| Next changeset 1:26abc7846e6f (2021-09-14) |
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Commit message:
"planemo upload for repository https://gitlab.com/paulklemm_PHD/proteinortho commit 889335c0a31f156c3f90d4c2048cb4df155a53b2" |
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added:
proteinortho.xml proteinortho_macros.xml test-data/C.fasta test-data/C.gff test-data/C2.fasta test-data/C2.gff test-data/E.fasta test-data/E.gff test-data/L.fasta test-data/L.gff test-data/M.fasta test-data/M.gff test-data/result.blast-graph test-data/result.proteinortho-graph test-data/result.proteinortho.tsv |
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| diff -r 000000000000 -r 4850f0d15f01 proteinortho.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteinortho.xml Tue Feb 18 17:57:28 2020 -0500 |
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| b'@@ -0,0 +1,343 @@\n+<tool id="proteinortho" name="Proteinortho" version="@TOOL_VERSION@+galaxy@WRAPPER_VERSION@">\n+ <description>detects orthologous proteins/genes within different species</description>\n+ <macros>\n+ <import>proteinortho_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="version_command"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ ## the following ln-action is necessary, since the file names are used by proteinortho (output contains filenames => species names)\n+ #import re\n+ #for $f in $input_files#\n+ ln -sf \'$f\' \'${re.sub(\'[^\\w\\-_.]\', \'_\', f.element_identifier)}\' &&\n+ #end for\n+ #if $synteny.synteny_options == "specified":\n+ #for $f in $synteny.input_files_syn#\n+ ln -sf \'$f\' \'${re.sub(\'[^\\w\\-_.]\', \'_\', f.element_identifier)}\' &&\n+ #end for#\n+ #end if\n+ proteinortho \n+ --project=result\n+ --cpus="\\${GALAXY_SLOTS:-4}"\n+ --ram="\\${GALAXY_MEMORY_MB:-16000}"\n+ #if $more_options.selfblast:\n+ $more_options.selfblast\n+ #end if\n+ #if $more_options.singles:\n+ $more_options.singles\n+ #end if\n+ --p=$p\n+ --e=$evalue\n+ #if $more_options.cov:\n+ --cov=$more_options.cov\n+ #end if\n+ #if $more_options.sim:\n+ --sim=`LC_NUMERIC=C awk "BEGIN {printf \\"%.2f\\",$more_options.sim/100}"`\n+ #end if\n+ #if $more_options.identity:\n+ --cov=$more_options.identity\n+ #end if\n+ #if $more_options.isoform != "no":\n+ --isoform=$more_options.isoform\n+ #end if\n+ #if $synteny.synteny_options == "specified":\n+ --synteny\n+ --dups=$synteny.dups\n+ --cs=$synteny.cs\n+ --alpha=$synteny.alpha\n+ #end if\n+ #for $f in $input_files#\n+ ${re.sub(\'[^\\w\\-_.]\', \'_\', f.element_identifier)}\n+ #end for#\n+ #if $synteny.synteny_options == "specified": \n+ #for $f in $synteny.input_files_syn#\n+ ${re.sub(\'[^\\w\\-_.]\', \'_\', f.element_identifier)}\n+ #end for#\n+ #end if\n+ 2> >(sed -E "s/.\\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g" 1>&2)\n+ #if $synteny.synteny_options == "specified":\n+ &&\n+ mv result.poff-graph result.proteinortho-graph &&\n+ mv result.poff.tsv result.proteinortho.tsv &&\n+ mv result.poff.html result.proteinortho.html ;\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <param name="input_files" format="fasta" type="data" multiple="true" min="2" label="Select the input fasta files (>2)" help="The input fasta files. At least 2 are needed!"/> \n+ <param argument="--p" type="select" label="Similarity comparision algorithm" help="In the first step of proteinortho an all-versus-all reciprocal best hit graph is build from the input files (using this algorithm).">\n+ <option value="diamond" selected="true">diamond (aminoacid sequences)</option>\n+ <option value="autoblast">auto detect NCBI-BLAST (protein and nucleotide sequences)</option>\n+ <option value="blastp">NCBI-BLASTP+ (protein sequences)</option>\n+ <option value="blastn">NCBI-BLASTN+ (nucleotide sequences)</option>\n+ <option value="lastp">Last (aminoacid sequences)</option>\n+ <option value="lastn">Last (nucleotide sequences)</option>\n+ <option value="blatp">BLAT (aminoacid sequences)</option>\n+ <option value="blatn">BLAT (nucleotide sequences)</option>\n+ </param>\n+ <param argument="--evalue" type="float" value="0.001" min="0" label="E-value threshold of the blast algorithm" help="This is the main parameter for the generation of'..b'text text="E_10	C_10	"/>\n+ </assert_contents>\n+ </output>\n+ <output name="proteinorthograph">\n+ <assert_contents>\n+ <has_text text="E_10	C_10	"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[Proteinortho with POFF - An orthology detection tool\n+\n+**What it does**\n+\n+Proteinortho is a tool to detect orthologous proteins/genes within different species (at least 2). \n+\n+ | It compares similarities of given gene/protein sequences and clusters them to find significant groups.\n+ | The algorithm was designed to handle large-scale data and can be applied to hundreds of species at one.\n+ | Details can be found in (doi:10.1186/1471-2105-12-124).\n+ | To enhance the prediction accuracy, the relative order of genes (synteny) can be used as additional feature for the discrimination of orthologs. The corresponding extension, namely PoFF (details see doi:10.1371/journal.pone.0105015), is already build in Proteinortho. \n+\n+----\n+\n+**Proteinortho in a nutshell**\n+\n+----\n+\n+* **(i) Build adaptive reciprocal best hit graph (RBH)**\n+\n+ | Using the blast algorithm (diamond,blast,blat,...) all input sequences are compared against each other.\n+ | If two proteins find each other with respect to multiple criteria like minimal evalue, similarity compared to the best hit, ... then a edge is drawn between the two proteins.\n+ | The result of this step is outputted to RBH\n+\n+* **(ii) Cluster the RBH**\n+\n+ | Using two clustering algorithms, edges are removed that weakly connect two connected components to reduce false positive hits.\n+ | The resulting connected components are outputted in orthology-groups / -PAIRS \n+\n+----\n+\n+**Proteinortho output files**\n+\n+----\n+\n+* **RBH**\n+\n+ | The result of the (i) step, the reciprocal best hit graph. \n+ | First a comment line announces 2 species (# ecoli.faa human.faa), then each line corresponds to a reciprocal best hit between 2 proteins/genes of the announced species. The output format is shown below.\n+ | *seqidA*,*seqidB* = the 2 ids/names of the proteins involved \n+ | *evalue_ab* = evalue with seqidA as query and seqidB as part of the database \n+ | *bitscore_ab* = bitscore with seqidA as query ...\n+ | *evalue_ba* = evalue with seqidB as query ...\n+ | ...\n+\n+.. csv-table::\n+ \n+ seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba \n+\n+----\n+\n+* **orthology-groups**\n+\n+ | The result of the (ii) step, the clustered reciprocal best hit graph or the orthology groups.\n+ | Every line corresponds to an orthology group of proteins/genes. \n+ | The first 3 columns characterize general properties of that group: number of proteins, species and the algebraic connectivity. The higher the algebraic connectivity the more edges are there and the better the group is connected to itself in general. \n+ | Then a column for each species follows containing the proteins of that species. If a species contributes with more than one protein to a group of orthologs, then they are ordered by connectivity.\n+\n+.. csv-table::\n+ \n+ Species,Genes,Alg.-Conn. \n+\n+----\n+\n+* **orthology-pairs**\n+\n+ | The same as orthology-groups but every edge is printed one-by-one here. The output is formatted the same as the RBH graph:\n+\n+.. csv-table::\n+ \n+ seqidA,seqidB,evalue_ab,bitscore_ab,evalue_ba,bitscore_ba \n+\n+----\n+\n+**Proteinortho-Tools for downstream analysis**\n+\n+* `proteinortho grab proteins` : find gene(s)/protein(s) in a given fasta file and retrieve their sequence(s). You can also use a orthology-groups file.\n+* `proteinortho summary` : Summaries the orthology-pairs/RBH files to determine how the species are connected to each other.\n+\n+More information can be found on github https://gitlab.com/paulklemm_PHD/proteinortho\n+]]>\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 4850f0d15f01 proteinortho_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/proteinortho_macros.xml Tue Feb 18 17:57:28 2020 -0500 |
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| @@ -0,0 +1,23 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">6.0.14</token> + <token name="@WRAPPER_VERSION@">2.9.1</token> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/1471-2105-12-124</citation> + <citation type="doi">10.1371/journal.pone.0105015</citation> + </citations> + </xml> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">proteinortho</requirement> + <requirement type="package">diamond</requirement> + <requirement type="package">blast</requirement> + <requirement type="package">blat</requirement> + <requirement type="package">last</requirement> + </requirements> + </xml> + <xml name="version_command"> + <version_command>proteinortho -v</version_command> + </xml> +</macros> |
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| diff -r 000000000000 -r 4850f0d15f01 test-data/C.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/C.fasta Tue Feb 18 17:57:28 2020 -0500 |
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| b'@@ -0,0 +1,1006 @@\n+>C_10 asd asd\n+VVLCRYEIGGLAQVLDTQFDMYTNCHKMCSADSQVTYKEAANLTARVTTDRQKEPLTGGY\n+HGAKLGFLGCSLLRSRDYGYPEQNFHAKTDLFALPMGDHYCGDEGSGNAYLCDFDNQYGR\n+SVRSPLKKLLGFGYNPTYGKSALGDELRLGLVFREEFRKINKALLTGGANVVKAGVSYKD\n+SKKQGHKLLCDEMDNAVSLLKVLHPKLGCCVGDDNHSYGALSDFFVTCRRLIGKGHIEKE\n+RKSANECLAKSFQPFCSDLNLTGGGVRQHPGILHLKYAIKLLQATPMYMLLCLHAGKTKL\n+CDNAADSSEFCQLQDRDIVAEYVAVWKSKKPQSAPHVLKGPHNKKALVVSSCFAADFRIV\n+AFVVLDSSNDYSDAKASLDDAKLCIESCVFIYAPSLKADGTKGGKYCGKGSIPENCQLRE\n+HVVACDRAGSDCSGEPSSWSCACKFAIGANMRSLARNSDAATQTIHGTAIRDYTPAVGRS\n+SGTFVGPECPLSKFVSSYLFVAKDNGGKLFVWVPGGNYHSLWRSFTMNLCNIGLAELPLS\n+AYRNIKKKGYDGGKAGTLVTLMEFVAQGRVANALFDWGSCNEEGAGLSKQCSETVVGFLQ\n+QSSDYHRLFPKGYGEVPPRCTLGPFPAFHMLMQAALKGSFRTAQQPSVLFSCKCVKLKYS\n+SCKYAL\n+>C_11\n+PQKDTVVRHTRSDIFTLPEAVHYPDGTCQTMLGTVKATRYTASGAGAKSAGYKEGHLGIR\n+KKPHSPCSLAAKASPAGRKGAAAACPLLIGFLPLMFVRFTKTGAYVGDSLWSLKEGIQYY\n+VRHSVRALARSENASKRFVEVIGTKMAPVGRALKSFFTCAHKKPGFLGKADYVIPNHHHG\n+LQPPHYQGYTKKNAQNKTGKGDDLILAHTAVVAPLTKNKHFTHSVKGMEHSGCLGDCSGK\n+HQIASGTKSPVWGCNYLVPGHGDFLLFVRDPRRDIGKLNSNYGLKKEAPVHCGEQREAF\n+>C_12\n+AWEAFVKVNNCDDKSSKGNHNVKDKSLHTHAEFAGTETGCEFSSLLVVSKVHNGIVKDRP\n+RKKLISEKIYKDLGYVGKGACKGPDWWTWHLIPDLKGKVFFHLEPVTCGAAAVGKPQIGS\n+SVHVQLLLKGDGIKVSNYFKICKYQYALATLKKKVEECWADDGGGQHKAEAPLCQVTFDH\n+VASCYAAKLICGEGCERASKTDKGELGEKLLHVPRGLRFQAAGTVLAKKRQNVPDMAAGC\n+DNLSSNRVVHARETPMSDKRQHAHGESKHFGSGGKIHSSKLTEETGLSLFSPGELTCAKE\n+RGGIHTALPGNAGYDGGECALKTQTAAFYLQPYQGVLREKSVEKCGVFGRCFIRPAGFMF\n+GTLPPCYWGDRGCNLGDFLLIVGGQERVPFKSDDNNQVEPMGVSLVGEATCRLYLYQTNG\n+PKLKSRNAKKWANTGESQPDPGVNGLLKVHMEFDESFKTTNGMTFQFGFARCPKKPYLCK\n+PVGIYADSMGFIVNTFLAEEEGKSPIAEELIADGISGHIDGAKTQTANFNFEATLLRVKS\n+GGFYASFLPGSPNEPVYVQGRVALTKSKAKTHLPSAVNGKKLGLPSIGVFVKAFCCGLVK\n+VMCGITSKIYCGCSVALMGNDQCGYEGEPAGMQSYLTIGLYATVSDSNTKRRGPPGAPGG\n+TGKSAFTASSTGDCKGFKGSLFKAKPPLPMVGMIGAFLSKVKSIGAPGMGLVKLTRLTKY\n+QTPAIKCQDKKSNFVCYGVVKKHAIQCQAL\n+>C_21\n+FWDAFIKMDSCEARTSKGYHNVKDTSLLGRAEHAGEDTGCEFSSLLVLNKPHNGITSAKH\n+RKKTIGELIAKSIGFVGQGACCKGQDWWKHWHAVPDAKGKVFFHMQPSTCASAPAGKPQR\n+IGRSIHVQILDKGDGIKVKTFSKTGAYVYGLLTLKKKVQDCWAADGKASSNKVNPPIPQV\n+TFDHIPSRYNTKHICGKGCEHNAKTDKGELGESLLHPRGLKFQFFGTVLQRKRQELPNMV\n+AGCDDLESNRVVVSRGVPTSHSRPEAHGESKFFGQLAGILSSKMTENTGFSLFPEGDTCG\n+KEVGSIHTHLPGAYQSEAKEKLGKAYDGGECALRLAAFYLHPYDGLLSERTFEKCSIFGR\n+CYIKPTGFSFVGLLPPCFWGDRGCHLGKFLLIINAKGRLALKWGDKNQVEPLGVDLMGEP\n+TCRLRLYQTNAFKLRSKSFLTWGKTGASQKSLRQGVHTKIHMEYEDSFKTPNGKTFQFGF\n+SRPQKPYEGVSIKYADSMGFIVHAFFADDEGQKSFTEELTAEYIQGSDTQTAHFDIKVTL\n+LITKSGGFYASFRQGSLAETVSVDFRASKAKSTSHLPAEPICPLFHKEGEALNAKELNLP\n+AMGVFVSGFCCGLVGVRCGITHKIYCGAGLVLRDHDQCGYDSGPANMQFYLTIGYTTVWD\n+GNTVRRGPNGLPLATGKGAFMCSGASTGECTGFEGCLFRQKGPPMVAQNGKYLTYFTAVF\n+TAFLERVKSIGASGMGLVELTRLSKYQTPAVCRAMSKFICLGVVKKNALETAAL\n+>C_13\n+DAVKREGSLCKVVGGCALNLTSDLAAGVVDVSEFDEAANAYAPALATTTDIYSGKLFSSA\n+VYATLGPKDILLDATVFSVCVVCCDICLVVEAELGVCPKICYSLKFKSYHCENLICKKNE\n+ARFTFKKADKDWILAVTTALVLIKKKCQKKPIVCTLFQEMYYAERGRYLMPFNDEPSNCP\n+ALLGVCEM\n+>C_14\n+PSGDLQDNSSLHFCHPHYLLTILGRQYIQNFGEDFVFCSERALFYDGDLMSKNQISVMFG\n+VSNAAVTSRQALHVTDCSDPQGPFGKGLKDPSGRFENQPKSAFLSKLAPYVEPRALQPKP\n+DNWVIAWAGRLNLAIPYQCKWIVQRGGGCCVGLVNTSARVFEQVADVHAHDHLRYIPWKC\n+SKGKWTGLTCKAGKSGKVFFKGKGTPVTRADTARPFSKADELCHGHAGTLTQAGAGDYFK\n+GTLKGLLGAHRRGLKAAKMRFLLQSSNFMKVLEAFAVGHNLRLLAKRNHWKGGRAASYAA\n+NIVKRTMENDAHLPFLVQCTQGHKLIFTGSCTIHEYNGQSKAKTFLPFGERSQQGADNYH\n+RADATSGKYLPADYANTTCKDANLKITISRQNACRNMHGWILSATGIEGVVAQEVKIKPI\n+KKKTDDVHEIKVGVEIDSIGVGLKGAQLWDNDKVCAVEYLADVSGNYLKSHYSLGSLSLM\n+GVSPIKVDKLSGRTLPKKHTVKSCLCRLKSLVKRGAQGCTPLQVCCCTNDKEFIPARGTE\n+CHVTDTSYEIKHLHQTESLKRLPITFAQGNLRNDLEVLNHLLTIPTGYRTCQVQHYLHLK\n+GSKPGQNPPTCALKQVHYVAKTRASDPEIPPHLLVSKNVQYALKGDLVTKEGRGPDVVIL\n+QSLLQLPVFVSSTNALEFLKAGPNPGEQKSQHVGDPCDIRCKSELMKMGDYGVDTPMNFD\n+LHGAEQDLDLGDADAKELKKAGEFAVPGPKAAIFNDKQLCHCNECGVGSTTDRRNSSMKF\n+ELVAGQKLTSVVGAIYHGTLTMNICNSLISDYFTSTAIQAIKYLY\n+>C_15\n+AKTSNYDQSFKTTMLHLHIKVRIPFYITTELGCKTCFLDISSSLMVYSTKAPTKLDAGLK\n+NGNDAEKLDDLQKEARVGSYLPARPKEKETPLRLKLKMRLSLAEQPIFEAHYYELNMPDV\n+GLICQVKHKGGLGGRKEHSSFVKTTCFIVGFYCELNYFFFGKVGAVFVIKKAASKPVFRT\n+VYGKTPLGTINATSENLRETQSEHTVYTVIGLIPTWHDLGDMVLALSLAGIENVPQEDDQ\n+GCNKREWKKSLAQSYKDADIHEGDQRCYKHRLNRGTAYKGDPAHGSTLIE'..b'QNIPETALGSCLDKW\n+NGLKAKLDYACSSSPQKRGGPKSSQKGMTDAGPAEIAAPQSHHGPAEKVCRLQVSGPCLT\n+KLMLVSALCHGDGKDMPKIYVSAKNCGYNYVIPASLASAFMGSVTLLFKAIVRFRRTSTR\n+STVLAAEILKSKILCCAVTGALVSFPPVQTASTAEYLMSSDIQTTVPWSPRCSRVAITKS\n+IIFLNSSEEQQARSCPIAKAHSQIKSVFVGQHEAYHVLKCSREPKVPGGVEHPLKSVAPM\n+ASMACCGHMGDVQWAQHSFHSPIVGLSLPESVDGFFRKLIFCTDGQFIGVKRSAYHRSLR\n+AGMVDTLGCAAFAQEKLETVKLKFSEGVHCATRFPINTRNTASAYGQWCGGWYNKAHVKE\n+DKSPPLGGSVVVLGAGIFPTKPSTSLDKVLAQENLTEVEGAVDPVLTVWLGVGGGPAMQH\n+>C_248\n+LAFSWIGEYNMQIGLPRGTSKRSFYRDARKGVLKVTESLFLESQNLPDVSLGNCLDKWTG\n+ICAKLDYACSSPPQKRGGPKKSQKGVTDAGPAERCAPQSHNGGADKVCPLKVSGPCLTKH\n+LLVSVLCHGDGKDMPMIYVNAKDCGLNCRIPASLGTAFMGSLALLFKAIVRLRRTSDRSS\n+VLAAEILKSKVLCCEQPVTGGLVSFPPVQTASTAEYLMTSDIQSTRPWTPRCSRVNITKN\n+IIFLNSSEEQQAVERRCPIALPHSGIKSVFVGQHEGYHVVQCSREPKVPGDVEHPLQSVA\n+TMASMSCCGHMVDVNWIQHGFHAPIVGLALPESVEGIFRKLIFCTDGQFIGVKRTAYRRS\n+LRAGMVDALGCAAFAQEKLKTVKLKFAEGVHCSTAFPIDTRTTASGYGQFCGGWYNKAHV\n+KEDKSPLLGGSVTVLGAGTFPTKPSASLDKVFAQENLMEVEGSVDPVLTLWLGVGGGAAM\n+QH\n+>C_249\n+LAFSWIGECNLQINLRGASSQSWYRDARKGLPVLKVTTSLFLESQNIPDTSLGNCLDKWT\n+GLRAKLDYSCSSSPPKRGGPKSSQKGVTDAGPAEICAPQSHHGPANKVCRLEVSGQCLTK\n+LLLVSVLCHGDGKDMPKIYHSAKNCGYNCLTPASLATAFMGPLTLLFKAIVRVRRSGVLA\n+AEILKSKILCCAHPVTGAVVSFPPVQTASTAEYLMTSDIQTTRPRTPRCSRVNITKSFIF\n+LNSNEEQQARSCAIAKSHSQIKSVFVEQHPGYHVVHCSRAPKVPGGVNHPLKSCVPMVAM\n+ACCGHMGDVNWAQHGFHAPIIGLALPESVGGFFRKLIFCTDGQFIGVKRSAYRRSLRAGM\n+VDTLGCAAFVQEKLKTVNLKFAQGVHCSSAFPIDTRTTAGAYGQFCGGWYNKNHVKEDKS\n+GELGGSVVVLGAGIFPGKPSASLDKLFAQENLMEGEGSQDPVLTVWLGAGGGTAMQH\n+>C_250\n+LAYSWIGEYSMQINLPRGPSTQSFYRDDRKGLPVLKITVSLFLDSQNIPDTSLGNCLDKW\n+TGLRAKLDYACSSSPQKRGGPKVSQKGVTDAGPSEICAPQSHHGPADKACRLQVSGPCLT\n+KLLLVSVKCHGDGKDMPKINVAAKNCGYTCLIPGSLATAFFGTLTLQFKAIVQLRRYSTR\n+SSVLAAESLELKSKMLCCVQPITGALVSFPPVQTASTADYLMTSDIQTTRPWTPRCSRVN\n+ITKGFTFLNSSEEQQARSCPINKSHSQAKKVFVGQHEGYHVVQCSREPKVPGGVEHPLKS\n+VAPMASMACCGHMGDVNWAQNGFHAPIVSLALPESVDSFFRKLIFCTDGQFIGVKRSAYR\n+RSLRAVDTLACAAFTQAKLKTVKLKFAEGAHCSTGLCLVAFPIDTRTTASAYGQFCGGWY\n+NKAQVKEEKSPLLGGSVVVFGAGMYPTRPSASLDKVFSQENLMEVEGVDPVLTVWLGVGG\n+ATAMQH\n+>C_251\n+LFSWIGGYNMQINLPIGPSTQSFYHDARKGLPVLKVTVSLFLESQNDPDTSLGNCLDKWI\n+GLRVKLDYACSSSSQKRGGPKSSQKGVTDDGPAEICAPQSHHGPVDKVCRLQVSGPCLTK\n+LLLVEVLCHGDGKDMPKIYVSGKNCGYNCLIPASLATAFMGSLTLLFKAIVRLRRTSTRS\n+SVLAAHPEILKSKVLCCVQPVTGALVSFPPVQTASTAEYLMKMTSGIQVTRPWTPRCSRV\n+NITKSFIFLNSSEEQQARSCPIAKSHSQIKSVFVGQHEGYHIVQCNREPKVPGGVEHPLK\n+SVAPMPSMACCGHMGNVNWAQHGFHGPIVGLALPESTDGFRKLIFCTDGQFIGVKRSAYR\n+RSLRAGLVDTLGCAAFAQEKLKTVKLKIAEGVHCSTAFAIDTRTANAYGQFCGGWFNKAH\n+VKENSSPLLGGGVVVLGSGILPTKPSASLDKVFAQENLMEVEGSVDPVLTVWLGVGGGTA\n+MQH\n+>C_252\n+LAFSWIGEYNMQVNLPRGPSTQSFYRDARKGLPVLKVTVSLFLESQNIPDTSIGNCLDKW\n+TALRAKLDYACSSSPQKRGGLKSSQKVVTDAGPAEICAPQSHHGPADKVCRLQVSGPCLT\n+KLVLVCVLCHGDGKNMPKIYVSAKNCGYNCLIPASLATAFMGSLTLLFKRIIRLRRTSTR\n+GSILACEILKSKVLCCTQPVTGALVSFPPVQTASTAEYLMTSDIQTTRPWTPRCSRVNVT\n+KSFIFLNTSEEQEVRSCPIAKDSHSQIKSVFVGQHEGYHVVECSRDPKVPGGVEHPLKSV\n+TPMASMACCGHLGDVNWAQHGFFAEIIGLALPEAVDGFFRKLIFCTDGQFIGVKRSAYRR\n+SLRAGLVDTLGCAEFAQEKLKTVKLKFEEGVHCNTAFPIETRTTASVYVQFCGGWYNTAH\n+VKEDKSPLLGGGVVVLGAGIFPTKPSASLDKVFMQENLMEVEGSVDPVLTVRLGVPGGTA\n+MQN\n+>C_253\n+LAIGEYNMHINLPKGPATQSFYRNARKALPVLKVTVSLFLASQNIPDTSLGNCLNKWTGL\n+RAKLDYACSSSPQKRSGPKSGQKGVTDAGPAEICAPQSHHGPADKVCRLQVSGPCLTKLL\n+LVSVLCHGDGKDMPKICVSAKNCGYKCLIPASLATAFMGTLTLLFKAIVRLRRTSTRSSV\n+LAAEILKSKVLCCTQPVTGALVSFPPVQTASTAEYLMTSDIQTTRPWTPRCSRLNITKSF\n+IYLNSAEEEQGRSCPIAKSHSQIKNVFVGQHEGNVTQCSREPKVPGTVEHPMKSVAPMAS\n+MACCGHMGDVDWAQHGFHPPIVGLALPESADGFFRKLIFCTEGQFIGVKRSAYRRSLRAG\n+MVDTLGCGAFAQEKLKLVKLKFAEGVHCSTAFPLDTRSTASAYGQFCGGWYNKAHVKEEK\n+SPLLGGSVVVMGEAGIFPTKPSASLDKVFAQENLMEVEGSVDPVLTVWLGVGGGTAMQQ\n+>C_254\n+LAFSWIGEYDMQINLPRGASTQSFYRDDKKGLPVLKVTVSLFLESQNIPDTSLTNCLNKW\n+TGLRAKLDYACSASPQKRGGPKSSQKGVTDAGPAEICAPGSHHGPADKICRLQVSGPCLT\n+KLLLVSVLCHGDGKDMPKIYVSAKNCGYNCLIPAGLATNFMGSLTLFFNAIVRLRRASTR\n+SSVLAAEILKSKVLCCTQPVTGARVSFPPVQTASTADYLMTSDIQTTRPWTPRCRRVNIT\n+KSIIFLNSNEEQQARSCPIAKSHSQIKSVFVGEHEGYHVVQCSRESKVPGGVEHPLKSVA\n+PKATMDCCGHMGDVNWAQHGFHAPIQGLALPESVDGFFRKLIFCTNGQFIGVKRSAYRRS\n+LRAGMVDTLGCAAFAQEKTKSAKLKFAEGVHCSTSFPLDTRTTASAYGQFCGSWYTKAHV\n+KEDKSPLLGGSVVVLGAGIFPTKPSASLDKVFAQENLMEVEGSVDVLTAWLGVGGGSAMQ\n+H\n' |
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| diff -r 000000000000 -r 4850f0d15f01 test-data/C.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/C.gff Tue Feb 18 17:57:28 2020 -0500 |
| b |
| b'@@ -0,0 +1,308 @@\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t1\t1\t.\t+\t.\tID=C_1;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t2\t2\t.\t+\t.\tID=C_2;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t3\t3\t.\t+\t.\tID=C_162;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t4\t4\t.\t+\t.\tID=C_163;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t5\t5\t.\t+\t.\tID=C_164;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t6\t6\t.\t+\t.\tID=C_165;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t7\t7\t.\t-\t.\tID=C_180;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t8\t8\t.\t-\t.\tID=C_179;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t9\t9\t.\t-\t.\tID=C_178;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t10\t10\t.\t-\t.\tID=C_177;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t11\t11\t.\t-\t.\tID=C_176;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t12\t12\t.\t+\t.\tID=C_254;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t13\t13\t.\t+\t.\tID=C_255;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t14\t14\t.\t+\t.\tID=C_256;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t15\t15\t.\t+\t.\tID=C_257;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t16\t16\t.\t+\t.\tID=C_258;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t17\t17\t.\t+\t.\tID=C_259;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t18\t18\t.\t+\t.\tID=C_260;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t19\t19\t.\t+\t.\tID=C_261;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t20\t20\t.\t+\t.\tID=C_262;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t21\t21\t.\t+\t.\tID=C_263;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t22\t22\t.\t+\t.\tID=C_264;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t23\t23\t.\t+\t.\tID=C_265;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t24\t24\t.\t+\t.\tID=C_266;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t25\t25\t.\t+\t.\tID=C_267;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t26\t26\t.\t+\t.\tID=C_268;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t27\t27\t.\t+\t.\tID=C_269;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t28\t28\t.\t+\t.\tID=C_270;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t29\t29\t.\t+\t.\tID=C_271;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t30\t30\t.\t+\t.\tID=C_272;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t31\t31\t.\t+\t.\tID=C_273;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t32\t32\t.\t+\t.\tID=C_274;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t33\t33\t.\t+\t.\tID=C_275;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t34\t34\t.\t+\t.\tID=C_276;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t35\t35\t.\t+\t.\tID=C_277;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t36\t36\t.\t+\t.\tID=C_278;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t37\t37\t.\t+\t.\tID=C_279;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t38\t38\t.\t+\t.\tID=C_280;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t39\t39\t.\t+\t.\tID=C_281;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t40\t40\t.\t+\t.\tID=C_282;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t41\t41\t.\t+\t.\tID=C_283;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t42\t42\t.\t+\t.\tID=C_284;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t43\t43\t.\t-\t.\tID=C_252;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t44\t44\t.\t-\t.\tID=C_251;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t45\t45\t.\t-\t.\tID=C_250;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t46\t46\t.\t-\t.\tID=C_249;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t47\t47\t.\t-\t.\tID=C_248;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t48\t48\t.\t-\t.\tID=C_247;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t49\t49\t.\t-\t.\tID=C_246;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t50\t50\t.\t-\t.\tID=C_245;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t51\t51\t.\t-\t.\tID=C_244;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t52\t52\t.\t-\t.\tID=C_243;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t53\t53\t.\t-\t.\tID=C_242;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t54\t54\t.\t-\t.\tID=C_241;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t55\t55\t.\t-\t.\tID=C_240;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t56\t56\t.\t-\t.\tID=C_239;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t57\t57\t.\t-\t.\tID=C_238;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t58\t58\t.\t-\t.\tID=C_237;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t59\t59\t.\t-\t.\tID=C_236;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t60\t60\t.\t-\t.\tID=C_235;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t61\t61\t.\t-\t.\tID=C_234;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t62\t62\t.\t-\t.\tID=C_233;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t63\t63\t.\t-\t.\tID=C_232;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t64\t64\t.\t-\t.\tID=C_122;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t65\t65\t.\t-\t.\tID=C_121;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t66\t66\t.\t-\t.\tID=C_120;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t67\t67'..b'91;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t244\t244\t.\t-\t.\tID=C_8;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t245\t245\t.\t-\t.\tID=C_161;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t246\t246\t.\t-\t.\tID=C_7;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t247\t247\t.\t-\t.\tID=C_60;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t248\t248\t.\t-\t.\tID=C_59;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t249\t249\t.\t-\t.\tID=C_58;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t250\t250\t.\t-\t.\tID=C_57;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t251\t251\t.\t-\t.\tID=C_56;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t252\t252\t.\t-\t.\tID=C_72;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t253\t253\t.\t-\t.\tID=C_71;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t254\t254\t.\t-\t.\tID=C_70;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t255\t255\t.\t-\t.\tID=C_69;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t256\t256\t.\t-\t.\tID=C_160;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t257\t257\t.\t-\t.\tID=C_159;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t258\t258\t.\t-\t.\tID=C_158;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t259\t259\t.\t-\t.\tID=C_157;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t260\t260\t.\t-\t.\tID=C_156;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t261\t261\t.\t-\t.\tID=C_155;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t262\t262\t.\t-\t.\tID=C_154;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t263\t263\t.\t-\t.\tID=C_153;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t264\t264\t.\t-\t.\tID=C_152;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t265\t265\t.\t-\t.\tID=C_151;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t266\t266\t.\t-\t.\tID=C_150;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t267\t267\t.\t-\t.\tID=C_149;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t268\t268\t.\t-\t.\tID=C_148;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t269\t269\t.\t-\t.\tID=C_147;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t270\t270\t.\t-\t.\tID=C_146;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t271\t271\t.\t-\t.\tID=C_145;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t272\t272\t.\t-\t.\tID=C_144;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t273\t273\t.\t-\t.\tID=C_143;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t274\t274\t.\t-\t.\tID=C_142;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t275\t275\t.\t-\t.\tID=C_141;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t276\t276\t.\t-\t.\tID=C_140;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t277\t277\t.\t-\t.\tID=C_139;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t278\t278\t.\t-\t.\tID=C_138;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t279\t279\t.\t-\t.\tID=C_137;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t280\t280\t.\t-\t.\tID=C_136;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t281\t281\t.\t-\t.\tID=C_135;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t282\t282\t.\t-\t.\tID=C_134;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t283\t283\t.\t-\t.\tID=C_133;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t284\t284\t.\t-\t.\tID=C_132;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t285\t285\t.\t-\t.\tID=C_131;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t286\t286\t.\t-\t.\tID=C_68;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t287\t287\t.\t-\t.\tID=C_67;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t288\t288\t.\t-\t.\tID=C_66;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t289\t289\t.\t-\t.\tID=C_65;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t290\t290\t.\t-\t.\tID=C_55;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t291\t291\t.\t-\t.\tID=C_54;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t292\t292\t.\t-\t.\tID=C_53;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t293\t293\t.\t-\t.\tID=C_130;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t294\t294\t.\t-\t.\tID=C_52;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t295\t295\t.\t-\t.\tID=C_51;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t296\t296\t.\t+\t.\tID=C_11;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t297\t297\t.\t+\t.\tID=C_12;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t298\t298\t.\t+\t.\tID=C_21;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t299\t299\t.\t+\t.\tID=C_13;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t300\t300\t.\t+\t.\tID=C_14;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t301\t301\t.\t+\t.\tID=C_15;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t302\t302\t.\t+\t.\tID=C_16;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t303\t303\t.\t+\t.\tID=C_17;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t304\t304\t.\t+\t.\tID=C_64;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t305\t305\t.\t+\t.\tID=C_19;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t306\t306\t.\t+\t.\tID=C_22;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t307\t307\t.\t+\t.\tID=C_63;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t308\t308\t.\t+\t.\tID=C_20;\n' |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/C2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/C2.fasta Tue Feb 18 17:57:28 2020 -0500 |
| b |
| @@ -0,0 +1,15 @@ +>C_10 +VVLCRYEIGGLAQVLDTQFDMYTNCHKMCSADSQVTYKEAANLTARVTTDRQKEPLTGGY +HGAKLGFLGCSLLRSRDYGYPEQNFHAKTDLFALPMGDHYCGDEGSGNAYLCDFDNQYGR +SVRSPLKKLLGFGYNPTYGKSALGDELRLGLVFREEFRKINKALLTGGANVVKAGVSYKD +SKKQGHKLLCDEMDNAVSLLKVLHPKLGCCVGDDNHSYGALSDFFVTCRRLIGKGHIEKE +RKSANECLAKSFQPFCSDLNLTGGGVRQHPGILHLKYAIKLLQATPMYMLLCLHAGKTKL +CDNAADSSEFCQLQDRDIVAEYVAVWKSKKPQSAPHVLKGPHNKKALVVSSCFAADFRIV +AFVVLDSSNDYSDAKASLDDAKLCIESCVFIYAPSLKADGTKGGKYCGKGSIPENCQLRE +HVVACDRAGSDCSGEPSSWSCACKFAIGANMRSLARNSDAATQTIHGTAIRDYTPAVGRS +SGTFVGPECPLSKFVSSYLFVAKDNGGKLFVWVPGGNYHSLWRSFTMNLCNIGLAELPLS +AYRNIKKKGYDGGKAGTLVTLMEFVAQGRVANALFDWGSCNEEGAGLSKQCSETVVGFLQ +QSSDYHRLFPKGYGEVPPRCTLGPFPAFHMLMQAALKGSFRTAQQPSVLFSCKCVKLKYS +SCKYAL +>C_11 +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/C2.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/C2.gff Tue Feb 18 17:57:28 2020 -0500 |
| b |
| @@ -0,0 +1,2 @@ +gi|12345678|ref|NC_012345.1| sim CDS 210 210 . + . ID=C_10; +gi|12345678|ref|NC_012345.1| sim CDS 296 296 . + . ID=C_11; |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/E.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/E.fasta Tue Feb 18 17:57:28 2020 -0500 |
| b |
| b'@@ -0,0 +1,1012 @@\n+>E_10\n+CVLDNYQIALLRNVLPKLFMTKNFIEGMCGGGGEENYKAMTRATAKSTTDNQNAPLSGGF\n+NDGKMGTGCLPSAAKNYKYPENAVSGASNLYALIVGESYCGDENDDKAYLCDVNQYAPNV\n+RQRPLKQLIGYGYSPEYLGDDLHLFKLLDLAILKADFKNGDAALLIGGAAAVRIVTEYIS\n+IQKQADKVLCDDLDDPVRIKALRPRLGCGVGFSYQAFGALSPFLTACKKIVAKAEVERSK\n+MAKRKCLAGSFPPLCPAVKLISYGVKEWPCLNLKCAIFLFQVQPLLYTLLSKYAGKPKFC\n+NFAPGTKQFIELHAHGQLNFQYVTGFPEVRQSGAAPILKGPHNKKAFYISMCLTAPFRVL\n+VMGVRDESCDYSSAKVCGRNRLCIHCIGWARKDAIVSAKGTHPAHCAKSAHVVACRPGKR\n+ASDSVTYTVQEPAIKDYSVGVGRAGGNIVGPECTLNAFLQSYVFHANEEGGKLIGWTGGG\n+CGSYHGLWRAFGVQTCRAGLAKLQHSFGYRLLVKKGYNSGTSGAFMVLLDFIVQGRLIYA\n+LFVWGECNNLVDGTHKACAESVVYLQQQANYRKMFPWGYGEVAPACSKSPFPNHTAHRPN\n+HCNFTL\n+>E_11\n+PKFDSAGRAKHSRNELLNDPDAVVYSSGNAQTMAVKAKHDGAGMTGGKIGNYKLGKPLPY\n+GAKDKSVNKRVSSTKGLARTGGVADCELFPGFVPLIFVRLFWQKLETGTYFADANWGLAQ\n+GIHYAKLASGTAKKYIDLIGDKIHELGRELKVFFSCDHKKAGYKPDFLVGTNPKSLQASN\n+PYAGFEKRNAKQKNGKSGIILAKKRSFALTKVKQFDHSGCLGDCSGKHEVGEIGIKNLAW\n+GCNYLVPKQHNLFLFLRNEPWREIGPLGQSYSLRGEASVGCGPKKDGF\n+>E_313\n+FWEAIIKLSNVEAENSKGNVNATEIALHTHADHPGTERGCVFTSFLVLKKAHKGITADRP\n+RKKLANARLPKGLPFVGSESCCGPKWWRLQPKACSGFGTASGKTLVGRIVLLLKGEGLML\n+GNYFHTGAYANDLMTLAKKVNECWTSEQAACKHKPNGALCDITFQSGPAFESKVLYAKGC\n+YSAAKTDGGQLSDSLLQAKDFKLAPFRLDVQGLPDALTGGGNLSSGACIVASESPVGTTQ\n+SHIHGLESKFYGSFGGVHVAKLTEAGFFLFPAANLTCKAEQLAAILTETLHTTIGGVPFS\n+ATVDAARRYGGEDCSFRTVEKCGVFGRVLTPSGYTIILKLDACFWPGDRGCQLGAFRLIV\n+GGKNRTPIDWDARSEVQPRGLDLVGEDNCKRLRVSLSDTSLLSSQTANNWDECGDSRSVE\n+KKSMGVSLQVGMTYGQSFKVVTPNGKMFQYGHSRPEKLYSGIYAEGLGFVQNVIATTTFD\n+VNDEVAAFFADDFGKLSVGDQLMAEAIKGHVDGPVSQSNKFEYDRKMAGQVGSKIVKSQC\n+LAEETLCVGPFYAAFRHHGAVNENIYVNTKSSNSKAATNLHSAVEAKGLAKARVGLFMNS\n+LHCGLIKLRCGILNRVYCKALMVLRENNQCGFEGDPAHMQFLKPGLFSTKTAGQDKRRGP\n+DTLPIDRVAKLLNGNHLPGATTKGATNDPGQGRLVPFKDTGACKGAGCLFSLRPKPSVAM\n+KGDFHDVIKIVGEPRMPLVALQRLTKYRTPSLCITMTGNFISKGAVRKKTLHANFY\n+>E_315\n+FWEAFISTNRVLHSHSEHEGTDTGCEFPTFLLNEEKGIANDRPRKKLVRQRLPKELAYVG\n+SRPCCRGPSHWDLQPGTCEGVALATGTAASAKPLTGRRVHLTLLLKAEGILLSHYFYTGD\n+YMTNITSLKKMHVEECWAADQSACNHKVDAALCNITFDTGPAYGRKLAYAVGCCSTANTD\n+TGELSEKLLHPRFIKLQLSMLDIQNLPQMLSGCGSLSTASVIVAREEPVVTKQQHGHGLE\n+STFFFAQSGIHPSKLPQRGFSLYPGGEVTCMGQELAAILTESSHPEINEVRFSESRDAKG\n+YGGDNCSKRAVEKCGVHGRVLDPADFTILSKLPPCFWGGICGCVLGKFRLIVDAKEKVPF\n+KWDAKDQVDPNGLDLIGDDECRLQVYQANAFKLTSKVDEKNMGVTREIGMSYAETFKTPQ\n+GKTFQFGLSRPLKLYSAAGIYANSMGFIANAYFAQEIGNGCVADDLKAEGVSGNSDGADS\n+QSAHFDFNRKFDGYVKIVRSHCFADGHLCSVGFYLKSHDGAPTEHVFVDTRGSCAKPCAK\n+LPCVVNAKDLGAATVGAFMTKCCALVVKCGITRKIYCKTGIVLRDHDECGFEGDPTHMEK\n+YLNPSLIARAAGAPRRRGPPTLERGKEGKLNDGVHLSASGKGCTCKPQAGKSAFTERGQC\n+QGYNGCLTHLRPQPNVGMGGDFFDLSKVVRHPPMSDSLIALIRYAKYRCRPMKCPFVCAG\n+VNTCGL\n+>E_13\n+ASIESGGIECKVVPAITLTNIGSGVTDVDDFKESSGSYSSVKGATAALYNGSIFLSAGFP\n+ERVPHDILVDDTHYAVASGCCAICWHVAMEVPLAGQEKICATNDVSFPNCNQAKCRKEKS\n+RFNLQDPDRSRILVVETTMVLFKKKVRKTAAVCALYIEAEYYRERAHYLKSYAQEKGTGP\n+SPLVECQL\n+>E_14\n+PKLDMQKSSKEYCHAHTLLSFVGSPSLKFYGEGFHSCVARPPFYDGDLMGKNGIPLLFGT\n+DDPTKTSRQILHVTDCADFVEGPPVKGKDNVSRFDQDPFVSSTNGYYEPRAEQPKPKQLQ\n+ATWAGGHSLAVPYQMKWIGIRGAGCCIFGGVAKSAAVFETVSDMNGHGHVRYIRRGCTKA\n+KWVAQTCKSARSGRVFFSGRGTRAKKCCQITRAETTRPFASGNEGCHSQTGVFVNFFKAV\n+EPCATVKALPNRQGLGGADIRFLLQGTDFRAAFKAFTVEQNTDLLGKAHHWKGAQTEDDA\n+TITKTMPNENHLALLINSLAKSYKLVYTGKCSLIEYEAASKATSFLPFGKRTDQNFQDID\n+VRHSRHAYLSAHLTAGHITADEANVTCNEASLIVALTRQKTCRGMPGTVLEAGGESGIDG\n+VGMALNVNIKCVKKHTHDVRELKPNEKVNTGIGIKVAKLSICDVEYVEDLNAGAQRPSYL\n+HPSNTGNRLGLVGLCKIDKIANRTLFRPNPINKCLKCRLKTGIKRDARRCEKLAVCYCAN\n+HDDFAPARSVAFACHISDTCFEIRHLCTNDSKFRLCIGFEETSFRIEIEGQDHQYLYVPC\n+GFRRSKIQLFLLVKGPKNGQAPPKCVVTEGTGPEEAISQSLAQLPIFEWSGKSLELIKPG\n+PNPSERKSLRIADKCKVRCAKQRMGDYGVDSPTELILTSHQAAESDLNEADPKSLNRPGG\n+FFVREAAQKPGLKASIFNKQKFCHCEQYYVIGGKKKSALASDLIMRGVSKIGVLYQGGLA\n+MEVCQSLISKYYGAFQSVRPPKLY\n+>E_15\n+ANAETDYPESFKHINAVLHLELKKRFLALYVSTNLACSPYLDVAGYLKIYPFKAVTKLDS\n+SLKNGFANTDKVDEMQKQARVVGFLSTRPEKETTLRFELQKKLGVEASVFRAAYYDLMPE\n+SGMICEIKHGSPGLIELTEHSGLIYATCFQASYICELGYYFFSKVGATFPLKKAARRPVL\n+KSTFAMPAATSVVPVTDNLNGESVHSGYTHGKAHVVALVVCLHDLTSIVVACTLARLGHT\n+HQEEEKGCNKAWIKKLNLSYMESGVEKGPQQCYKLKLKRAVTYKHHAAHGSNLIDVFSLR\n+EKDGEAKHEIKTLGGSDKLNLFSYNLANNTAGIKHIKCLAYSYHLLGGWATPTRPSGPRG\n+GIHLSPCALKSSIDGSGVTLKQNMVDLRNWFTGDAYFNGYIGYSGWLG'..b'LAPRSGSGGRFPPPRLSLLEALFLGTPNADTRLCKS\n+FITGGCELLPH\n+>E_482\n+AHPKGKVLDGCLTASQSQIVWFCCERKRWTKFEAFVRLAQGDGSDVASFAYTPVKEAVAP\n+HIQGEGEDKFGKIKYYVERDKFPEHKCSPGATASESGCHAGSGKQHQHNILVSVGLASRH\n+MQTLATPSGGVSATENIYAPVGSLLLIQAEAFRKGAISAECHKVVRKFAFLIEYACLRSD\n+NLGTTNQFPDLDYLNFAQTKALARLKSGRVRVLLDFEWINEGSIKVSNHLGCEDNLGKGL\n+RHAVYLSVNDALGGYYEVTKYRHVPSRSRPDRHNLGDHLIDYRVTHDFANYANGMAPMKL\n+SPDSLRLKEQDPCSEGRAAVQQYGMVLSGTLEASTGQLEADDTTSDYSFGDEGKKDWVGD\n+AEAAKIATKLRHESGIIKRLCFKICIEHTKCPLRPFYLSPFLRAAADDGVNLCNYDIGSS\n+LISAAGGNADNQKRFHHKASNAFVRNHVCKSIGDEFLVGRPICVLTCKEKFRDFQALYGH\n+GQCLGQCACVKDCAILQAYSGVTVLQNASELERFTRNDDVDELGEFARLAKTYALGTFEQ\n+PTFSSPGLWSLHLKDNLITQIGGQSEKRSARIHLADAAQVAFGVNCLGGYYLRLKDDDDF\n+DWPEHTGGKIFNSKRMGMKIEEQQTLKESLGLLEMEVLFATTWAAGCQLVKPQYAGHQRG\n+PKGKRRALAPRPGSGGRFPVVQLTLLEAAFLGQPNLEHADNCLCKSYITGGCELLQQ\n+>E_483\n+AHLAGMVLHKCLTASESQIIWFCCEGRKRWKGETFVHLAQGEGSAVASFVFTPLKETTAA\n+HIQGEREDDHCKLGKIRYYKDREKFRAHKCSSQSTASDAGCIAGSGQYKKLQLSILDTVG\n+LESTHMDSLATPAGAVKRAELKGPAPFVLDKPHKRAEAVILSKHQLVSYEAIVLPVYGDA\n+CAKSKFRHVLKSTLPGNCSKSSERIYTPVGALQSIAREAFAISPECHRVVKTFAFLIEYT\n+CMGSFPDLQSMKLCHTKRLSRLICGRLRVLLDDWFNNDSIKVSNHLGCENEDLGKGLRPS\n+VYLSVNDLGGYYEATKYGHVPSKSHPPEERHELGDYLIEYRVTQDFANYKNGVAKMKLSQ\n+DCLRDKEQEPCSEARSAVQVFGLVLAGTLDLSTGLNMWSRVWQMEGDNSNGDYNFADNLN\n+KDWVALANAESVVARLRHNTGILKRVPFEICVEHTKCDLQPYHLTPFLRVADDEGVGSCN\n+YDIGSNLLGAKLCTPGGHSDNQKLFHHKAAAALIRHHGTKNVGDELLVSRSCVATCSEKF\n+KDREFDCAVTRAYAGVTATQNASDLERFTRNNELEQLGNIALAKTYALGAYQQPTFSTPV\n+LWKLHLEDNLITDLGDQSEKRSGRINLAAGTQVAFGVNCLGGKYFRLKNDDDFDWPEHAG\n+GKVFKSFHFMMKRVGLKIAELNTLKETPGLLDMEVAVTWTGACQLVRPHAAGNQPGPKGK\n+RRSLAPKVGSGGRLPLPRLTLLEAAFLGQPNADNRLCKSYITGGCQLLPH\n+>E_484\n+AHPQGKTLDGCLTASQSQAVWMCCYGQKKWGFETFVKLTQGDGSDVASFVFKPLKETLAA\n+HIQGEATEEHTLGKVKYYVEREKFRAIHKCPSGSTESDGDCRAGSKHYKQHQHTILLSVG\n+LEPTHMQAFASPPGAVKSAELKAPASFISANPHKRAAAVILPKHQLLIFEVIVLPVYENG\n+CAKSKFRHALKKTLPGNCSSSSERVYGPNGALLLIQQQAFAIVAECHKVLRNFAFLIDYA\n+CLRSFPDLQSMHLSQSKLLARLKSGRLRVLLDFEWINDGSIKVSNHLGCENDYGKGLRPT\n+VYLSADEALGGYYEEAHYGHVPSTAHPDHHALSQHSIEYRVSQDFANYKHGLAKMKLSPE\n+SLRDKEQGPCGAAPSAIPAYGLVSSGTSESSTGQMEGDESHGAYPFGDNLHKDFVTLADA\n+ESIDPKLRHISGIIKKLCFKICFEHTKCPLRPFPLTPFLRVAKDKVVGACNYDGEQLISA\n+ALCSPGGDADNQKRFHHNANSALVRHHVCKAVGADLLVGRPICVATCSEKFRDFQALGKP\n+YGHGQCLMQCGCVKDCEVTHSFSGETLLQNAAGLDRFTRKNELDEVGPFALAKTYGLGSF\n+EQPTFESPVLWSLHLKNNLITNIGDQWEKRSGRIHLVDGAQVAFGVACLGGFYLRLEDDD\n+DFEWSEHTGGIFKSFNFMINLVGLKVAEQKTQKETPGLLEMEVLVTWAGACQLVRPHISG\n+NQPGPKGKRKSLAPRSGSGGKFPVPRLTILEPAFLGQPNVDNRLCKSYCPGGCELLPH\n+>E_485\n+AHPQGKVLKYCLTASQSQVVWFCCEGRKRWDFKNFVRLNHGSGSDVAAFVFTPLKETLTA\n+HIQGSAEDEHCKLSKVKYYAKQQKRAARCSCLGTSSQAGCRAGSGHYKQHQHFILVSVGL\n+ASTSMQNLATPAVAVKSEELKPKASLVAAKAHKRAASVITPKHQLLSYEVVLHVYDNGCA\n+KSKRIYGPVGAILLIEQDAFAVSAECHKVTRKFSFLVEYACSRSFPDLQSMNLAQTRILS\n+RLKKGRLRVLLDFEWKNGGSVKVPNHLGCEDDLGRGLWPTVFLSGNDALGGYYGETKYGH\n+VPSKSHPDRHALGDHLIEYRVTQDFANYRNGMLKMKLEPDSLRNKGQEPCSNARRAVQVY\n+GLILSGTLEQSGGQVEGDDTDGDYAFGDPLYQDWVPTAEAEIDTKLRGNSIIRRLCAKIC\n+LEHTDCPLRAFHLNPFLRVADDDGIGSCNYDVGSSVISASLYSPGNNADNQKRFHHKASG\n+TLIRHHVCKNVCVATCADKFRDFQALGKPYGHGDCLMQCACVKDCAVLHGYSSVTVTQNE\n+SDLERFTFDTDLNNLGNFALAKTYALGSFEHPTFSSPVKLWSLHLKNNLVTNVGDQSEKR\n+SGRIHLADGGQVAFGVNCLGGYYLRQKDDDDSDRPENTGSKSFFMVKRAGLKIPEQKTLP\n+GLLGLEVLAAWAGGACQLVRTHAAGHQPGPNGKRRSLAYTRSGSGGRIPVPKLILLDASF\n+LEQPSSDNKMCKSYIVGGCALLPH\n+>E_486\n+AHPQGRPLVLDGCLTILKSIAQVCWFCCEGKKRWEFETFVWLAQGDGSDVASFVFTPLKE\n+TIAFAHIQGEAEEEHCRLGKAMYYTERNKGKAPKSSSGAEAPGAGCRAGSGGYKQHQHSI\n+LVSVGLDTTHMRTLATPAGAVKSAEFKPPAVWIFIAAEPHMRAAAIILAKHQLLSYEVLV\n+LPVYEDGCAKSKRIYGPVGLILLIQQSSFAITAECHKIVRTFKFLLEYACLRTFPDLQSM\n+TLDQTKILARLKAARTRILLNLEWINDGMIKVDNHLGCENDHGKGLRPTVYLCVSEAAGG\n+FYPEETKYGHVPSKCHPNRHALGDQLIEYRVTQKFAKYKNSMVTMNLEKDKLRAKEEEPC\n+SQARSAVQVYGLTLSGTLEPSKKPMEGDDSNGDYSFGDNQYKDWVSLAEPDSIDTKLRQN\n+STIIKRLCFKICIEHTKYPLRPPHMNPFFRVADDDGIGCCNYDVGSSSFSAALCPPAGCG\n+LYHRNKHYPGKTDNQKRFHHKASSALIRHNVCKDVCVAKCAEKFRDFQAQGKPYGHGQCV\n+MQCACIKDCAVTHGYSGVTVLQSASDLERFTRNNDLDELGKFNLANTYALGSFAHPTFSS\n+PVLWSLHLKEGLIADFGDQSEKRSGRSHLADDTLVSFGTDCIGGYTLRLKQDGDFDWPEH\n+TGGKIFKSFHFMVKRIGLKIGEQMTLKADPGLLEMEVLVVWTAACQLVRVHATGHQPQPK\n+AKKRKLAPRSGEGGKFPVERLTLLEAAILGQPDANVRLCKTFIVGGCEILQH\n' |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/E.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/E.gff Tue Feb 18 17:57:28 2020 -0500 |
| b |
| b'@@ -0,0 +1,310 @@\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t1\t1\t.\t-\t.\tID=E_319;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t2\t2\t.\t-\t.\tID=E_317;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t3\t3\t.\t+\t.\tID=E_366;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t4\t4\t.\t+\t.\tID=E_367;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t5\t5\t.\t+\t.\tID=E_368;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t6\t6\t.\t+\t.\tID=E_369;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t7\t7\t.\t+\t.\tID=E_432;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t8\t8\t.\t+\t.\tID=E_433;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t9\t9\t.\t+\t.\tID=E_434;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t10\t10\t.\t+\t.\tID=E_435;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t11\t11\t.\t+\t.\tID=E_436;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t12\t12\t.\t+\t.\tID=E_437;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t13\t13\t.\t+\t.\tID=E_438;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t14\t14\t.\t+\t.\tID=E_439;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t15\t15\t.\t+\t.\tID=E_440;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t16\t16\t.\t+\t.\tID=E_441;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t17\t17\t.\t+\t.\tID=E_442;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t18\t18\t.\t+\t.\tID=E_443;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t19\t19\t.\t+\t.\tID=E_444;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t20\t20\t.\t+\t.\tID=E_445;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t21\t21\t.\t+\t.\tID=E_446;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t22\t22\t.\t+\t.\tID=E_447;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t23\t23\t.\t+\t.\tID=E_448;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t24\t24\t.\t+\t.\tID=E_449;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t25\t25\t.\t+\t.\tID=E_450;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t26\t26\t.\t+\t.\tID=E_451;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t27\t27\t.\t+\t.\tID=E_452;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t28\t28\t.\t+\t.\tID=E_453;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t29\t29\t.\t+\t.\tID=E_454;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t30\t30\t.\t+\t.\tID=E_455;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t31\t31\t.\t+\t.\tID=E_456;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t32\t32\t.\t+\t.\tID=E_457;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t33\t33\t.\t+\t.\tID=E_458;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t34\t34\t.\t+\t.\tID=E_459;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t35\t35\t.\t+\t.\tID=E_461;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t36\t36\t.\t+\t.\tID=E_462;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t37\t37\t.\t+\t.\tID=E_463;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t38\t38\t.\t+\t.\tID=E_464;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t39\t39\t.\t+\t.\tID=E_465;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t40\t40\t.\t+\t.\tID=E_466;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t41\t41\t.\t+\t.\tID=E_467;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t42\t42\t.\t+\t.\tID=E_468;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t43\t43\t.\t+\t.\tID=E_469;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t44\t44\t.\t-\t.\tID=E_594;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t45\t45\t.\t-\t.\tID=E_593;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t46\t46\t.\t-\t.\tID=E_592;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t47\t47\t.\t-\t.\tID=E_591;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t48\t48\t.\t-\t.\tID=E_590;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t49\t49\t.\t-\t.\tID=E_589;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t50\t50\t.\t+\t.\tID=E_540;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t51\t51\t.\t+\t.\tID=E_541;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t52\t52\t.\t+\t.\tID=E_542;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t53\t53\t.\t-\t.\tID=E_384;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t54\t54\t.\t-\t.\tID=E_383;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t55\t55\t.\t-\t.\tID=E_431;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t56\t56\t.\t-\t.\tID=E_382;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t57\t57\t.\t-\t.\tID=E_381;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t58\t58\t.\t-\t.\tID=E_380;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t59\t59\t.\t-\t.\tID=E_379;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t60\t60\t.\t-\t.\tID=E_378;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t61\t61\t.\t-\t.\tID=E_377;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t62\t62\t.\t-\t.\tID=E_376;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t63\t63\t.\t-\t.\tID=E_375;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t64\t64\t.\t-\t.\tID=E_374;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t65\t65\t.\t-\t.\tID=E_373;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t66\t66\t.\t-\t.\tID=E_372;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t6'..b'2345678|ref|NC_012345.1|\tsim\tCDS\t246\t246\t.\t-\t.\tID=E_419;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t247\t247\t.\t-\t.\tID=E_418;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t248\t248\t.\t-\t.\tID=E_417;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t249\t249\t.\t-\t.\tID=E_416;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t250\t250\t.\t-\t.\tID=E_415;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t251\t251\t.\t-\t.\tID=E_414;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t252\t252\t.\t-\t.\tID=E_413;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t253\t253\t.\t-\t.\tID=E_412;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t254\t254\t.\t-\t.\tID=E_411;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t255\t255\t.\t-\t.\tID=E_410;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t256\t256\t.\t-\t.\tID=E_409;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t257\t257\t.\t-\t.\tID=E_408;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t258\t258\t.\t-\t.\tID=E_407;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t259\t259\t.\t-\t.\tID=E_406;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t260\t260\t.\t-\t.\tID=E_405;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t261\t261\t.\t-\t.\tID=E_404;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t262\t262\t.\t-\t.\tID=E_403;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t263\t263\t.\t-\t.\tID=E_566;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t264\t264\t.\t-\t.\tID=E_402;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t265\t265\t.\t-\t.\tID=E_401;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t266\t266\t.\t-\t.\tID=E_400;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t267\t267\t.\t-\t.\tID=E_399;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t268\t268\t.\t-\t.\tID=E_398;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t269\t269\t.\t-\t.\tID=E_397;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t270\t270\t.\t-\t.\tID=E_396;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t271\t271\t.\t-\t.\tID=E_395;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t272\t272\t.\t-\t.\tID=E_394;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t273\t273\t.\t-\t.\tID=E_393;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t274\t274\t.\t-\t.\tID=E_392;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t275\t275\t.\t-\t.\tID=E_391;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t276\t276\t.\t-\t.\tID=E_390;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t277\t277\t.\t-\t.\tID=E_389;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t278\t278\t.\t-\t.\tID=E_388;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t279\t279\t.\t-\t.\tID=E_387;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t280\t280\t.\t-\t.\tID=E_386;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t281\t281\t.\t-\t.\tID=E_339;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t282\t282\t.\t-\t.\tID=E_328;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t283\t283\t.\t-\t.\tID=E_327;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t284\t284\t.\t-\t.\tID=E_326;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t285\t285\t.\t-\t.\tID=E_323;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t286\t286\t.\t-\t.\tID=E_321;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t287\t287\t.\t-\t.\tID=E_337;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t288\t288\t.\t-\t.\tID=E_1;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t289\t289\t.\t-\t.\tID=E_430;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t290\t290\t.\t+\t.\tID=E_3;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t291\t291\t.\t+\t.\tID=E_4;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t292\t292\t.\t+\t.\tID=E_5;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t293\t293\t.\t+\t.\tID=E_6;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t294\t294\t.\t+\t.\tID=E_7;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t295\t295\t.\t+\t.\tID=E_8;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t296\t296\t.\t+\t.\tID=E_340;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t297\t297\t.\t+\t.\tID=E_338;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t298\t298\t.\t+\t.\tID=E_9;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t299\t299\t.\t+\t.\tID=E_10;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t300\t300\t.\t+\t.\tID=E_11;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t301\t301\t.\t+\t.\tID=E_313;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t302\t302\t.\t+\t.\tID=E_315;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t303\t303\t.\t+\t.\tID=E_13;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t304\t304\t.\t+\t.\tID=E_14;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t305\t305\t.\t+\t.\tID=E_15;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t306\t306\t.\t+\t.\tID=E_16;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t307\t307\t.\t+\t.\tID=E_17;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t308\t308\t.\t+\t.\tID=E_18;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t309\t309\t.\t+\t.\tID=E_19;\n+gi|12345678|ref|NC_012345.1|\tsim\tCDS\t310\t310\t.\t+\t.\tID=E_20;\n' |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/L.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/L.fasta Tue Feb 18 17:57:28 2020 -0500 |
| b |
| b'@@ -0,0 +1,506 @@\n+>L_10\n+CVLCKYEIAALGNVLNKLFMTKLEDKVCGGDSQVYYKADARLTPAKTSTDNANSPLAGGY\n+HDNKLAFMGCYPTSAKKYNYPQQTIKAQKTDIFTLTARDHYDENTAGSYYCSFESVYACD\n+TRRCTNKPVVRAVKKLLGYGYRAKHESPYGRSTLGDNLHNVKQFTAKFYLKLSVFRDDFR\n+SVPKKLLIGSAAVYRAVTDYKSVSVGEQYETLTKKGNKENLGGTYSPVCAARGIDVACAD\n+KDGSQRKQVLSPRLACCVVFDYTAFGAIGELLLTVMSLITKVEAAKEKEGTNKCLVGSFP\n+CAENTLSGAGVKDWPGCLSLKCTFTLIQVTPMLYLMLCKYAQKPKFCNLGSNTRAFHQLQ\n+SHQMVSEYVEAFKENKPVGADPVLKGPREEKALYVGHCVPLSFRILSKGAVGEETDYSSS\n+QMAKTSLDQEHLCVGCTPWDARKGAAYKCKGTQQEHSAKSANVVASKVGKPDCIKGRSAW\n+NCMCKFVIGKDRITRTGDAVARTHENAIKKYAVAVASGVGTIMGPECVISDFVLQAYLFV\n+AGGTGGNVISWTPAGCGTYQALWKKYGVNTCWSGLVGLPLESYRQQLQKGYNRDSGGLLH\n+IMMGFVVQGRLVSALFPWGECRADLIQLTQKLTAQGGGYLQQSVKYRKLFPPAQGPVPPP\n+CTIGTFLTFHNLVEQGLKGTFNTAKRPNSCAFTF\n+>L_11\n+PKFDSVVNKSRSDLFNAPEAVLFTNSECQTITVKAKNKGTGVAAEKVNGYNVSQPLEPYS\n+MSKKPVPNCGLEGSKELGRRNAAATCIFPGLIPLVFIRFQDTGTYLGDPSWALLEGVHYY\n+THHNVRDLAHKPNTHKSAKKYINIFGAKLRPAGKELKSFFDCKKAAIRLHNKAGFLGETD\n+DYILGTNTDALQAYHPFEGFANKNGKRKNGKGGVILARARAIALKAKRQFHSVTLNFIGP\n+IGDCSGKHHIGQGLAKAVWGCTYLVPSHADQILLLLMDTPYREVGPLGKNYSLGHLGCEE\n+KKDGF\n+>L_313\n+FWHGFDKLNPHGAKNSQSTLNVRNKSLTTVANHSGKETGCAFKAFLVLKSQHKDITADRP\n+RNKLVNPYVTSEEVHFSREKLPKDLGYVGARYCVSGPKWWHLQPTECGLSDSTKPLCGRK\n+VLLLKVIGIMLHNYFATGAYMDDLFTLKRQTQECLAVCDPNFQSGPNFEAKVEYKNGSFA\n+PAKTNAGQLGTKLLQPRGIKPLPFELNVQNLPDMLGGCGDLGSGHDGPVIIARDTAVLAK\n+AQNKHGLESKFFASMGGTHSELAEAGFFLFPAGNYLICAGEKLAILTQIYTLHAQAGGLR\n+FKLSATLKNQFGRVYGSEECSFHTLECGIFGRVLEPTSFTIVGKLPPCFWGGDRGCALVQ\n+YMLVTGGKGRHPIEWEARPQSADVVGDDTCERSPVYQSHAFKLTSENANNWDEIGDSQKM\n+MNVGRQFGMEYGEGIKTDNDKIFQFGLSRSQKLYSTVTIYDDSIGFTSAGFFPDQIVTPS\n+VAKALFASGVAGHFQGADAQSEGYEFESKEEGVISIAKSCLVEDTLSPGFYTDFHHGTPE\n+NGVYCDTRGSHTKASCSLPSAVQSKELGTGAVGLFMSAFCCGLVKIMCTVTSKALCKTGF\n+LVVRDNDQCGFEKSPAHMRTYLSTGKYTPRTDGATKREKPPTIPLTPKIAKLGAGDQMHS\n+ATAAGCTNKPGVGLSGFTDAGEETKGFESCMFRLRALPTLGIQGDFFGIVPVVGEPKMNL\n+VTLRRLTRYRPPAICRTVKIAKFICTGGVRDKLLHTHGN\n+>L_619\n+EAVKKECQVVAACTLELGCDLVDGVTDLRSKFKKSNGGYTPALDLTSSLFSGKAFASGGY\n+VIVRNKDIVNANQFACCMSCCNTGWQVVIEAPLASSEKVGYKAHVNFPNCEEIVCKTERS\n+RFNLNSPARPDTLVVADAMVLKKSCKKTPVVCTLYIQKYYADRVQYLKDYSQGKISIGCD\n+I\n+>L_621\n+DSVKRDEASCKVVGACTLNIGKSDLAGGVSDVSGLKQSEGGFSPALGTSSGLFNVKIFAE\n+AGYAVLQPKDILVEEAHFSVCMSCCAVAWQIAIDPPLAALEITGYTVHVKFPNCEQIVCR\n+KEGSRLDLNDPRPVTLVIAAAMVLKKACKKTPFVCALYKQKYYNDRGQYLKGYAQDKAKC\n+IGYRV\n+>L_623\n+DSVKKSIAQLAYNKRDGVCKVVGACTLHLGKSALADGVTDVDELKQSEGGFGPALGTTSG\n+HYNVKIYAAAGYAVVQPKDVLDATHFAVCMSCPAIGWQVAIEPPLAGTGTPGSTVHVGFP\n+NCEQIVCRKGRSRLNLHHPERPKTLIVAEAMVLKKACKKTPFVCALYIQKYYNDRGQYLK\n+SYCQEKAKCIGYQI\n+>L_14\n+PQADIQRKFCHANALLFVNAPRVENFGDGFEACVARAPFYEGNLAGKGGVLLLFGTNDPI\n+MTAHKAGQVTGCVEVKGPFFHGRDPTGRYDHQKKSRLEAFVSELKSYFKQRAEQSIPRQW\n+EATWVGKMSLAVPYNIKWLKVRAGGCVSYGLVSKSAAVFDQVAAKVHDEHGHIRYVVWKC\n+TNARRHALTCKAGRGGTVFFCGRGTRVKKCSSTRTDKNQPFSSANQLCQTETGVLLDYFN\n+GTLGALPAAQGLSAGDVRFLLLSTNYNGPIKIYAVGRNKELLAKHHKWKGAQTAGDATIK\n+KTAPNESFLPFLVRNQKSHKLVFTGKSSLKAYASLAKSRAILAFGPHPEQGRTIYNGARS\n+IGSRYSVNEAAESCAKANSIVALTRKKSYRNMHNRILELSGESGLDGVIALNWNIKSAKK\n+QDDDAHEIKPDALIDHTVAGIEGAKLWICQVEYLADLNASAPVADYLHSAYGNGLMGVCR\n+INKIASRTMPRQHDVNSCVTCRQKSGISGAKKCATRHVRYSTEHKEFFMARSTHFRCNRM\n+DTGSFEILHANQADARGNKRLCVSFAQASGRTSKAGQDNLYIYISIGFKRCQERRPKKCK\n+IRCGKKKVGEVDTPPNYVLNYSQGDADLQDLIPALNKPGDFFVRSATDKQSANASIFNEK\n+QFCNCNQSGVAAVVGKKSRALSSEQIVKGPSNVGGLYQDGTAMQVCEPLISNYGCGTYTS\n+IRPIKYLC\n+>L_15\n+PKGTNYQGFRTETLHLDAKTTFTPAFYVTKELACAPCYLHVEGFLMVYSLKEITKADEGP\n+LKNGKATAKVNDLQEEARVATFENRLKSELQKRLGVESADFQAQYYSLLNDVGLVCDSKY\n+KAGLIGHSNHKELIDAACFQCGYHCDAYIFFSRVGSQFPKRKAAGKGPFRGVFATPPAKA\n+VSTIHDHLSEGHWVHTIYTNGKAHVVALNPVWHDLGVLAVAVSLGPLAELDEGKNRGCGK\n+NWVKRLTLGYLESNIPYVEGTVKCYKVKLKRATAVGSHPNDGYVMANVYPLKMPSGVGAS\n+KHEVDAFGNSENLSLFETNLGNYTNGTKKEKCQDVEYRLWGGSNPPTKPAGARGGPHLCG\n+SSPTGATGVTEKENMEELRRFAAGDGFFKGYIQYGGWFGGLKDKAWLEKFREEFGVVSNG\n+RDKRTGELKHVECPIQVQKPYNNPLILHHEKDCGRKTRVHGSGGEKDVGPWRGDTNTKQD\n+KQKFGSGKL\n+>L_16\n+LDDDETQLSDIKDEECRLFDFPGKHVGGFGACASQAAAGLGQIFHCAVGTGRLGLVNVAD\n+VRNSSSTRAHHVKLTHDSGLGPSAFKILLVPQAIKLVSITDESSNPVDVADLPFHNPWND\n+ASYFAQRTHGKWENGVLKTATDKDASHLRFLTRNLYHQVSFIEIQTLADESLHVSGISPR\n+YYHQSRAFDEYLSVPPAERRKLDECTSDYNGKQAKLAAQIVTRPFGIDSNIALLESAGNS\n+'..b'HGDASVAKSKELESLKVQGFEDSTTILGRGDGDVNEPVYDHTKFTLAVVGRLGQVLCST\n+ILTSQMPTVKGQTCDNVLISHYCLLMALPCQTLVVVKNHKRLKYQSYSNSFMGDARNEHY\n+GSPNSTAIKHVRVLSVCKNNFFEPCLHPTSVAGMKGVLAGACGEDRCKETQDQEPSTEPR\n+ECPGLKMVQHMRVSAGNLIAYNVSFFIKDTALSNANEAHTGGVASLRTATHTWGVTANRV\n+DYFNAVLKGYHTALVKTTRCGVGFLKGAILQFIPLVKCFVVTKVAHVCVRVDQKSGNDIR\n+DCRSWLGKAKGAQDDVTNFAKSPALENSKGKGANSRSPDGTAICMSSVAVEKCLGGRCVY\n+GKTEPEGLTNSEFEEPKGRAESYTDSVATLETLAQCGYAISDTAALPLFCLLLGAHDTQL\n+APFDRYGPESSKGIQLNELAYLEAYVSGNCQNKLSQKVGLDEGEFSLQKPIAVPAPYPKD\n+TCVGTMVSKSNSALVSNTHSETASQPFVCCGSKHLVLKVEACNLVVKNGTKKDIVTAEKE\n+PCQYNCGHGAVIAKLTTEDSQLYGPDVVCMKGPALCNSKKDIEPSKLPALVWSMGGKKCP\n+AENLELRYINFRLLYPEQAEPENSDLAHKSS\n+>L_5\n+NCESGNAEADESGSGNYAKCICSGFRREIWQLTMEADANIEHEHKGASEEPISPKGDNVN\n+VLGKDCEKPLVHQKSKDDLKASARLLIKCVSKNAWHNPLQGNSLPGYANKWGVALLNLIL\n+LYSFKALSRAIALRYTGGAKDSPPFINESVVFGAPAAHILVTSMSGNMHGEKHPQRSSVS\n+CAAVDRSKPDTKRAADPRKAQLEGIFDERLHKCVKVSTGEVVNGVHALYAKLYRTPPPVT\n+DAKCFVSKDKGAINEEGKLIGQKVGGVLAPIGRGHAHLFVGNKAAFPMPVNVACLSTGSG\n+MADTGEGTNGDDIAADKSANEQIKIVGALQNHGRPLEFNKGSGPFQLNDKLEEAYFYQCT\n+QHEHAAAHKHARVTSCANGAQTSIWGCQFALLFLPAGFKTTPGLQRFWEFGHAGHLDTQL\n+HGETCLMKAPKTCAHLVVVERWTYSLQLEPFATSQNKAVIFEKESSRSLFNCYPLKEKKN\n+SGVGDTKKTPEVGTFECVIKPYRWQILADAKKNKTLRGTSFAFCSALHLTSPVLRNQIAL\n+RCHTDKVSEETWQMPATFASSVFGVKVIFNERCVTHMSCSSEGEAGLHDLVKAGLQRAKN\n+PLSHPPVSYPLTIVYKVDAKNVGQLSAPCNRQAIQKEKMQSNGLVSKCCCTRTDTAPSTL\n+TKASEVFPLPISAVQVAGLAATHADEPYESFAWAMFTIGEYTQKVKNGQKADTGLGVPCL\n+VHEYGPAEAFDRHYRGSQDCDLRQGALWENASANLRVNVKPEAVANNTCGKTGGSDKGDH\n+DLVSVETVKETLNSANVAEVTAHFNQSIGCILCLKQLECGLSAQSIVKKQNGKKKIETPK\n+VQTVQAALKLKGRCSVRQHNVWAFTNSPVVVAGSQYAHKGIKLLEINAEEQVLIAGNAPR\n+FPGQLGTGSQF\n+>L_6\n+QLPFSWYFKPDVRLIIKEELACHTTAAQKMREPMLPLRRITDAEPAGFIEPLNGLIVKPH\n+DDHPVGDAFKPRIWCNTEYVLFQGYAGHHTAGHNLHKHFLARQERPNEYLTPMGMGPGDV\n+LKGRQGGGFFYVQKELPLWHAIGAGKVKKLKKAFYIRKADMRFHPSFKNHQCVELSIVDG\n+LLNAMATPGSPQLFLNRGDEDLRGEECNSVNTFADKLLRTTMDPCEASGYHASKTFGRES\n+IGDHPSYVLPGGLRMTWDTDEECMIMKAYLIKAENYLLSKPKATTTMVSPYSFFDFARLH\n+HLLPPLGASATGLDCAVYDYVVTDTIFREHVKNQACPAVVYSVNGWSKELIHGKLSVGGG\n+WEQGLDGPFKYHHTQEPFEDKVDVKGAIPVDTKFKAGKFKKHKQSQLINGGGSLYKESCF\n+AHKMKRERNKTPDTGAKNGQGIVQANMSGFTVDGMRALQPEPAQSANVTAGVLAVAVAAV\n+SYFDRVQTTNCEVYASGFWPQAVRGKIKMNQAPPIAEAFFKLGKSELCDGEQFTIGADQP\n+DSKVLIGRASGLCHFLMTPPIEAGWLTTNISQYENDAGTHQDVAKDASVTANFFCEVTVV\n+GISITHGLSADKRSIFRGVISATQSGSVPLTGLALVPPVGLSPQTLTNRLAGLIGYGKLA\n+CLKCTVYKSTRRTLAIVLLEYRVSVWIAKEPRAKLVMNAKAHALHLTHRHSSDRMPFAFS\n+GRNCKAADQPGILTHNKMCQCGDFGLPHEKYGFAHLSRSSFGVSCTACSNPTIVSALHRA\n+ESIHRSGAWLNSQDSTETGTNLFGPTSKESRESICGNQFSVTATIGQLGYVTDVLAHGMV\n+LAFCDFAKTASAGPPKEKVNCDDGHGGLMLEANVFSEESDVRKHLGLSEKGYHCVLTSKT\n+LVKFLIKNQTFHCGAEGCVPTGSGAFGD\n+>L_8\n+CRLPGGVNERAFGHVNDKDLCMLPSPVFCTQKGKEHPPNKEYQMAGSKPPTWPAAQVVDC\n+RHELRTYTGQLPMRSATDLGPNVKSIYTVSERGFKVGQTNHAVCFEAGNVEDKKWKMCHG\n+KNYGRSESWLYFSMNEKANGHLKDLHPSAYQRPKKWTGMRDFGATTKTGLRLVAFSDPSG\n+ACVDMPYLSDCPRGKLSRPTIPPGAGLTVEFTAASARCNKLAEIANAAAKAQKFFTTGIM\n+TSAFLAAKSAVTPTHENKTNGLSLQHPNKSGEELKDYAVKPFGLVQSKLAGTAHAQMIYK\n+DPAGSGYFNNFVTNYPKITHDLIFCPKGGLEFTNGVPFGSPLAGCQLYKSTFPVKSLGKA\n+CEIFSLRRMALSQENKQHVNDHLTAKVGANGPSRGIDVQVGCAHEPNCGGPQLREDFFCL\n+TLGAAHGRFVKSLARDSLQLCFHADITPPLVISISTKILGKVVKLRGASGETVELASAQA\n+VASRPSKQAERARIGFCCGSFSIHADATLQSGSCTGGTDKKLALEQDDDPCVTARQGSGL\n+QRAGQPIKSRSHEACKADSLSDKAAPGQSWTMEIGVETYQVMQGNGPRRTSRSTLYAEGG\n+VIDWFKGAHNSYEFTGIVCSGIRDMLTPQDFQDIKEQTGDLSCMAVNCNAANDIHCSAGQ\n+VLPFKERLVCRHATSGKLINDLSGTSSKVGGMKLPLSSTHFLKLTINEGGPVRTGADSHC\n+SGFSCGCKALKLKDFIPSRQLGSVTGGKQVVTLPNKEGGDTTNLPKEYANTGGMCAVCPN\n+SAHGTGGMTVLSLGAFGYRYTCLVGVEDASKDLLVGNGLAFYHTLYVSLHGKVNHTDSPG\n+DWVSFGIHTSENKSTCTGNGCILHVSVHSQQFGDFLACKHGKQRVPDKERYYYDFAANAV\n+PGTTTPSGILLRTVRTAKSPAKFHFG\n+>L_9\n+LALHHDDACICTRAVGFFYTQFKQEAPVSCASVNKEFDHFSVDKKDPWAAIGLASAAGNN\n+GHNFVAKNKTKQYRSRQRYSRAGSGPIVRALFTAYATTIQNTHTFTTPLGKKRIVDNALR\n+DGSVSRACLPLELSPFVRIRCACSGGLAGAAGFFTVVVPLLLVLLQVNGSLKLTWLGAMY\n+AVFPVLDLRRVLLVVTADTGLETFRPAPNGRHSKDCAT\n+>L_648\n+LYLHHDDACICTRAVGFFYTKFHQEAAVACASVNKEFDHFSVDKKDPWAAIGLTGSTVGN\n+NHHNFVARDKTKQYHSRTEDQRYSRAGSGPIVRALPTAYATTIQNTHTFTTPLGKKRIVD\n+NALKDGSVSRECLPLELSPFVRIRCPCSGGLGAAAFFTVVVPLLAVLLQKSGSVKLKWLG\n+AMYAVFPVLDLRRVLLVVTADTGLETFRPSPNGRHPKDCAT\n' |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/L.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/L.gff Tue Feb 18 17:57:28 2020 -0500 |
| b |
| @@ -0,0 +1,41 @@ +gi|12345678|ref|NC_012345.1| sim CDS 1 1 . - . ID=L_319; +gi|12345678|ref|NC_012345.1| sim CDS 2 2 . - . ID=L_317; +gi|12345678|ref|NC_012345.1| sim CDS 3 3 . + . ID=L_617; +gi|12345678|ref|NC_012345.1| sim CDS 4 4 . + . ID=L_6; +gi|12345678|ref|NC_012345.1| sim CDS 5 5 . + . ID=L_7; +gi|12345678|ref|NC_012345.1| sim CDS 6 6 . + . ID=L_8; +gi|12345678|ref|NC_012345.1| sim CDS 7 7 . + . ID=L_9; +gi|12345678|ref|NC_012345.1| sim CDS 8 8 . + . ID=L_648; +gi|12345678|ref|NC_012345.1| sim CDS 9 9 . + . ID=L_10; +gi|12345678|ref|NC_012345.1| sim CDS 10 10 . + . ID=L_11; +gi|12345678|ref|NC_012345.1| sim CDS 11 11 . + . ID=L_313; +gi|12345678|ref|NC_012345.1| sim CDS 12 12 . - . ID=L_623; +gi|12345678|ref|NC_012345.1| sim CDS 13 13 . + . ID=L_333; +gi|12345678|ref|NC_012345.1| sim CDS 14 14 . + . ID=L_2; +gi|12345678|ref|NC_012345.1| sim CDS 15 15 . + . ID=L_3; +gi|12345678|ref|NC_012345.1| sim CDS 16 16 . + . ID=L_4; +gi|12345678|ref|NC_012345.1| sim CDS 17 17 . + . ID=L_5; +gi|12345678|ref|NC_012345.1| sim CDS 18 18 . - . ID=L_635; +gi|12345678|ref|NC_012345.1| sim CDS 19 19 . - . ID=L_633; +gi|12345678|ref|NC_012345.1| sim CDS 20 20 . - . ID=L_631; +gi|12345678|ref|NC_012345.1| sim CDS 21 21 . - . ID=L_629; +gi|12345678|ref|NC_012345.1| sim CDS 22 22 . - . ID=L_627; +gi|12345678|ref|NC_012345.1| sim CDS 23 23 . + . ID=L_323; +gi|12345678|ref|NC_012345.1| sim CDS 24 24 . + . ID=L_637; +gi|12345678|ref|NC_012345.1| sim CDS 25 25 . + . ID=L_639; +gi|12345678|ref|NC_012345.1| sim CDS 26 26 . + . ID=L_641; +gi|12345678|ref|NC_012345.1| sim CDS 27 27 . + . ID=L_643; +gi|12345678|ref|NC_012345.1| sim CDS 28 28 . + . ID=L_645; +gi|12345678|ref|NC_012345.1| sim CDS 29 29 . + . ID=L_647; +gi|12345678|ref|NC_012345.1| sim CDS 30 30 . + . ID=L_336; +gi|12345678|ref|NC_012345.1| sim CDS 31 31 . + . ID=L_328; +gi|12345678|ref|NC_012345.1| sim CDS 32 32 . + . ID=L_331; +gi|12345678|ref|NC_012345.1| sim CDS 33 33 . - . ID=L_621; +gi|12345678|ref|NC_012345.1| sim CDS 34 34 . - . ID=L_619; +gi|12345678|ref|NC_012345.1| sim CDS 35 35 . + . ID=L_14; +gi|12345678|ref|NC_012345.1| sim CDS 36 36 . + . ID=L_15; +gi|12345678|ref|NC_012345.1| sim CDS 37 37 . + . ID=L_16; +gi|12345678|ref|NC_012345.1| sim CDS 38 38 . + . ID=L_17; +gi|12345678|ref|NC_012345.1| sim CDS 39 39 . + . ID=L_18; +gi|12345678|ref|NC_012345.1| sim CDS 40 40 . + . ID=L_19; +gi|12345678|ref|NC_012345.1| sim CDS 41 41 . + . ID=L_20; |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/M.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/M.fasta Tue Feb 18 17:57:28 2020 -0500 |
| b |
| b'@@ -0,0 +1,512 @@\n+>M_10\n+CVLHKYEIAALGNVLNKLFMTKLEDKVCGGDSQVYYKAKSPLTAITSTDNANSPLAGGYH\n+DHKLAFMGCIPTSAKKYNYPEETIKAQKTDIFTLSFATARDHYDESSAKSYLCNFESVYA\n+CDTRRCTNKPSVRAVKKLLGYFGYRAKHESPYGRHTLGDNLHSVKQFTSKNYLKLSVFRD\n+DFRRVPKKLLIGGAAVYRVVSDYKSTKKGNKESLGGTYSPVCAARGVDVHCAKKDGPDRK\n+QVLSPKLKCCVVFDYTAFGAIGELLLTVMSLITTIEAAKEKEGTNKCLVGSFPCAEITLS\n+GAGIKDWPGCLSLKCTFTLFQVTPMLYLMLCKYAQKPKFCNLGSNTRSFCQLNSHQLVAE\n+YVETFKEKKPVGADPVLKGPREEKALYVGNCVPLSFRILSKGAVGEETDYSSSQMARTSL\n+DQDHLCVECTPWDARKGAKCKGTQQEHSAKSANVGGCKVGKPQCIKGRSAWNCMCKFVIG\n+SDRLARNGDAVARTHENAIKNYAVSVARGVGTIIGPECVISDLVLQEYLFVAGGTGGNVA\n+SWTPAGCGTYQALWKKFGVNTCWSGLVALPLESYRNQVKNGYNRESGGLHIMMGFIVQPR\n+LVSALFSWGECRADLIELTQKLDAESGGYLQQSVEYRKLFPPAQGPVPPSCTISTFLTFH\n+NLVEEGLKGTFNTAKRPNACTFT\n+>M_11\n+PKFDSVVNHSRSDLFNNPEAVLFTNSECQTISVKAKNKGTGVAAEKVDGYAVSQPLEPYS\n+MSKKPVPNCGLEGSKELGRRDAAATCIFPGLVPLVFIRFQDTGQYLGDPSWALLEGVHYY\n+ASHGVSDLARKPNTHKSAKKYINIFGAKLNPTGSELKSYFDCKKAAIRLHNRADFLGETN\n+DYILGTNTEALQAYHPFEGFANKDGKKKLGKGGVILARPRTIALKTKRQFHSVTGLNFIG\n+PTGDCSGKHHIGQGLAKAVWGCTYLVPSHADILLLLMDMAYREVGPLGKGYSLGHLGCEE\n+KKDGF\n+>M_313\n+FWRGFAKLNPHDAKNSQGTLNVKNKSLTTVANHSGTETGCAFKAFLVLKSAHKEITADRP\n+QNKLVNPYVTSEEVHFSREKLPKTLAYAGARNCVSGPKWWHLQPTECGLSDSTKPLCGRK\n+VLLLKVIGIMLSNYFATGAYADDLFTLKRQQERIATCDPSFQSGPNFEAKVVYKIGSFTP\n+AKTDAGQLGSKLLQPRGIKPLPFELNVQNLPDMLGGCGDLGSGHDGPVIIARDTAVLPKA\n+QNKHGLESKFFASMGGIHSELALDETGFNLFPAGNYLICAVEKLAILTQIYTLHAAGGLR\n+FKLSASNQFGRVYGGEECSFHTLECGIFGRVLEPTSFTIVGKLRPCFSGNDRGCALVQYL\n+LVVGGKGRHPIEWEARPQGADVVGEDTCERSPVYSHAFKLTSENANNWDEIGDSQKLMNV\n+GRQFGMEYGEGFKTDNNKIFQFGLSRCQKLYSTVGIYDDSIGFTSAVFFPDQIVTPSVAK\n+QLFASGVVGHFQGADAQQEGYEFESKEEGTISIATSCLVEDTLSPGGFYTDFHHGTPENG\n+IYCDTRGSNTKSSCNIPSAVQAKELGTGPVGLFMSAFCCGLVKILCGSKILTKTGFIVVR\n+DNDQCGFEKGPAHMRTYLSTGKYTPRTDGATKREKPPSFCTGTIPLAPKIAKLGAGDQMH\n+GATAAGCTNKPGTGLSGFTDTGEETKGFEGCMFRLRALPTLNMQGDFFGIVSVVGEPKMN\n+LVTLRRLTRYRPPAICRTVKIAKFACTGSVRKKLLHTHGN\n+>M_619\n+DGVKKECQVVGACTLQLGSDLVGGVTDVEKFKKSNGGYTPALNLTDSLFSGKAFAAAGYV\n+IVRPKDILVNENQFACCLSCCDTNWQVVVEAPLASSIRVGYKVHVNFPNSEEIVCKKERS\n+RLSLGSPARPDTLVVADAMVLKKSCKKVPIVCTLYIMKYYADRQQYLKGYAQEKIHSIGC\n+DI\n+>M_621\n+DSVKRDDVSCKVVGACTLNIGKSDLAGGVSDVSELKQSEGGFSPALGTTSGLYNVKIFAA\n+AGYAVLQPKDILVDEAHFSVCMSCCAVAWQIAIHPPLAALEITGYTVHVKFPNCEQIVCR\n+KERSRLDLNDPERPITLVIAAAMVLKKQCKKTPFVCALYKQKYYNDRGQYLKGYAQEKAK\n+CIGYRV\n+>M_623\n+DSVKKSIAQLAYNKRDGICKVVGACTLHLGKSALADGVTDVDDLKQSEGGFGPALGTTSG\n+LYNVKIYAAAGYAVVQPKDVLDATHFSVCMSCPAIGWQVAIEPPLAGTGTPHSTVHVGFP\n+NCEQIVCRKGRSRLNLHHPERPKTLIVAAAMVLKKSCKKTPFACALYIQKYYNDRGQYLK\n+SYSQEKAKCIGYI\n+>M_14\n+PQANIQRKFCHDNALLAVNAPRVENFGDGFEACVARAPFYEGDLMGKGGVLLLFGTNEPI\n+MTAHKAGQVTGSSEVKGPFFHGRDPTGRYDHQKKSHLEVFVSELTSYFKQKAEQSIPRQW\n+EATWVGKMSLAVPYNIKWLKVRGGGCVSYGLVSKSAAVFDQVAAKVHEEHGHVRYVVWKC\n+TNARRHALTCKAARGGHVFFCGRGTRVKKCTSTKTDKNRPFSSANQLCQTETGVLLDYFK\n+GTLAALPAAQGLSAGDVRFLLLSTNYRGLIKAYAVGREKELLVKHHKWKGAQTAGDATNK\n+KTAPNESFLPFLVKGQKSHKLVFTGKSTLEMTRKEYASAAKSRSILGFGPHPEQGRTIYN\n+GARSIGSRYPVNEAAESCTKANSIVALTKKKSCRNMHNRILEASGENGLDGVIALNLNYK\n+CAKKETDDAHEIKPDALIDHTVVGIDGAKLWICQVEYLADLHASALVANYLHSTYGNGLM\n+GICRINKIASRTMPRQHTVQSCVTCRLKSGISGAKKCAPKHVRYTTEHKDFFMVRSTQFR\n+CNKMDEGSFEFLHANQNQPKLGSFGQHDHVESHNEPGKYIEKGHGPHHPIEDARGNKRLC\n+VSFTQASGRTSKAGQDNLYIYISIGFKRCQERRPKKCKIRCGKKKVGEVDTPPNYVLNYS\n+QGDADLEDLIPALNKSGDFFVRSATDKPGASASIFNEKRFCNCEQCNVAAVGGKKSRALS\n+SEEIVKGPSNVGGLYQGGTAMQVCEPLIPNYCGTYTSIRPVKYLC\n+>M_15\n+PKGTNYQGFRTETLHLDIKTTFTPAFYVTKELACSPCYLQVEGFLMVYSLREITKADEGP\n+LKNGKKATAKVNDLQEEARVSTFENRLKSELQKRLGVESADFQAQYYSLLNDVGLICDSK\n+YKAGLIGQADHRELIATACFQCQYHCDAYIFFSRVGSQFPKRKAAGKGPFRGVFATPPAK\n+AVSTIHDQLAEGHWVHTIYTNGKAHIVALAPVWHDLGVLAVAVPLGPLAALDAGSNRQCG\n+KNWVKRLTLGYLESNIPYVEGTVKCYEVKNKRATAVKSHPEHGSVMATIYPLKSGVGASK\n+HEVDAFGGSENLSLFSTNLGNYTDSTNSTKKEKCQDCEYRLWGGSNPPTKPAGARGGPHL\n+CGSAPTGSNTGTGVTEKENMAELRCFAAGDGFFKGYIQYGGWFGGLNDKAWLAKFREEFG\n+NVSNGRDKRTGELRHVECPIQVQKPYNNPILHHEKDCGGKTRVHGSGGEKDVGPWRTDTS\n+TKQDNQKFASGKL\n+>M_16\n+LEDDETQLSDIDDEECRLFDFPGKHVGGFGACASQAAAGLGQIFDCAVGTGRLGLVNVAD\n+VRSSSSTRAHVKLTHDSGLGPSNPVDVAALPFHDPWNDASYFAQRTHGKWENGVLKTATE\n+KDASHLRFLTKNLYHQVSFIGIQTLADESLHVSGISPRYYHQSRAFDEYLSGVPPAEKRK\n+LDECTSDYNGHQFKLAAQIVTRPFGIDSNI'..b'ANLIAYNVGFMTKDTALSNANEAHTGGVASLRTATHT\n+WGVTANRVDYFNAVLKGYHTALVERCGVGFLKGAILEFIPLVKCFVVTKVAHVVRVDQKT\n+GNEIRDCRSWLGKAKGAQGDVSNFAKKPALENSKGKGANSRSPDGTAICMESVAVIKCLG\n+ERCVYGKSEPENLTNSEFEEPKGRAESYTDSIATLETLAQCGYAIADTAALPLFCLLLGA\n+EDTQLASFDERYGPEATSKGIQLNDVTYLEAYYSGNGQNKLGQQVGLDEGEFRLQKPIAV\n+PAPYPKDTCVGTMVSKSNSALVSDTHKATASQPFVCCGSKQLILKVEACDLVVKNGTKDD\n+IVTADTEPCQYNCGHGAVIAKLTTEDSQLYGPDVVCMKNPAKCNSKKDIEPSQLAALVWA\n+MGGKKCPAENLELMYINFKLLYSEQADAENSDLAHKGS\n+>M_5\n+NCESGNAEADESGSGNYAKSICAGFRREVWKLTMEADANIEHEHKGATEEPISPKGNNVN\n+VLGKGCEKPLVHQKSKDDLKAEAQLLIKCEAKNAWHKPLQGNSLPGYAPKWGVALLDLVL\n+LYSFKALARAIPLRYTGGAKDSPPFINESVVFGQPLEHILVTSRYEMSGNLHSEKHPQRS\n+KPDTKPADPRKAQLEGIFDERLHDCVKVSTGEVVNGNDNTTVHTLYAKLYRTPPPVNDAK\n+CFVSKDKGGINEEGKLIGQKVGGVLDPIARGHAHLFVGNKAAYPMKANVACLSTGSGTAD\n+SGDGTNGDDIAADKSANEDIKIVGALQNHGRPMEFNKGSGPFQLNHKLEEPYFYQCTQHD\n+HAKAHKNARVTSCANGQQSSVWGCQFSLLFLPAAFKTTPGLQRFWEFGHAAHLDTQLHPE\n+TCLMSAPKTCAHLVVVEKWTYTLQLEPFATSQNQSLIFEKNSSCSLFNCYPLKEKKNSGV\n+EADAVDQPGDTKKTPEIGTFECVILPYRWQILADAKKNKTMRGTSFAFCNALNLTSPVLR\n+NQIALRCHTDKVSEETSQMPATFASSVFGVKVIFNERCQSHMSCSEEGEAGVHDLVKAGL\n+QRAKNFPLSHPPISYPLTIVYKVNPKNVGHLSAPCNRQAIAKEKMQSNGLVSKCCCTRTG\n+TAPSTLTKASELFPLPISAVEVAGLAATHADEPYESFAWAMFTIGEYTQKVKNGQKAGSG\n+MGVPCLVHAYGPAEAFDRHYRGSQECDMRQGALWENASQELRVNTNPEAVANDTCGKTGG\n+SDKGDNDLVSVETVKETLNSARGSGYGVAEVTAHFNEAVARIGCILCLKQLECGLSAQSI\n+VKKHNGKKKIETPKVHTVQVALKLKGRCSVRQHNLPAFTNSPVVVAESQYAHKGIKLLEI\n+NDEEQVLITGNAPRFPGELGTGSQF\n+>M_6\n+QLPFSWYFKPDVRLEIKEELACHTTAAQKMKEPRRIEDAEPAGFTEPLNGLIVKPHDENP\n+VGDVFGPRIWCDTDYVLFAGYAGNHTAGHNLQKHFLAHQARPNEYLTPRQGGGFFYVQKE\n+LPLWHAIGAGKVKKNKKSFYIRKADMRFHPSFKNHQCVALSIVDGLLNAVATPGSPKLFL\n+NRGDGELRGEECNSVNTFADKLLRTTMQPCGASPFGRESIGDHPSYVLPGGLRMTWDTDE\n+ECMIMKAFLIKAENYLLSNPKATTTMVSPDGFFDFARLHHLLPPLAASATGLDCDVSVYD\n+YVVSDTIFREHVKNKACPAVVYSVNGWSKEIHGKLSVGGGWEQGLDGPFKYHHTQEPFED\n+KVDIKGAIPVDTMFKASMFKKHKQSQLVTGGGSLYKESCFKHKMKRERNKSADKGANLGQ\n+GILQTAMSGFTVDGMQALQPEPAQSANVTAGVLAVAVAAVSYFDRVQTTNCEVYASGFWP\n+QAVRGNISVNQGPPFSEAFFKLGKPELCDGEQFTIGTDQPDSKVLIGRASGLCHFLMTPS\n+IEAGWLTTNVSQYENDAGTHPDVGAKDAGVTENFFCQEVTVIGISITHGLSADKRSIFRG\n+VISATQSGKVQLTGLALVPPVGLSPQTLTNRLAGLIGYGKLACLKCTVYKSTRRTLAIVL\n+LEYRVAVSVAKEPRAKLVMNAKLHTLYVTHRHSSDLMPFAFTGRNCKATNQPGILTHNKM\n+CQCAEAGLPHEKYGFAHLSRSSFGVSCTGCSDPTIVQALHRAESIHRSGAWLNSQNSTET\n+GAILFGPTSKETRDSICGNQAFSVAATIGQLGYIVDVLAHGMVLAFCDYAKTAGGSPPKE\n+KVSCDDGHGGLMLEANVFSEDDHVRKHLGLSENGYHCVLTSKTLVKFLIRHQTIHCGTEG\n+CVPTGSGDFSD\n+>M_7\n+SENNIKWPQLGGVALYGEDANMELGADGVPSLASLGMPWPVLFNANLSGKQCAQCRIFIV\n+CHLTQPHGCGAMQVGMSGDSEAKDQVKLNGGACKDKFRGRTLMAMYPFGRVLFATPSTVA\n+FDKFILKEGFGFLGRCAAKVAATQPLNGVTTAVQVVNKCCNKSKKSLEPLLTGRDHAAEG\n+CGYASAFTVALIKNSYHCDYYSDHAKYASKSYSKSSRALASYFLIQFISCTKGLCSESHE\n+CVKNEFLVKIWAGSKMGTSIPTDYTMLTDPGYPYECDDHQNNRHCSGEKMPKLQNHPSYS\n+AFTQRRKSFTKQLTPSKGERKFDKNAVHLDIGKVTPTASDEYVEALSLVHPTALNPAFGM\n+KAVYQYLKRAYKKGLLGLDVHVSKNNTEASKKDYHVVT\n+>M_8\n+CRLPGGVNERAFGHVNDKDLCMLPSAVFCTQKGKENPQNKEYQMAGSKPQTWPAAQVLDC\n+RHELRTYTGQLPLRAATDLGPDVKSIYTVSQRGFKVGQTNHAVCVFEAGNVADKKWKMCH\n+GKNYGRSESWIYFSLNEKANGHLKALHPSAFQKHKKWTGMRDFGATTKTGLRLVAFSDPT\n+GACAQVPYLSDCPRGKLSRPTIPPGAALTVEFTAASARCKKLAEIANADEPASSAKAQKF\n+FTTGAMASSFLAAKSAVTPTLENKTNGSSLQHPSKSGDQLKDYTVKPFSLVQPKLAGTAH\n+ALMIYKDPPGSGYFINFVTKYQKIKRFWGVPVKARPQNAKASFCTHDLIFCPKGGLEFLN\n+GVPFGSPLAGCQLERSTFPVKGLGKACAILSLSRVALSQENKQHVNDHHEAKVGANGPSR\n+AIDVQVGCAVEPNCGDTQLREDFFCYTLGAAHGRFVLSLARDTLQLCFHADITPPLVISI\n+STKILGSVVKLRGASGETVELASAQAVASKPLKQAERARIGFCRGSLAIHADATLQSGSC\n+TGGTDKKLELEQDNDPCVTAKQGSGLKRAGQPIKSRSHDACKADSLSDKAAPGRSWTMEI\n+GTETYPVMQGNGPRRASRSTLYAEGGVIDWFKGAHNSYEFTGITCSGVRDMLTPQDFEDI\n+KEQTGDLSCMAVNCNAANDCHCSAGLVLPFKETLVCRHATSGKLINDVSGPSVKVGGMKL\n+PLSSNHFLPLTINQGGPVRTGADSDCSGFCCGCKALKLKLAEFIPSRPLGSVTGGKEVVS\n+FPNKEGGDTTNLPKEYANTGGMCAVCPNGAHGTGGMTILSLGAFGYQYTCLVGVDGASKD\n+LLVGNGLEIYHALYVSLHKKVKHTDSPGQWVGFSIHTSEDKSTCTGNGCILHVSVHSQQF\n+GDFLACKHGKQRVPDKEKYYYDFAANPVPGTTTPSGLLLRTVRTAKTPTKFHFG\n+>M_9\n+LSYLHYDDACVVTRAVGFFYTQFKQEAPVSCANVNKEFDHFSVDKKDPWAAIGLTSATGN\n+RAHNFVAADKTKHYRSRQRYARAGSGPIVRALFETAYATTIQNTHTFSTPLKRIVDNGLD\n+DGSVSRACLPLELAPFVRLRCACSGGLFFTGVVPLLTVLLQVNGSVKLTWLGAMYATFPV\n+LDLRRMLLVVTQDTGLATFRPSPNGRHPKDCAT\n' |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/M.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/M.gff Tue Feb 18 17:57:28 2020 -0500 |
| b |
| @@ -0,0 +1,40 @@ +gi|12345678|ref|NC_012345.1| sim CDS 1 1 . - . ID=M_319; +gi|12345678|ref|NC_012345.1| sim CDS 2 2 . - . ID=M_317; +gi|12345678|ref|NC_012345.1| sim CDS 3 3 . + . ID=M_617; +gi|12345678|ref|NC_012345.1| sim CDS 4 4 . + . ID=M_6; +gi|12345678|ref|NC_012345.1| sim CDS 5 5 . + . ID=M_7; +gi|12345678|ref|NC_012345.1| sim CDS 6 6 . + . ID=M_8; +gi|12345678|ref|NC_012345.1| sim CDS 7 7 . + . ID=M_9; +gi|12345678|ref|NC_012345.1| sim CDS 8 8 . + . ID=M_10; +gi|12345678|ref|NC_012345.1| sim CDS 9 9 . + . ID=M_11; +gi|12345678|ref|NC_012345.1| sim CDS 10 10 . + . ID=M_313; +gi|12345678|ref|NC_012345.1| sim CDS 11 11 . - . ID=M_623; +gi|12345678|ref|NC_012345.1| sim CDS 12 12 . + . ID=M_333; +gi|12345678|ref|NC_012345.1| sim CDS 13 13 . + . ID=M_2; +gi|12345678|ref|NC_012345.1| sim CDS 14 14 . + . ID=M_3; +gi|12345678|ref|NC_012345.1| sim CDS 15 15 . + . ID=M_4; +gi|12345678|ref|NC_012345.1| sim CDS 16 16 . + . ID=M_5; +gi|12345678|ref|NC_012345.1| sim CDS 17 17 . - . ID=M_323; +gi|12345678|ref|NC_012345.1| sim CDS 18 18 . + . ID=M_627; +gi|12345678|ref|NC_012345.1| sim CDS 19 19 . + . ID=M_630; +gi|12345678|ref|NC_012345.1| sim CDS 20 20 . + . ID=M_632; +gi|12345678|ref|NC_012345.1| sim CDS 21 21 . + . ID=M_634; +gi|12345678|ref|NC_012345.1| sim CDS 22 22 . + . ID=M_636; +gi|12345678|ref|NC_012345.1| sim CDS 23 23 . + . ID=M_638; +gi|12345678|ref|NC_012345.1| sim CDS 24 24 . + . ID=M_640; +gi|12345678|ref|NC_012345.1| sim CDS 25 25 . + . ID=M_649; +gi|12345678|ref|NC_012345.1| sim CDS 26 26 . + . ID=M_642; +gi|12345678|ref|NC_012345.1| sim CDS 27 27 . + . ID=M_644; +gi|12345678|ref|NC_012345.1| sim CDS 28 28 . + . ID=M_646; +gi|12345678|ref|NC_012345.1| sim CDS 29 29 . + . ID=M_336; +gi|12345678|ref|NC_012345.1| sim CDS 30 30 . + . ID=M_328; +gi|12345678|ref|NC_012345.1| sim CDS 31 31 . + . ID=M_331; +gi|12345678|ref|NC_012345.1| sim CDS 32 32 . - . ID=M_621; +gi|12345678|ref|NC_012345.1| sim CDS 33 33 . - . ID=M_619; +gi|12345678|ref|NC_012345.1| sim CDS 34 34 . + . ID=M_14; +gi|12345678|ref|NC_012345.1| sim CDS 35 35 . + . ID=M_15; +gi|12345678|ref|NC_012345.1| sim CDS 36 36 . + . ID=M_16; +gi|12345678|ref|NC_012345.1| sim CDS 37 37 . - . ID=M_20; +gi|12345678|ref|NC_012345.1| sim CDS 38 38 . - . ID=M_19; +gi|12345678|ref|NC_012345.1| sim CDS 39 39 . - . ID=M_18; +gi|12345678|ref|NC_012345.1| sim CDS 40 40 . - . ID=M_17; |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/result.blast-graph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.blast-graph Tue Feb 18 17:57:28 2020 -0500 |
| b |
| @@ -0,0 +1,169 @@ +# file_a file_b +# a b evalue_ab bitscore_ab evalue_ba bitscore_ba +# E.fasta C.fasta +# 1.90009e-124 442.2 1.4375e-126 444.9 +E_10 C_10 3.8e-124 434.9 2.8e-126 442.2 +E_11 C_11 5.9e-51 190.7 5.6e-50 187.6 +E_13 C_13 1.1e-26 109.4 1.7e-25 105.5 +E_14 C_14 9.4e-163 563.5 2.5e-161 558.9 +E_15 C_15 5.4e-100 354.4 3.3e-100 355.1 +E_16 C_16 2.7e-45 171.8 7.1e-47 177.2 +E_17 C_17 4.4e-183 631.3 5.0e-182 627.9 +E_18 C_64 6.7e-64 234.2 1.6e-63 233.0 +E_19 C_22 2.2e-30 121.3 5.2e-30 120.2 +E_19 C_63 3.0e-32 127.5 1.2e-31 125.6 +E_313 C_12 4.1e-131 458.4 1.0e-129 453.8 +E_315 C_12 1.8e-128 449.5 7.5e-128 447.6 +E_317 C_1 1.6e-136 476.5 1.8e-133 466.5 +E_366 C_1 9.4e-131 457.2 2.4e-130 456.1 +E_368 C_1 1.5e-134 469.9 4.4e-132 461.8 +E_437 C_1 1.0e-130 457.2 2.9e-128 449.1 +# L.fasta C.fasta +# 2.95e-95 363.6 2.1e-95 364.35 +L_10 C_10 2.9e-128 448.7 1.6e-130 455.3 +L_11 C_11 1.8e-58 215.7 1.0e-57 212.2 +L_14 C_14 5.1e-123 431.4 7.9e-124 433.3 +L_15 C_15 2.3e-87 312.4 2.7e-87 311.2 +L_16 C_16 1.4e-41 159.5 2.3e-43 164.5 +L_17 C_17 7.1e-170 587.4 3.1e-169 584.3 +L_18 C_64 9.2e-66 240.4 1.8e-65 238.4 +L_19 C_63 7.2e-29 116.3 4.7e-29 115.9 +L_2 C_164 3.0e-94 335.1 1.0e-93 332.4 +L_2 C_166 1.2e-90 323.2 8.0e-91 322.8 +L_2 C_167 5.2e-91 324.3 3.9e-90 320.5 +L_2 C_2 5.9e-95 337.4 4.2e-95 337.0 +L_20 C_20 2.5e-172 595.5 2.2e-170 588.2 +L_313 C_12 1.4e-115 406.8 1.0e-114 402.9 +L_313 C_21 1.8e-110 389.8 2.5e-111 391.7 +L_323 C_1 1.2e-136 476.9 6.7e-134 466.8 +L_336 C_1 2.5e-134 469.2 6.9e-131 456.8 +L_621 C_13 3.3e-34 134.4 4.2e-33 129.8 +L_627 C_1 4.6e-136 474.9 5.1e-134 467.2 +L_631 C_1 1.5e-139 486.5 4.5e-138 480.7 +# C2.fasta C.fasta +# 0 1391.7 0 1391.7 +C_10 C_10 0.0e+00 1391.7 0.0e+00 1391.7 +# C2.fasta E.fasta +# 2.8e-126 442.2 5.4e-126 434.9 +C_10 E_10 2.8e-126 442.2 5.4e-126 434.9 +# M.fasta C.fasta +# 3.5e-119 418.7 1e-117 412.9 +M_10 C_10 1.3e-128 449.9 1.3e-129 452.2 +M_11 C_11 2.0e-57 212.2 4.4e-56 206.8 +M_14 C_14 9.4e-128 447.2 2.6e-130 454.9 +M_15 C_15 1.2e-83 300.1 4.4e-85 303.9 +M_16 C_16 8.3e-36 140.2 9.6e-37 142.5 +M_17 C_17 7.6e-156 540.8 2.3e-156 541.6 +M_18 C_64 8.0e-70 253.8 1.1e-68 249.2 +M_19 C_63 6.3e-25 103.2 5.5e-25 102.4 +M_2 C_164 1.2e-92 329.7 1.2e-91 325.5 +M_2 C_166 5.1e-91 324.3 1.1e-90 322.4 +M_2 C_167 7.7e-95 337.0 1.0e-93 332.4 +M_2 C_2 8.5e-94 333.6 2.3e-93 331.3 +M_20 C_20 7.9e-174 600.5 1.3e-170 589.0 +M_313 C_12 3.5e-119 418.7 1.0e-117 412.9 +M_323 C_1 6.6e-135 471.1 4.8e-132 460.7 +M_331 C_1 2.0e-131 459.5 5.9e-130 453.8 +M_336 C_1 2.2e-135 472.6 2.0e-133 465.3 +M_621 C_13 6.4e-38 146.7 8.3e-37 142.1 +M_630 C_1 9.3e-129 450.7 2.8e-127 444.9 +M_632 C_1 3.3e-134 468.8 1.6e-130 455.7 +M_636 C_1 3.7e-130 455.3 1.1e-128 449.5 +# C2.fasta L.fasta +# 1.6e-130 455.3 4.1e-130 448.7 +C_10 L_10 1.6e-130 455.3 4.1e-130 448.7 +# C2.fasta M.fasta +# 1.3e-129 452.2 1.8e-130 449.9 +C_10 M_10 1.3e-129 452.2 1.8e-130 449.9 +# M.fasta L.fasta +# 0 1374.8 0 1372.5 +M_10 L_10 0.0e+00 1223.0 0.0e+00 1218.4 +M_11 L_11 6.4e-164 565.1 4.2e-163 562.4 +M_14 L_14 0.0e+00 1300.8 0.0e+00 1302.0 +M_15 L_15 1.7e-262 893.3 2.6e-263 896.0 +M_16 L_16 1.8e-135 470.3 3.4e-135 469.5 +M_17 L_17 0.0e+00 1636.7 0.0e+00 1640.9 +M_18 L_18 3.1e-214 732.6 1.5e-213 730.3 +M_19 L_19 5.0e-74 265.4 5.1e-74 265.4 +M_2 L_2 3.2e-230 785.8 7.4e-230 784.6 +M_20 L_20 0.0e+00 1709.1 0.0e+00 1704.1 +M_3 L_3 6.1e-212 724.9 1.4e-211 723.8 +M_313 L_313 0.0e+00 1374.8 0.0e+00 1372.5 +M_317 L_317 0.0e+00 1416.0 0.0e+00 1416.4 +M_319 L_319 0.0e+00 1484.9 0.0e+00 1478.8 +M_323 L_323 0.0e+00 1548.9 0.0e+00 1549.3 +M_328 L_328 0.0e+00 1488.8 0.0e+00 1486.9 +M_331 L_331 0.0e+00 1570.8 0.0e+00 1571.2 +M_333 L_333 0.0e+00 1570.8 0.0e+00 1572.8 +M_336 L_336 0.0e+00 1474.9 0.0e+00 1480.7 +M_4 L_4 0.0e+00 1317.0 0.0e+00 1316.2 +M_5 L_5 0.0e+00 1607.4 0.0e+00 1611.7 +M_6 L_6 0.0e+00 1635.9 0.0e+00 1634.0 +M_617 L_617 0.0e+00 1493.4 0.0e+00 1491.1 +M_619 L_619 5.6e-83 295.4 1.7e-82 293.9 +M_621 L_621 2.6e-99 349.7 2.6e-99 349.7 +M_623 L_623 2.8e-109 382.9 3.8e-109 382.5 +M_627 L_627 0.0e+00 1325.8 0.0e+00 1327.8 +M_632 L_631 0.0e+00 1254.2 0.0e+00 1250.0 +M_632 L_633 0.0e+00 1239.2 0.0e+00 1234.2 +M_634 L_635 0.0e+00 1310.4 0.0e+00 1312.7 +M_636 L_635 0.0e+00 1350.9 0.0e+00 1350.9 +M_636 L_637 0.0e+00 1300.4 0.0e+00 1300.8 +M_638 L_637 0.0e+00 1350.9 0.0e+00 1347.0 +M_638 L_639 0.0e+00 1350.1 0.0e+00 1344.3 +M_640 L_641 0.0e+00 1493.0 0.0e+00 1490.7 +M_640 L_643 0.0e+00 1485.3 0.0e+00 1485.7 +M_642 L_641 0.0e+00 1503.4 0.0e+00 1499.6 +M_642 L_643 0.0e+00 1526.5 0.0e+00 1526.1 +M_644 L_645 0.0e+00 1695.2 0.0e+00 1694.9 +M_644 L_647 0.0e+00 1631.7 0.0e+00 1633.2 +M_646 L_645 0.0e+00 1704.1 0.0e+00 1703.7 +M_646 L_647 0.0e+00 1664.4 0.0e+00 1666.4 +M_649 L_641 0.0e+00 1446.8 0.0e+00 1445.6 +M_8 L_8 0.0e+00 1676.4 0.0e+00 1681.4 +M_9 L_9 5.2e-104 365.5 2.7e-103 363.2 +# L.fasta E.fasta +# 1.4000000075e-147 526 1.000265e-151 531 +L_10 E_10 5.9e-127 444.5 3.9e-128 447.2 +L_11 E_11 6.2e-65 237.3 3.8e-65 236.9 +L_14 E_14 1.8e-163 565.8 1.1e-165 572.4 +L_15 E_15 3.8e-104 368.2 4.2e-104 367.1 +L_16 E_16 4.7e-59 217.6 1.0e-59 218.8 +L_17 E_17 8.2e-201 690.3 4.2e-201 690.3 +L_18 E_18 4.8e-81 291.2 6.3e-82 293.1 +L_19 E_19 3.7e-31 124.0 4.6e-32 125.9 +L_313 E_313 1.8e-177 612.5 8.9e-178 612.5 +L_317 E_437 1.5e-155 539.7 5.3e-155 537.0 +L_323 E_368 2.0e-182 629.0 6.4e-182 626.3 +L_617 E_432 2.8e-147 512.3 2.0e-151 525.0 +L_621 E_13 3.3e-37 144.4 4.8e-37 142.9 +L_623 E_13 1.1e-38 149.4 5.7e-38 146.0 +L_627 E_368 2.6e-185 638.6 5.6e-186 639.8 +L_631 E_317 2.6e-174 602.1 5.7e-175 603.2 +L_631 E_368 3.2e-180 621.7 2.7e-180 620.9 +L_635 E_317 6.9e-175 604.0 1.4e-176 608.6 +# M.fasta E.fasta +# 1.4e-164 569.7 9.9e-167 575.9 +M_10 E_10 5.2e-128 448.0 1.1e-127 445.7 +M_11 E_11 4.5e-63 231.1 1.0e-62 228.8 +M_14 E_14 2.3e-164 568.9 9.7e-167 575.9 +M_15 E_15 7.2e-103 364.0 3.2e-104 367.5 +M_16 E_16 1.3e-50 189.5 1.1e-50 188.7 +M_17 E_17 2.2e-198 682.2 6.1e-200 686.4 +M_18 E_18 1.3e-81 293.1 1.1e-81 292.4 +M_19 E_19 4.5e-29 117.1 4.3e-30 119.4 +M_313 E_313 1.2e-178 616.3 3.1e-178 614.0 +M_319 E_367 2.8e-157 545.4 2.8e-158 547.7 +M_323 E_317 3.6e-171 591.7 6.6e-171 589.7 +M_323 E_368 6.3e-176 607.4 4.5e-175 603.6 +M_328 E_432 4.0e-156 541.6 1.6e-153 531.9 +M_331 E_368 1.3e-173 599.7 3.8e-174 600.5 +M_336 E_317 1.5e-166 576.2 2.6e-167 577.8 +M_336 E_366 3.6e-168 581.6 3.3e-167 577.4 +M_336 E_368 1.5e-174 602.8 7.6e-175 602.8 +M_621 E_13 4.5e-42 160.6 5.0e-42 159.5 +M_627 E_368 2.4e-180 622.1 1.4e-181 625.2 +M_632 E_368 2.3e-178 615.5 6.2e-177 609.8 +M_634 E_317 1.4e-164 569.7 9.9e-167 575.9 +M_636 E_317 1.4e-164 569.7 1.1e-165 572.4 +M_636 E_366 1.1e-159 553.5 2.5e-159 551.2 |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/result.proteinortho-graph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.proteinortho-graph Tue Feb 18 17:57:28 2020 -0500 |
| b |
| @@ -0,0 +1,144 @@ +# file_a file_b +# a b evalue_ab bitscore_ab evalue_ba bitscore_ba +# E.fasta C.fasta +# 1.90009e-124 442.2 1.4375e-126 444.9 +E_10 C_10 3.8e-124 434.9 2.8e-126 442.2 +E_11 C_11 5.9e-51 190.7 5.6e-50 187.6 +E_13 C_13 1.1e-26 109.4 1.7e-25 105.5 +E_14 C_14 9.4e-163 563.5 2.5e-161 558.9 +E_15 C_15 5.4e-100 354.4 3.3e-100 355.1 +E_16 C_16 2.7e-45 171.8 7.1e-47 177.2 +E_17 C_17 4.4e-183 631.3 5.0e-182 627.9 +E_18 C_64 6.7e-64 234.2 1.6e-63 233.0 +E_19 C_22 2.2e-30 121.3 5.2e-30 120.2 +E_19 C_63 3.0e-32 127.5 1.2e-31 125.6 +E_313 C_12 4.1e-131 458.4 1.0e-129 453.8 +E_315 C_12 1.8e-128 449.5 7.5e-128 447.6 +E_368 C_1 1.5e-134 469.9 4.4e-132 461.8 +# L.fasta C.fasta +# 2.95e-95 363.6 2.1e-95 364.35 +L_10 C_10 2.9e-128 448.7 1.6e-130 455.3 +L_11 C_11 1.8e-58 215.7 1.0e-57 212.2 +L_14 C_14 5.1e-123 431.4 7.9e-124 433.3 +L_15 C_15 2.3e-87 312.4 2.7e-87 311.2 +L_16 C_16 1.4e-41 159.5 2.3e-43 164.5 +L_17 C_17 7.1e-170 587.4 3.1e-169 584.3 +L_18 C_64 9.2e-66 240.4 1.8e-65 238.4 +L_19 C_63 7.2e-29 116.3 4.7e-29 115.9 +L_2 C_164 3.0e-94 335.1 1.0e-93 332.4 +L_2 C_166 1.2e-90 323.2 8.0e-91 322.8 +L_2 C_167 5.2e-91 324.3 3.9e-90 320.5 +L_2 C_2 5.9e-95 337.4 4.2e-95 337.0 +L_20 C_20 2.5e-172 595.5 2.2e-170 588.2 +L_313 C_12 1.4e-115 406.8 1.0e-114 402.9 +L_313 C_21 1.8e-110 389.8 2.5e-111 391.7 +L_323 C_1 1.2e-136 476.9 6.7e-134 466.8 +L_621 C_13 3.3e-34 134.4 4.2e-33 129.8 +L_627 C_1 4.6e-136 474.9 5.1e-134 467.2 +# C2.fasta C.fasta +# 0 1391.7 0 1391.7 +C_10 C_10 0.0e+00 1391.7 0.0e+00 1391.7 +# C2.fasta E.fasta +# 2.8e-126 442.2 5.4e-126 434.9 +C_10 E_10 2.8e-126 442.2 5.4e-126 434.9 +# M.fasta C.fasta +# 3.5e-119 418.7 1e-117 412.9 +M_10 C_10 1.3e-128 449.9 1.3e-129 452.2 +M_11 C_11 2.0e-57 212.2 4.4e-56 206.8 +M_14 C_14 9.4e-128 447.2 2.6e-130 454.9 +M_15 C_15 1.2e-83 300.1 4.4e-85 303.9 +M_16 C_16 8.3e-36 140.2 9.6e-37 142.5 +M_17 C_17 7.6e-156 540.8 2.3e-156 541.6 +M_18 C_64 8.0e-70 253.8 1.1e-68 249.2 +M_19 C_63 6.3e-25 103.2 5.5e-25 102.4 +M_2 C_164 1.2e-92 329.7 1.2e-91 325.5 +M_2 C_166 5.1e-91 324.3 1.1e-90 322.4 +M_2 C_167 7.7e-95 337.0 1.0e-93 332.4 +M_2 C_2 8.5e-94 333.6 2.3e-93 331.3 +M_20 C_20 7.9e-174 600.5 1.3e-170 589.0 +M_313 C_12 3.5e-119 418.7 1.0e-117 412.9 +M_621 C_13 6.4e-38 146.7 8.3e-37 142.1 +M_630 C_1 9.3e-129 450.7 2.8e-127 444.9 +# C2.fasta L.fasta +# 1.6e-130 455.3 4.1e-130 448.7 +C_10 L_10 1.6e-130 455.3 4.1e-130 448.7 +# C2.fasta M.fasta +# 1.3e-129 452.2 1.8e-130 449.9 +C_10 M_10 1.3e-129 452.2 1.8e-130 449.9 +# M.fasta L.fasta +# 0 1374.8 0 1372.5 +M_10 L_10 0.0e+00 1223.0 0.0e+00 1218.4 +M_11 L_11 6.4e-164 565.1 4.2e-163 562.4 +M_14 L_14 0.0e+00 1300.8 0.0e+00 1302.0 +M_15 L_15 1.7e-262 893.3 2.6e-263 896.0 +M_16 L_16 1.8e-135 470.3 3.4e-135 469.5 +M_17 L_17 0.0e+00 1636.7 0.0e+00 1640.9 +M_18 L_18 3.1e-214 732.6 1.5e-213 730.3 +M_19 L_19 5.0e-74 265.4 5.1e-74 265.4 +M_2 L_2 3.2e-230 785.8 7.4e-230 784.6 +M_20 L_20 0.0e+00 1709.1 0.0e+00 1704.1 +M_3 L_3 6.1e-212 724.9 1.4e-211 723.8 +M_313 L_313 0.0e+00 1374.8 0.0e+00 1372.5 +M_317 L_317 0.0e+00 1416.0 0.0e+00 1416.4 +M_319 L_319 0.0e+00 1484.9 0.0e+00 1478.8 +M_328 L_328 0.0e+00 1488.8 0.0e+00 1486.9 +M_331 L_331 0.0e+00 1570.8 0.0e+00 1571.2 +M_333 L_333 0.0e+00 1570.8 0.0e+00 1572.8 +M_336 L_336 0.0e+00 1474.9 0.0e+00 1480.7 +M_4 L_4 0.0e+00 1317.0 0.0e+00 1316.2 +M_5 L_5 0.0e+00 1607.4 0.0e+00 1611.7 +M_6 L_6 0.0e+00 1635.9 0.0e+00 1634.0 +M_617 L_617 0.0e+00 1493.4 0.0e+00 1491.1 +M_619 L_619 5.6e-83 295.4 1.7e-82 293.9 +M_621 L_621 2.6e-99 349.7 2.6e-99 349.7 +M_623 L_623 2.8e-109 382.9 3.8e-109 382.5 +M_627 L_627 0.0e+00 1325.8 0.0e+00 1327.8 +M_632 L_631 0.0e+00 1254.2 0.0e+00 1250.0 +M_632 L_633 0.0e+00 1239.2 0.0e+00 1234.2 +M_636 L_635 0.0e+00 1350.9 0.0e+00 1350.9 +M_638 L_637 0.0e+00 1350.9 0.0e+00 1347.0 +M_638 L_639 0.0e+00 1350.1 0.0e+00 1344.3 +M_640 L_641 0.0e+00 1493.0 0.0e+00 1490.7 +M_640 L_643 0.0e+00 1485.3 0.0e+00 1485.7 +M_642 L_641 0.0e+00 1503.4 0.0e+00 1499.6 +M_642 L_643 0.0e+00 1526.5 0.0e+00 1526.1 +M_644 L_645 0.0e+00 1695.2 0.0e+00 1694.9 +M_644 L_647 0.0e+00 1631.7 0.0e+00 1633.2 +M_646 L_645 0.0e+00 1704.1 0.0e+00 1703.7 +M_646 L_647 0.0e+00 1664.4 0.0e+00 1666.4 +M_649 L_641 0.0e+00 1446.8 0.0e+00 1445.6 +M_8 L_8 0.0e+00 1676.4 0.0e+00 1681.4 +M_9 L_9 5.2e-104 365.5 2.7e-103 363.2 +# L.fasta E.fasta +# 1.4000000075e-147 526 1.000265e-151 531 +L_10 E_10 5.9e-127 444.5 3.9e-128 447.2 +L_11 E_11 6.2e-65 237.3 3.8e-65 236.9 +L_14 E_14 1.8e-163 565.8 1.1e-165 572.4 +L_15 E_15 3.8e-104 368.2 4.2e-104 367.1 +L_16 E_16 4.7e-59 217.6 1.0e-59 218.8 +L_17 E_17 8.2e-201 690.3 4.2e-201 690.3 +L_18 E_18 4.8e-81 291.2 6.3e-82 293.1 +L_19 E_19 3.7e-31 124.0 4.6e-32 125.9 +L_313 E_313 1.8e-177 612.5 8.9e-178 612.5 +L_317 E_437 1.5e-155 539.7 5.3e-155 537.0 +L_323 E_368 2.0e-182 629.0 6.4e-182 626.3 +L_617 E_432 2.8e-147 512.3 2.0e-151 525.0 +L_621 E_13 3.3e-37 144.4 4.8e-37 142.9 +L_627 E_368 2.6e-185 638.6 5.6e-186 639.8 +# M.fasta E.fasta +# 1.4e-164 569.7 9.9e-167 575.9 +M_10 E_10 5.2e-128 448.0 1.1e-127 445.7 +M_11 E_11 4.5e-63 231.1 1.0e-62 228.8 +M_14 E_14 2.3e-164 568.9 9.7e-167 575.9 +M_15 E_15 7.2e-103 364.0 3.2e-104 367.5 +M_16 E_16 1.3e-50 189.5 1.1e-50 188.7 +M_17 E_17 2.2e-198 682.2 6.1e-200 686.4 +M_18 E_18 1.3e-81 293.1 1.1e-81 292.4 +M_19 E_19 4.5e-29 117.1 4.3e-30 119.4 +M_313 E_313 1.2e-178 616.3 3.1e-178 614.0 +M_319 E_367 2.8e-157 545.4 2.8e-158 547.7 +M_323 E_317 3.6e-171 591.7 6.6e-171 589.7 +M_336 E_366 3.6e-168 581.6 3.3e-167 577.4 +M_621 E_13 4.5e-42 160.6 5.0e-42 159.5 +M_627 E_368 2.4e-180 622.1 1.4e-181 625.2 +M_634 E_317 1.4e-164 569.7 9.9e-167 575.9 |
| b |
| diff -r 000000000000 -r 4850f0d15f01 test-data/result.proteinortho.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/result.proteinortho.tsv Tue Feb 18 17:57:28 2020 -0500 |
| b |
| @@ -0,0 +1,35 @@ +# Species Genes Alg.-Conn. C.fasta C2.fasta E.fasta L.fasta M.fasta +2 5 0.16 * * * L_641,L_643 M_640,M_642,M_649 +4 6 0.115 C_12,C_21 * E_313,E_315 L_313 M_313 +3 6 0.301 C_164,C_166,C_167,C_2 * * L_2 M_2 +2 4 0.489 * * * L_645,L_647 M_644,M_646 +3 3 0.312 * * E_367 L_319 M_319 +4 5 0.165 C_63,C_22 * E_19 L_19 M_19 +3 3 0.812 C_20 * * L_20 M_20 +2 2 1 * * * L_9 M_9 +2 2 1 * * * L_8 M_8 +2 2 1 * * * L_619 M_619 +2 2 1 * * * L_6 M_6 +2 2 1 * * * L_5 M_5 +2 2 1 * * * L_4 M_4 +2 2 1 * * * L_333 M_333 +2 2 1 * * * L_3 M_3 +5 5 0.714 C_10 C_10 E_10 L_10 M_10 +4 4 0.803 C_64 * E_18 L_18 M_18 +4 4 0.762 C_17 * E_17 L_17 M_17 +4 4 0.758 C_16 * E_16 L_16 M_16 +4 4 0.78 C_15 * E_15 L_15 M_15 +4 4 0.793 C_14 * E_14 L_14 M_14 +4 4 0.718 C_11 * E_11 L_11 M_11 +3 3 0.316 * * E_432 L_617 M_617 +4 4 0.725 C_13 * E_13 L_621 M_621 +2 2 1 * * * L_328 M_328 +2 2 1 * * * L_623 M_623 +3 3 0.331 * * E_437 L_317 M_317 +2 3 0.333 * * * L_637,L_639 M_638 +2 2 1 * * * L_635 M_636 +4 6 0.126 C_1 * E_368 L_627,L_323 M_627,M_630 +2 3 0.331 * * * L_631,L_633 M_632 +2 2 1 * * * L_331 M_331 +2 3 0.329 * * E_317 * M_634,M_323 +3 3 0.322 * * E_366 L_336 M_336 |