGVGCGIVLNFGGSFLGLMVFLIYLGGMMVVFGYTTAMATEQYPEIWLSNKAVLGAFITGLLMEFFMVYYVLKDKEVEIVFEFNGLGDWVIYDTGDSGFFSEEAMGIAALYSYGTWLVIVTGWSLFIGVVVIMEITRGN\n+>NC_020324:nad6-1-7837-8265 Pholcus phalangioides\n+MMAVIFLCGAMVFINHPMIMVGGLIVFTVWMSFISYMSLLTFWYGNLIMLVILSGVLVVFTYMASLSPNEGFFLDYWGLAVFMVLVGAAGLGLEGSEDMSLVSIKLWVSVDGSMNLFAVVLLFLAMLVVVWVGSYWSGPIHV\n+>NC_015654:nad6--1-12451-12975 Chaenocephalus aceratus\n+MLYCGYLLMLGVVVGMVVVAANPSPFYAALGVVMVAAAGCGFIMCVGGTFLCLVLFLIYLGGMLVVFAYSAALCAEVHPTGLSEGSVLKCMMGYFGVVLGVGLLQGNPEAPLYWWFVGEEAEMNVVQGETEGVSEAYGSGGMCLVICAWVLLVALYVALEVSRGSSRGPVRPIK\n+>NC_009983:nad6-1-12593-13084 Bothriometopus macrocnemis\n+MGEVKLLFMMFVGLMGIFCLNISPMMGMIYLLVSTTIFTTILLIVKGSFVGFLFFLSTISGLFILFSIFMMSMKIKFFSKTLVLKSKIFFMIILSSLTMMSMFSSPPNEWGTYLWLEEQILSKSGLMIWIYVFLIFLLLLSLPIVDQILKDISSSNRSEKEKD\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureProt/nad6.fas.phr |
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| Binary file test-data/refseq63m/featureProt/nad6.fas.phr has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureProt/nad6.fas.pin |
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| Binary file test-data/refseq63m/featureProt/nad6.fas.pin has changed |
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| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureProt/nad6.fas.psq |
| b |
| Binary file test-data/refseq63m/featureProt/nad6.fas.psq has changed |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureProtHMM/nad6.db --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq63m/featureProtHMM/nad6.db Fri Mar 27 17:53:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,517 @@\n+HMMER3/f [3.1b1 | May 2013]\n+NAME nad6\n+LENG 165\n+ALPH amino\n+RF yes\n+MM no\n+CONS yes\n+CS no\n+MAP yes\n+DATE Sun Oct 18 17:14:23 2015\n+NSEQ 3753\n+EFFN 7.090276\n+CKSUM 1917954243\n+STATS LOCAL MSV -10.7336 0.70794\n+STATS LOCAL VITERBI -11.3203 0.70794\n+STATS LOCAL FORWARD -4.8220 0.70794\n+HMM A C D E F G H I K L M N P Q R S T V W Y \n+ m->m m->i m->d i->m i->i d->m d->d\n+ COMPO 2.74207 4.03774 3.79615 3.28699 2.67755 2.74966 4.22543 2.48065 3.23006 1.99245 2.95471 3.32591 3.66626 3.71895 3.62649 2.53604 2.95032 2.31178 4.21507 3.18531\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01110 4.90209 5.62444 0.61958 0.77255 0.00000 *\n+ 1 2.73823 4.29628 4.15875 3.68404 3.06276 3.16073 4.24795 2.74935 3.44841 2.42293 1.97497 3.75809 4.32570 3.35181 3.78500 3.03810 3.01969 2.01014 4.90749 2.10436 1 m x - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.06020 4.90209 2.97604 0.61958 0.77255 0.48576 0.95510\n+ 2 2.82943 4.30747 4.73396 4.22106 2.64387 4.09014 4.41246 2.34017 3.86411 1.56450 2.35960 3.81029 4.47251 4.16980 4.06005 2.98308 2.17096 2.19995 4.87072 3.39102 2 l x - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.03298 5.08056 3.64113 0.61958 0.77255 0.59856 0.79763\n+ 3 2.97549 4.40687 4.76493 3.09127 2.07923 4.16479 4.47130 2.35219 3.25167 1.82631 2.46711 4.04768 2.96217 3.80880 4.08464 3.24994 3.10089 2.34629 4.20620 3.02549 3 l x - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.04359 5.23628 3.28795 0.61958 0.77255 0.44579 1.02253\n+ 4 3.09340 3.34438 4.97740 3.68382 2.01415 4.13604 4.61617 2.38738 3.74728 2.09420 2.50655 3.99040 4.64909 4.36166 4.24600 2.55433 2.36909 2.40232 4.25467 2.56767 4 f x - -\n+ 2.68622 4.42223 2.77544 2.73141 3.46226 2.40532 3.72376 3.29345 2.67767 2.69332 4.24723 2.90357 2.73763 3.18179 2.89834 2.37895 2.77514 2.98430 4.58503 3.61509\n+ 0.37270 1.49131 2.45282 0.88371 0.53315 0.41971 1.07071\n+ 5 2.90868 4.06129 5.10574 4.48987 1.90723 4.28875 4.63881 1.99814 4.27307 1.36342 2.79452 4.09782 4.64628 4.40286 4.27863 3.24012 3.10591 2.29354 4.41338 3.75803 13 l x - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00735 5.41324 5.85383 0.61958 0.77255 0.66605 0.72100\n+ 6 3.08603 4.35146 5.12752 4.50097 1.51296 3.95049 4.66393 2.19157 4.29606 1.38036 2.86120 4.46866 4.69372 4.42647 4.27032 3.24677 3.23883 2.44782 4.70001 3.85464 14 l x - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00713 5.45369 5.86782 0.61958 0.77255 0.71736 0.66951\n+ 7 2.84823 2.98319 5.09486 4.19936 2.95413 3.28274 4.64969 2.53810 4.17413 1.56027 2.41732 4.03610 4.65452 4.37743 4.306'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00580 5.54942 6.27177 0.61958 0.77255 0.48576 0.95510\n+ 158 2.25966 4.56071 3.43298 2.69885 3.33885 2.35308 3.74554 3.67692 2.42983 2.49339 3.94232 3.19539 3.98991 3.05267 2.39179 2.29367 3.06443 3.09861 4.95618 4.00925 480 a . - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00603 5.50947 6.23182 0.61958 0.77255 0.48576 0.95510\n+ 159 2.62473 4.91381 2.69113 2.77149 3.54673 2.48725 4.11716 3.12424 2.49947 2.63028 3.75417 3.05348 2.60279 2.89163 2.52877 2.65941 3.17834 3.00394 4.96463 4.18129 481 g . - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00607 5.50249 6.22483 0.61958 0.77255 0.48576 0.95510\n+ 160 2.49690 5.10861 3.13185 2.41036 3.67252 3.10993 4.01887 3.27238 2.28211 2.38838 3.87460 3.01093 3.50130 3.08205 2.45529 2.28184 3.01777 2.89173 5.15367 4.24694 482 s . - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00635 5.45851 6.18085 0.61958 0.77255 0.48576 0.95510\n+ 161 2.64398 4.40479 3.47941 2.97650 3.66088 3.37631 4.06726 3.31465 2.36428 2.20769 3.67920 2.68409 3.30925 3.04588 2.23194 2.61419 3.25197 2.71597 5.35224 2.99904 483 l . - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00749 5.29410 6.01645 0.61958 0.77255 0.48576 0.95510\n+ 162 2.91409 4.92430 3.53688 2.89034 2.99920 3.65385 3.89045 3.14431 2.19572 2.69379 3.70123 3.16206 3.22997 2.91109 2.21823 2.53744 2.91794 2.36001 4.04958 3.86839 484 k . - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00874 5.14019 5.86253 0.61958 0.77255 0.48576 0.95510\n+ 163 2.69559 4.70020 3.52191 3.00924 3.07553 2.96681 4.03107 2.77738 2.55235 2.69161 3.12967 3.15365 3.65318 2.97236 2.92915 2.16987 2.75831 2.69688 3.73913 3.33742 485 s . - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00935 5.07244 5.79478 0.61958 0.77255 0.48576 0.95510\n+ 164 2.51866 5.02724 3.09262 2.64514 2.98425 3.37358 3.69313 3.23515 2.20191 3.03733 3.65916 2.34803 3.57893 2.78299 2.61778 2.55789 2.91810 3.24544 5.49916 3.49763 486 k . - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01219 4.80944 5.53179 0.61958 0.77255 0.48576 0.95510\n+ 165 2.72202 4.65396 3.34314 2.77225 3.16965 3.08215 3.80014 2.83109 2.45521 2.26584 3.66697 3.04575 3.97157 2.94918 2.92005 2.44775 2.83452 2.50632 5.03383 3.31001 487 l . - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90346 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00822 4.80548 * 0.61958 0.77255 0.00000 *\n+//\n' |
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| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureProtHMM/nad6.db.h3i |
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| Binary file test-data/refseq63m/featureProtHMM/nad6.db.h3i has changed |
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| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureProtHMM/nad6.db.h3m |
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| Binary file test-data/refseq63m/featureProtHMM/nad6.db.h3m has changed |
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| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/featureProtHMM/nad6.db.h3p |
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| Binary file test-data/refseq63m/featureProtHMM/nad6.db.h3p has changed |
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| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/ncRNA/OL.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq63m/ncRNA/OL.cm Fri Mar 27 17:53:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,284 @@\n+INFERNAL1/a [1.1.2 | July 2016]\n+NAME OL\n+STATES 103\n+NODES 26\n+CLEN 33\n+W 72\n+ALPH RNA\n+RF no\n+CONS yes\n+MAP yes\n+DATE Thu May 24 22:04:50 2018\n+COM [1] /work/berntm/progz/infernal-1.1.2/src//cmbuild -F metazoa/cleaned/OL.cm metazoa/cleaned/OL.stk\n+COM [2] /work/berntm/progz/infernal-1.1.2/src//cmcalibrate --cpu 8 metazoa/cleaned/OL.cm\n+PBEGIN 0.05\n+PEND 0.05\n+WBETA 1e-07\n+QDBBETA1 1e-07\n+QDBBETA2 1e-15\n+N2OMEGA 1.52588e-05\n+N3OMEGA 1.52588e-05\n+ELSELF -0.08926734\n+NSEQ 821\n+EFFN 821.000000\n+CKSUM 625725364\n+NULL 0.000 0.000 0.000 0.000 \n+EFP7GF -7.6753 0.73996\n+ECMLC 0.66646 -5.32898 3.74545 1600000 507768 0.002363\n+ECMGC 0.42409 -13.50951 1.11839 1600000 197811 0.002022\n+ECMLI 0.64950 -4.93781 4.20090 1600000 453896 0.002644\n+ECMGI 0.44313 -12.13032 1.75670 1600000 188195 0.002125\n+CM\n+ [ ROOT 0 ] - - - - - -\n+ S 0 -1 0 1 6 1 1 72 118 -15.595 -15.535 -0.396 -2.336 -4.839 -7.136 \n+ IL 1 1 2 1 6 1 5 73 120 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 \n+ IR 2 2 3 2 5 1 6 73 120 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+ [ MATP 1 ] 1 44 U A - -\n+ MP 3 2 3 7 6 2 8 72 118 -3.583 -15.139 -0.133 -13.915 -14.195 -7.885 -12.245 -12.523 -11.563 -1.433 -9.914 -11.708 0.213 -10.829 -11.666 -8.732 -11.787 -10.921 3.816 -12.080 -1.656 -4.074 \n+ ML 4 2 3 7 6 1 7 70 117 -4.633 -14.486 -0.348 -2.527 -14.336 -11.866 -9.074 -5.575 -9.989 1.991 \n+ MR 5 2 3 7 6 1 6 69 115 -12.205 -10.934 -3.866 -10.912 -0.107 -9.125 1.937 -5.921 -2.872 -5.708 \n+ D 6 2 3 7 6 0 3 67 114 -12.605 -11.303 -7.100 -7.782 -7.800 -0.025 \n+ IL 7 7 5 7 6 1 9 71 118 -8.577 -0.191 -3.065 -10.495 -11.272 -10.932 0.000 0.000 0.000 0.000 \n+ IR 8 8 6 8 5 1 9 71 117 -7.534 -0.012 -11.045 -9.212 -10.318 0.000 0.000 0.000 0.000 \n+ [ MATP 2 ] 3 42 C G - -\n+ MP 9 8 6 13 6 2 9 70 116 -15.480 -15.419 -0.000 -14.196 -14.475 -14.870 -12.518 -12.793 -11.840 -1.303 -3.500 -11.987 3.560 -4.553 -11.942 -8.991 -12.064 -11.181 1.854 -12.355 -7.895 -4.460 \n+ ML 10 8 6 13 6 1 5 68 115 -11.630 -11.976 -0.220 -2.846 -11.826 -9.356 -4.488 0.595 -5.435 1.276 \n+ MR 11 8 6 13 6 1 5 67 114 -12.115 -10.844 -6.753 -10.823 -0.018 -9.036 -5.602 -7.321 1.986 -6.353 \n+ D 12 8 6 13 6 0 3 67 114 -13.102 -11.800 -0.082 -8.279 -8.297 -4.372 \n+ IL 13 13 5 13 6 1 4 69 116 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 \n+ IR 14 14 6 14 5 1 4 69 115 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+ [ MATP 3 ] 4 41 U A - -\n+ MP 15 14 6 19 6 2 8 68 114 -15.541 -15.480 -0.003 -9.131 -14.536 -14.931 -12.590 -12.872 -11.908 -9.109 -10.258 -12.052 2.130 -11.173 -12.011 -9.080 -12.131 -11.276 3.504 -12.424 -1.897 -10.813 \n+ ML 16 14 6 19 6 1 4 66 113 -8.904 -9.250 -0.144 -3.659 -9.100 -6.629 -1.201 0.668 -2.036 0.792 \n+ MR 17 14 6 19 6 1 5 66 113 -12.115 -10.844 -6.753 -10.823 -0.018 -9.036 1.989 -6.982 -6.320 -6.494 \n+ D 18 14 6 19 6 0 0 62 109 -9.0'..b'1.46634 0.26236 7.53642 0.00053\n+ 12 1.83612 1.49620 1.70228 0.83398 13 u - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00593 8.73588 5.15890 1.46634 0.26236 4.06055 0.01739\n+ 13 0.98227 2.01203 1.58025 1.25213 14 a - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00448 8.73571 5.44615 1.46634 0.26236 0.75520 0.63472\n+ 14 1.11124 2.32579 1.16199 1.34599 15 a - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 1.71340 0.99378 0.79945 1.32787 0.30794 1.12924 0.39050\n+ 15 0.70590 2.04290 1.07328 3.35816 24 a - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00179 8.36268 6.46928 1.46634 0.26236 1.49874 0.25285\n+ 16 0.85515 1.98512 1.04452 2.45859 25 a - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00039 8.54873 8.54873 1.46634 0.26236 0.47655 0.97001\n+ 17 0.79045 2.18263 1.23384 1.94881 26 a - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00028 8.86339 8.86339 1.46634 0.26236 1.10064 0.40445\n+ 18 0.62336 1.98713 1.35995 2.65784 27 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00095 8.91671 7.11772 1.46634 0.26236 6.65867 0.00128\n+ 19 0.66450 2.49725 1.13821 2.49169 28 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00027 8.91603 8.91603 1.46634 0.26236 0.32701 1.27682\n+ 20 0.39595 3.30860 1.51733 2.64369 29 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00198 8.98909 6.28932 1.46634 0.26236 5.39286 0.00456\n+ 21 0.41263 3.52137 1.29556 3.35852 30 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00025 8.98736 8.98736 1.46634 0.26236 0.00859 4.76092\n+ 22 0.46174 2.79813 1.59827 2.23829 31 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00024 9.01578 9.01578 1.46634 0.26236 1.09861 0.40547\n+ 23 0.26536 3.96146 1.90095 2.73939 32 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00024 9.01578 9.01578 1.46634 0.26236 1.09861 0.40547\n+ 24 0.10496 4.35372 2.83298 3.57756 33 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00024 9.01578 9.01578 1.46634 0.26236 1.09861 0.40547\n+ 25 1.31170 3.49244 0.35695 7.81404 34 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00820 9.01578 4.82284 1.46634 0.26236 1.09861 0.40547\n+ 26 1.67860 4.62692 0.21926 7.67265 35 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00273 9.00783 5.95033 1.46634 0.26236 4.22270 0.01477\n+ 27 7.92571 0.07602 3.51183 3.14664 36 C - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06155 9.00534 2.82061 1.46634 0.26236 1.96893 0.15037\n+ 28 3.46326 3.57794 0.06156 7.71503 37 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00828 8.94554 4.81436 1.46634 0.26236 0.00357 5.63733\n+ 29 4.12151 8.09120 0.05283 3.35436 38 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.03444 3.44062 6.31266 0.00762 4.88064 0.03162 3.46965\n+ 30 1.93438 8.38419 0.18067 3.88520 40 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00473 9.01410 5.38327 1.46634 0.26236 0.12663 2.12914\n+ 31 0.33086 8.31034 1.26898 8.01221 41 A - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04141 9.01131 3.20789 1.46634 0.26236 3.68247 0.02548\n+ 32 1.49713 8.32172 0.29297 3.50844 42 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.27396 2.70446 1.75604 0.00380 5.57559 2.60448 0.07682\n+ 33 0.12383 7.74949 2.40777 3.64879 44 A - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00015 8.78458 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/ncRNA/rrnS.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq63m/ncRNA/rrnS.cm Fri Mar 27 17:53:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,6313 @@\n+INFERNAL1/a [1.1.2 | July 2016]\n+NAME rrnS\n+STATES 2806\n+NODES 754\n+CLEN 899\n+W 1088\n+ALPH RNA\n+RF no\n+CONS yes\n+MAP yes\n+DATE Sat Jun 2 15:41:50 2018\n+COM [1] /work/berntm/progz/infernal-1.1.2/src//cmbuild -F metazoa/cleaned/rrnS.cm metazoa/cleaned/rrnS.stk\n+COM [2] /work/berntm/progz/infernal-1.1.2/src//cmcalibrate --cpu 8 metazoa/cleaned/rrnS.cm\n+PBEGIN 0.05\n+PEND 0.05\n+WBETA 1e-07\n+QDBBETA1 1e-07\n+QDBBETA2 1e-15\n+N2OMEGA 1.52588e-05\n+N3OMEGA 1.52588e-05\n+ELSELF -0.08926734\n+NSEQ 3825\n+EFFN 7.678628\n+CKSUM 1907880127\n+NULL 0.000 0.000 0.000 0.000 \n+EFP7GF -52.6454 0.69740\n+ECMLC 0.65922 -7.89826 0.70865 1600000 349387 0.003435\n+ECMGC 0.14649 -151.52630 -140.88600 1600000 1901 0.210416\n+ECMLI 0.59973 -7.72721 1.58888 1600000 320360 0.003746\n+ECMGI 0.16646 -97.16450 -87.73462 1600000 1922 0.208117\n+CM\n+ [ ROOT 0 ] - - - - - -\n+ S 0 -1 0 1 4 0 1 1088 1333 -8.345 -8.552 -0.214 -2.919 \n+ IL 1 1 2 1 4 597 696 1090 1336 -1.686 -2.369 -1.117 -4.855 0.000 0.000 0.000 0.000 \n+ IR 2 2 3 2 3 597 696 1090 1336 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 1 ] 1 - u - - -\n+ ML 3 2 3 5 3 596 695 1088 1334 -9.110 -0.144 -3.421 0.027 0.206 -0.923 0.379 \n+ D 4 2 3 5 3 594 693 1087 1332 -8.103 -0.757 -1.306 \n+ IL 5 5 3 5 3 596 695 1089 1335 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 2 ] 2 - A - - -\n+ ML 6 5 3 8 3 595 694 1088 1333 -9.119 -0.041 -5.248 1.270 -1.439 -1.175 -0.364 \n+ D 7 5 3 8 3 593 692 1085 1331 -8.054 -1.954 -0.438 \n+ IL 8 8 3 8 3 596 694 1088 1334 -1.442 -0.798 -4.142 0.000 0.000 0.000 0.000 \n+ [ MATL 3 ] 3 - A - - -\n+ ML 9 8 3 11 3 594 693 1087 1332 -9.469 -0.582 -1.597 1.039 -0.986 -1.118 -0.030 \n+ D 10 8 3 11 3 592 691 1085 1330 -6.950 -1.607 -0.592 \n+ IL 11 11 3 11 3 596 694 1088 1333 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 4 ] - 949 - u - -\n+ MR 12 11 3 14 3 595 693 1087 1332 -8.936 -0.012 -7.254 0.142 -0.276 -0.844 0.598 \n+ D 13 11 3 14 3 591 690 1084 1329 -9.506 -1.523 -0.620 \n+ IR 14 14 3 14 3 595 694 1087 1332 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 5 ] - 948 - a - -\n+ MR 15 14 3 17 3 594 693 1086 1331 -9.217 -0.011 -7.400 0.938 -0.742 -1.077 0.019 \n+ D 16 14 3 17 3 590 689 1082 1328 -8.973 -2.100 -0.387 \n+ IR 17 17 3 17 3 594 693 1086 1331 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 6 ] - 947 - A - -\n+ MR 18 17 3 20 3 593 692 1085 1330 -9.314 -0.013 -7.090 1.036 -1.188 -0.580 -0.250 \n+ D 19 17 3 20 '..b'1.46634 0.26236 1.43687 0.27138\n+ 878 2.19575 1.03333 1.80136 1.00014 928 u - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02375 4.50241 4.39135 1.46634 0.26236 1.58455 0.22946\n+ 879 2.26373 3.27027 0.24038 2.63510 929 G - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02242 4.50222 4.50222 1.46634 0.26236 1.59651 0.22640\n+ 880 3.24537 4.17716 0.08110 3.74639 930 G - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02240 4.50322 4.50322 1.46634 0.26236 1.48251 0.25756\n+ 881 0.05941 4.13115 3.82622 3.92096 931 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02492 4.50544 4.30051 1.46634 0.26236 1.44896 0.26764\n+ 882 0.05845 4.20201 3.77474 3.97029 932 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02804 4.50509 4.09834 1.46634 0.26236 1.51340 0.24867\n+ 883 1.17448 1.95608 0.89209 1.96746 933 g - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02568 4.50094 4.25042 1.46634 0.26236 1.67885 0.20652\n+ 884 1.68362 1.92684 0.70576 1.74321 934 g - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02262 4.49806 4.48900 1.46634 0.26236 1.59107 0.22779\n+ 885 3.07741 2.80609 2.96351 0.17216 935 U - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02380 4.49988 4.38945 1.46634 0.26236 1.72136 0.19702\n+ 886 1.83291 2.21996 0.53276 1.93477 936 G - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02450 4.49858 4.33702 1.46634 0.26236 1.68196 0.20581\n+ 887 2.06620 0.90773 1.90946 1.13403 937 c - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02410 4.49732 4.36821 1.46634 0.26236 1.63814 0.21609\n+ 888 1.16701 1.75837 1.24755 1.47329 938 a - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02318 4.49725 4.44191 1.46634 0.26236 1.74475 0.19199\n+ 889 2.53019 0.62848 2.05478 1.35157 939 C - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02789 4.49682 4.11301 1.46634 0.26236 1.68963 0.20406\n+ 890 2.85433 0.86933 2.60600 0.79997 940 u - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02806 4.49252 4.10575 1.46634 0.26236 1.53416 0.24288\n+ 891 3.44374 2.65524 3.48355 0.14263 941 U - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04235 4.49113 3.49785 1.46634 0.26236 1.68843 0.20433\n+ 892 1.20261 2.19475 0.83640 1.86475 942 g - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06955 4.47238 2.88665 1.46634 0.26236 1.25804 0.33437\n+ 893 2.05230 3.00120 0.30998 2.42623 943 G - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04227 4.43959 3.52046 1.46634 0.26236 2.18278 0.11960\n+ 894 0.55401 2.15931 2.23114 1.59677 944 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04333 4.42357 3.49295 1.46634 0.26236 2.26336 0.10982\n+ 895 0.86953 1.87009 2.12358 1.18045 945 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04499 4.40782 3.44803 1.46634 0.26236 2.54094 0.08207\n+ 896 1.01077 1.79326 2.02548 1.08556 946 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.09936 4.38845 2.49901 1.46634 0.26236 2.53579 0.08251\n+ 897 0.69400 2.15614 1.77448 1.53673 947 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.09248 4.31656 2.59038 1.46634 0.26236 2.96962 0.05269\n+ 898 0.76162 1.87572 2.08942 1.36225 948 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.21908 4.25039 1.70108 1.46634 0.26236 3.20944 0.04122\n+ 899 1.28800 1.57528 1.95219 0.98012 949 u - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01760 4.04890 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/ncRNA/tRNA.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq63m/ncRNA/tRNA.cm Fri Mar 27 17:53:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,549 @@\n+INFERNAL1/a [1.1.2 | July 2016]\n+NAME tRNA\n+STATES 224\n+NODES 59\n+CLEN 70\n+W 292\n+ALPH RNA\n+RF no\n+CONS yes\n+MAP yes\n+DATE Wed Jul 11 20:38:39 2018\n+COM [1] /work/berntm/progz/infernal-1.1.2/src//cmbuild -F metazoa/cleaned/tRNA.cm metazoa/cleaned/tRNA.stk\n+COM [2] /work/berntm/progz/infernal-1.1.2/src//cmcalibrate --cpu 8 metazoa/cleaned/tRNA.cm\n+PBEGIN 0.05\n+PEND 0.05\n+WBETA 1e-07\n+QDBBETA1 1e-07\n+QDBBETA2 1e-15\n+N2OMEGA 1.52588e-05\n+N3OMEGA 1.52588e-05\n+ELSELF -0.08926734\n+NSEQ 82262\n+EFFN 82262.000000\n+CKSUM 1064118658\n+NULL 0.000 0.000 0.000 0.000 \n+EFP7GF -2.1327 0.74584\n+ECMLC 0.52308 -6.13287 4.44432 1600000 303379 0.003955\n+ECMGC 0.35220 -9.19117 3.81519 1600000 39040 0.010246\n+ECMLI 0.45989 -3.74821 7.70110 1600000 232232 0.005167\n+ECMGI 0.41215 -3.09079 7.83649 1600000 36141 0.011068\n+CM\n+ [ ROOT 0 ] - - - - - -\n+ S 0 -1 0 1 4 1 1 292 582 -21.254 -22.499 -0.022 -6.067 \n+ IL 1 1 2 1 4 8 25 294 583 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 \n+ IR 2 2 3 2 3 8 27 294 584 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 1 ] - 254 - a - -\n+ MR 3 2 3 5 5 11 29 293 583 -21.280 -0.001 -11.664 -12.226 -12.709 0.966 -2.506 -0.134 -0.061 \n+ D 4 2 3 5 5 5 23 291 581 -0.615 -5.362 -4.216 -2.202 -4.278 \n+ IR 5 5 3 5 5 8 26 292 582 -1.292 -2.445 -15.694 -1.293 -14.967 0.000 0.000 0.000 0.000 \n+ [ MATP 2 ] 2 251 g c - -\n+ MP 6 5 3 10 6 11 29 292 582 -22.212 -22.151 -0.004 -9.146 -11.033 -12.171 -4.827 -3.071 -6.469 2.251 -6.637 -7.934 1.310 -5.207 -6.452 2.464 -7.883 0.340 0.685 -6.203 -5.149 -3.228 \n+ ML 7 5 3 10 6 6 24 287 577 -13.293 -13.640 -3.201 -0.239 -13.489 -4.508 0.799 -1.805 -0.087 0.047 \n+ MR 8 5 3 10 6 7 24 290 580 -17.023 -15.752 -0.199 -10.915 -3.333 -5.111 -3.154 -3.305 -3.841 1.894 \n+ D 9 5 3 10 6 4 20 279 569 -16.168 -14.866 -3.907 -11.345 -11.362 -0.101 \n+ IL 10 10 5 10 6 7 24 291 580 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 \n+ IR 11 11 6 11 5 7 24 290 580 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+ [ MATP 3 ] 3 250 a u - -\n+ MP 12 11 6 16 6 9 27 290 580 -7.865 -7.913 -0.022 -9.696 -13.446 -7.608 -7.365 -2.929 -8.698 2.871 -5.763 -9.903 0.562 -8.174 -7.168 1.795 -10.373 -1.434 1.614 -7.593 -3.408 -4.719 \n+ ML 13 11 6 16 6 6 24 286 576 -14.570 -14.916 -4.979 -0.104 -14.766 -4.728 -0.489 -2.114 -4.279 1.587 \n+ MR 14 11 6 16 6 6 22 283 573 -14.245 -12.974 -4.742 -12.953 -0.442 -2.144 1.325 -1.500 -1.594 -0.304 \n+ D 15 11 6 16 6 4 20 278 568 -16.789 -15.487 -5.521 -8.394 -8.462 -0.040 \n+ IL 16 16 5 16 6 11 30 289 579 -11.127 -11.390 -0.002 -13.045 -13.821 -13.481 0.000 0.000 0.000 0.000 \n+ IR 17 17 6 17 5 11 30 289 579 -10.190 -0.002 -13.701 -11.869 -12.975 0.000 0.000 0.000 0.000 \n+ [ MATP 4 ] 5 248 a u - -\n+ MP 18 17 6 22 6 12 30 288 578 -6.814 -6.815 -0.027 -12.261 -10.974 -12.951 '..b'0.36767 1.17879 4.46387 0.01158\n+ 49 1.42843 2.79983 0.50555 2.34006 173 G - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.16503 5.25652 1.91788 0.00053 7.54309 2.75562 0.06568\n+ 50 1.96677 2.55471 0.33275 2.72686 175 G - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.10581 2.91432 3.07562 1.41885 0.27706 1.31387 0.31304\n+ 51 2.27672 2.40501 3.79364 0.24258 184 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.07544 2.75302 4.71801 1.29238 0.32105 0.83373 0.56992\n+ 52 2.54125 3.14149 2.61107 0.21746 193 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01176 13.48466 4.44864 1.46634 0.26236 2.10175 0.13038\n+ 53 1.05103 0.94825 2.71981 1.62396 194 c - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00721 13.49070 4.93652 1.46634 0.26236 1.70908 0.19971\n+ 54 0.52648 2.82517 1.36749 2.35098 195 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.05125 3.29465 4.35233 0.87714 0.53780 0.91599 0.51103\n+ 55 0.17870 2.77985 3.77096 2.54378 201 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02780 13.54230 3.59667 1.46634 0.26236 1.62317 0.21974\n+ 56 0.83657 1.65195 1.94107 1.46283 202 a - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.17221 2.89979 2.27141 1.14124 0.38481 2.37086 0.09805\n+ 57 2.23676 1.79692 3.33746 0.36837 210 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.23778 3.14765 1.77978 1.30349 0.31688 0.73793 0.65028\n+ 58 2.60369 0.29665 2.95594 2.03513 218 C - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01883 4.51156 4.86976 0.39604 1.11773 0.61323 0.78001\n+ 59 2.41747 0.52241 2.69361 1.38578 221 C - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02260 3.85691 6.71530 0.18355 1.78564 1.21771 0.35085\n+ 60 1.55317 1.28965 1.65641 1.13248 224 u - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01214 4.53156 6.64399 0.38305 1.14500 1.64722 0.21392\n+ 61 1.56472 1.43203 1.53114 1.09142 227 u - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04515 3.12518 8.43425 0.10786 2.28036 0.31084 1.31988\n+ 62 2.42113 0.92869 1.83743 1.03035 230 c - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.12192 2.25624 4.60186 0.40478 1.09999 0.04610 3.09997\n+ 63 1.60595 0.91982 2.75966 1.08649 236 c - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01241 4.44616 7.40093 0.30491 1.33632 3.29854 0.03764\n+ 64 1.48929 1.50040 1.69717 0.99906 239 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01379 4.36169 6.97335 0.50793 0.92066 1.71132 0.19922\n+ 65 1.43588 1.69759 1.97637 0.82008 242 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00900 4.74596 8.22337 0.44177 1.02972 1.59800 0.22602\n+ 66 1.25750 1.49265 1.95613 1.05138 245 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01056 4.72569 6.41132 0.43182 1.04789 2.87355 0.05816\n+ 67 1.46070 1.36694 1.63149 1.14758 248 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00425 5.47954 9.52723 0.00059 7.43734 0.33415 1.25859\n+ 68 1.64875 1.46681 2.27447 0.74613 250 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00001 13.61600 11.71165 1.46634 0.26236 0.18004 1.80324\n+ 69 2.22739 1.05136 1.82946 0.96174 251 u - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00985 4.62540 13.61464 9.13024 0.00011 0.00537 5.22887\n+ 70 0.72539 3.03998 1.48425 1.42148 254 a - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 6.25473 0.00192 * 0.00019 8.55554 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 test-data/refseq63m/ncRNA/trnY.cm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq63m/ncRNA/trnY.cm Fri Mar 27 17:53:42 2020 -0400 |
| [ |
| b'@@ -0,0 +1,549 @@\n+INFERNAL1/a [1.1.2 | July 2016]\n+NAME trnY\n+STATES 224\n+NODES 59\n+CLEN 70\n+W 171\n+ALPH RNA\n+RF no\n+CONS yes\n+MAP yes\n+DATE Wed Jul 11 21:03:42 2018\n+COM [1] /work/berntm/progz/infernal-1.1.2/src//cmbuild -F metazoa/cleaned/trnY.cm metazoa/cleaned/trnY.stk\n+COM [2] /work/berntm/progz/infernal-1.1.2/src//cmcalibrate --cpu 8 metazoa/cleaned/trnY.cm\n+PBEGIN 0.05\n+PEND 0.05\n+WBETA 1e-07\n+QDBBETA1 1e-07\n+QDBBETA2 1e-15\n+N2OMEGA 1.52588e-05\n+N3OMEGA 1.52588e-05\n+ELSELF -0.08926734\n+NSEQ 3596\n+EFFN 23.577213\n+CKSUM 2475394320\n+NULL 0.000 0.000 0.000 0.000 \n+EFP7GF -16.7615 0.72134\n+ECMLC 0.65949 -4.52240 3.88423 1600000 306877 0.003910\n+ECMGC 0.38382 -13.35512 0.28299 1600000 75065 0.005329\n+ECMLI 0.57047 -3.82037 5.52297 1600000 247755 0.004843\n+ECMGI 0.41384 -8.89743 3.42146 1600000 65482 0.006109\n+CM\n+ [ ROOT 0 ] - - - - - -\n+ S 0 -1 0 1 4 0 1 171 297 -9.597 -10.843 -0.012 -7.274 \n+ IL 1 1 2 1 4 2 20 172 298 -2.817 -4.319 -0.613 -2.698 0.000 0.000 0.000 0.000 \n+ IR 2 2 3 2 3 2 22 173 299 -1.925 -0.554 -4.164 0.000 0.000 0.000 0.000 \n+ [ MATR 1 ] - 125 - A - -\n+ MR 3 2 3 5 5 2 23 172 298 -9.674 -0.013 -9.489 -9.435 -7.586 1.690 -1.983 -1.883 -2.008 \n+ D 4 2 3 5 5 0 16 169 295 -5.356 -0.711 -2.951 -4.413 -2.408 \n+ IR 5 5 3 5 5 2 20 171 298 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+ [ MATP 2 ] 1 124 g c - -\n+ MP 6 5 3 10 6 4 24 171 297 -10.844 -10.783 -0.027 -6.028 -9.577 -9.966 -2.129 -3.045 -2.673 1.922 -4.456 -4.287 -0.295 -4.434 -3.515 2.793 -4.195 0.545 0.627 -3.418 -1.216 -2.760 \n+ ML 7 5 3 10 6 1 18 168 294 -6.255 -6.601 -1.303 -1.010 -6.451 -3.981 0.385 -0.416 -0.139 0.051 \n+ MR 8 5 3 10 6 1 17 168 294 -6.999 -5.728 -1.637 -5.706 -0.840 -3.757 0.349 -0.379 -0.213 0.131 \n+ D 9 5 3 10 6 0 12 162 288 -9.333 -8.031 -3.828 -4.510 -4.528 -0.257 \n+ IL 10 10 5 10 6 2 19 170 296 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 \n+ IR 11 11 6 11 5 2 20 169 296 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+ [ MATP 3 ] 2 123 g c - -\n+ MP 12 11 6 16 6 4 23 169 295 -10.823 -10.762 -0.008 -9.085 -9.399 -10.001 -4.970 -3.541 -4.378 1.762 -5.896 -5.391 -0.091 -5.343 -4.951 2.940 -5.476 1.318 -0.561 -4.347 -2.125 -1.942 \n+ ML 13 11 6 16 6 1 18 166 292 -6.946 -7.292 -1.839 -0.600 -7.142 -4.672 0.047 -0.073 -0.744 0.505 \n+ MR 14 11 6 16 6 1 17 166 292 -7.000 -5.729 -1.637 -5.707 -0.819 -3.920 0.348 -0.379 -0.214 0.133 \n+ D 15 11 6 16 6 0 12 160 286 -9.358 -8.056 -3.853 -4.535 -4.552 -0.252 \n+ IL 16 16 5 16 6 1 19 168 294 -2.579 -2.842 -0.760 -4.497 -5.274 -4.934 0.000 0.000 0.000 0.000 \n+ IR 17 17 6 17 5 2 19 167 294 -2.408 -0.496 -5.920 -4.087 -5.193 0.000 0.000 0.000 0.000 \n+ [ MATP 4 ] 3 122 U A - -\n+ MP 18 17 6 22 6 3 21 167 293 -7.115 -6.676 -0.050 -8.632 -8.990 -6.311 -3.6'..b'1.46634 0.26236 8.34953 0.00024\n+ 49 1.27153 2.98213 0.67193 1.84395 86 G - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02063 10.30427 3.89315 1.46634 0.26236 3.74445 0.02393\n+ 50 1.54200 3.17556 0.60235 1.62581 87 G - - <\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.21425 10.28861 1.64602 1.46634 0.26236 1.85461 0.17021\n+ 51 2.68135 3.23684 3.28314 0.15697 88 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04224 10.11695 3.18633 1.46634 0.26236 2.10155 0.13041\n+ 52 1.67695 3.54669 2.97478 0.31037 89 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.29453 10.13097 1.36617 1.46634 0.26236 0.90669 0.51728\n+ 53 1.68373 1.01723 2.01555 1.14107 90 c - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.06294 10.04743 2.79757 1.46634 0.26236 3.42284 0.03316\n+ 54 0.68355 1.75890 1.45389 2.41592 91 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.37435 1.17358 5.80746 2.13502 0.12584 2.68248 0.07084\n+ 55 0.18700 2.99442 3.37961 2.44843 108 A - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.01311 10.04288 4.34463 1.46634 0.26236 0.93875 0.49613\n+ 56 1.06980 2.29106 1.13844 1.44628 109 a - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00513 10.23190 5.28244 1.46634 0.26236 0.76575 0.62546\n+ 57 1.73466 1.70998 2.69812 0.55280 110 U - - _\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.04915 10.35620 3.03811 1.46634 0.26236 0.19891 1.71269\n+ 58 1.95411 0.62199 2.02442 1.66407 111 C - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00722 10.42406 4.93858 1.46634 0.26236 1.34038 0.30347\n+ 59 1.91853 0.85757 3.07275 0.96052 112 c - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.08150 10.43492 2.54798 1.46634 0.26236 1.02109 0.44660\n+ 60 2.99540 0.97043 3.14437 0.63872 113 U - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00006 10.37568 10.37568 1.46634 0.26236 2.15787 0.12281\n+ 61 3.43169 0.77457 3.23915 0.76021 114 u - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00036 10.38966 8.02263 1.46634 0.26236 8.14999 0.00029\n+ 62 4.10756 0.61701 7.42964 0.81328 115 C - - >\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02546 4.24541 4.52700 0.00429 5.45424 0.23808 1.55185\n+ 63 2.13841 1.61334 4.68281 0.39499 117 U - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00077 10.46017 7.21076 1.46634 0.26236 4.29745 0.01370\n+ 64 2.61974 0.81956 3.00861 0.82738 118 c - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00256 10.45986 5.97896 1.46634 0.26236 7.00154 0.00091\n+ 65 1.99711 1.61542 3.11254 0.47646 119 U - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00206 10.45735 6.20241 1.46634 0.26236 2.21395 0.11571\n+ 66 2.37728 1.66142 2.73956 0.42659 120 U - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.02126 4.40348 4.73336 0.00468 5.36617 0.63197 0.75831\n+ 67 0.37858 3.43947 1.51419 2.76308 122 A - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00156 10.46740 6.48426 1.46634 0.26236 3.31988 0.03683\n+ 68 3.64405 0.72837 2.93265 0.82576 123 c - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00016 10.46673 8.90739 1.46634 0.26236 0.23949 1.54660\n+ 69 2.18345 0.76716 3.03302 0.98124 124 c - - )\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00006 10.48563 10.48563 1.46634 0.26236 0.03118 3.48339\n+ 70 0.17408 2.95040 2.79176 3.07620 125 A - - :\n+ 1.38629 1.38629 1.38629 1.38629\n+ 0.00003 10.49064 * 1.46634 0.26236 0.00000 *\n+//\n' |
| b |
| diff -r 000000000000 -r dd589aa77943 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,8 @@ +<?xml version="1.0"?> +<tables> + <!-- Locations of data downloaded for the megan tools --> + <table name="mitos" comment_char="#"> + <columns>value, name, type, path</columns> + <file path="tool-data/mitos.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r dd589aa77943 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Mar 27 17:53:42 2020 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of indexes in the Bowtie2 mapper format --> + <table name="mitos" comment_char="#"> + <columns>value, name, type, path</columns> + <file path="${__HERE__}/test-data/mitos.loc" /> + </table> +</tables> |
