| Previous changeset 0:40b87aef5241 (2021-08-26) Next changeset 2:33092577d65d (2021-10-21) |
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Commit message:
"planemo upload commit 87560553f1dbbd3e0ab7d7157fa5a7f32f61dca1" |
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modified:
funannotate_predict.xml macros.xml |
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added:
test-data/compare/Genus_species.gbk test-data/compare/Other_beast.gbk test-data/compare/Other_species.gbk test-data/compare/Yet_another.gbk test-data/funannotate_db/Pfam-A.clans.tsv test-data/funannotate_db/Pfam-A.hmm test-data/funannotate_db/Pfam-A.hmm.h3f test-data/funannotate_db/Pfam-A.hmm.h3i test-data/funannotate_db/Pfam-A.hmm.h3m test-data/funannotate_db/Pfam-A.hmm.h3p test-data/funannotate_db/dbCAN.hmm test-data/funannotate_db/dbCAN.hmm.h3f test-data/funannotate_db/dbCAN.hmm.h3i test-data/funannotate_db/dbCAN.hmm.h3m test-data/funannotate_db/dbCAN.hmm.h3p test-data/funannotate_db/go.obo test-data/funannotate_db/interpro.tsv test-data/funannotate_db/merops.dmnd test-data/funannotate_db/merops.formatted.fa test-data/funannotate_db/ncbi_cleaned_gene_products.txt test-data/funannotate_db/uniprot.dmnd |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 funannotate_predict.xml --- a/funannotate_predict.xml Thu Aug 26 06:55:33 2021 +0000 +++ b/funannotate_predict.xml Mon Oct 04 19:37:44 2021 +0000 |
| [ |
| b'@@ -32,6 +32,8 @@\n --database \'$database.fields.path\'\n #end if\n \n+$force\n+\n --species \'${organism.species}\'\n --isolate \'${organism.isolate}\'\n --strain \'${organism.strain}\'\n@@ -46,7 +48,7 @@\n --parameters \'${parameters}\'\n #end if\n \n-#if $evidences.rna_bam:\n+#if $evidences.rna_bam\n --rna_bam ${evidences.rna_bam}\n #end if\n \n@@ -71,6 +73,9 @@\n --p2g_pident ${evidences.p2g_pident}\n --p2g_prefilter ${evidences.p2g_prefilter}\n \n+--busco_seed_species \'${busco.busco_seed_species}\'\n+--busco_db \'${busco.busco_db}\'\n+\n #if $augustus.augustus_species != \'none\':\n --augustus_species \'${augustus.augustus_species}\'\n #end if\n@@ -85,9 +90,6 @@\n --soft_mask ${genemark.soft_mask}\n #end if\n \n---busco_seed_species \'${busco.busco_seed_species}\'\n---busco_db \'${busco.busco_db}\'\n-\n $evm.repeats2evm\n #if $evm.evm_partitioning.evm_partition == "yes":\n --evm-partition-interval ${evm.evm_partitioning.evm_partition_interval}\n@@ -145,6 +147,8 @@\n </options>\n </param>\n \n+ <param argument="--force" type="boolean" checked="true" truevalue="" falsevalue="--force" label="Check the genome sequence" help="Disable at your own risk if you want to ignore problems in the genome sequence reported by Funannotate" />\n+\n <section name="organism" expanded="true" title="Organism">\n <param argument="--species" type="text" optional="false" label="Name of the species to annotate" help="e.g. Genus species">\n <validator type="empty_field" />\n@@ -179,18 +183,31 @@\n </param>\n </section>\n \n+ <section name="busco" expanded="true" title="Busco">\n+ <param argument="--busco_db" type="select" label="BUSCO models to align" help="BUSCO will be used to perform initial training of ab initio predictors (e.g. Augustus).">\n+ <expand macro="busco_species"/>\n+ </param>\n+ <param argument="--busco_seed_species" type="select" label="Initial Augustus species training set for BUSCO alignment" help="Used when BUSCO runs Augustus internally.">\n+ <expand macro="augustus_species"/>\n+ </param>\n+ </section>\n+\n+ <section name="filtering" expanded="true" title="Filtering">\n+ <param argument="--min_intronlen" type="integer" value="10" label="Minimum intron length" />\n+ <param argument="--max_intronlen" type="integer" value="3000" label="Maximum intron length" />\n+ <param argument="--min_protlen" type="integer" value="50" label="Minimum protein length" />\n+ <param argument="--keep_no_stops" type="boolean" checked="false" truevalue="--keep_no_stops" falsevalue="" label="Keep gene models without valid stops" />\n+ <param argument="--repeat_filter" type="select" label="Repetitive gene model filtering" help="\'overlap\' drops gene models that are more than 90% contained within a repeat region; \'blast\' compares the amino acid sequences to a small database of known transposons">\n+ <option value="overlap blast" selected="True">overlap + blast</option>\n+ <option value="overlap">overlap</option>\n+ <option value="blast">blast</option>\n+ <option value="none">none</option>\n+ </param>\n+ </section>\n+\n <param argument="--parameters" type="data" format="json" optional="true" label="Ab-initio training parameters from a previous run" help="If specified, will over-rule any other training presets based on sepcies selection." />\n \n- <section name="other_predictors" expanded="false" title="Other annotations">\n- <param argument="--stringtie" type="data" format="gtf" optional="true" label="StringTie GTF result" />\n- <param argument="--maker_gff" type="data" format="gff3" optional="true" label="MAKER2 GFF file" help="Parse results directly to EVM" />\n- <param argument="--pasa_gff" type="data" format="gff3" optional="true" label="PASA generated gene models" />\n- '..b'not_gbk">\n <assert_contents>\n@@ -470,6 +510,77 @@\n <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>\n </assert_stderr>\n </test>\n+\n+ <!-- proteins -->\n+ <test>\n+ <param name="input" value="genome_masked.fa" />\n+ <param name="database" value="2021-07-20-120000" />\n+ <section name="organism">\n+ <param name="species" value="Genus species" />\n+ </section>\n+ <section name="evidences">\n+ <conditional name="prot_evidence">\n+ <param name="prot_evidence_source" value="custom" />\n+ <param name="protein_evidence" value="predict_scratch/Genus_species.proteins.fa" />\n+ </conditional>\n+ </section>\n+ <section name="busco">\n+ <param name="busco_seed_species" value="fly" />\n+ <param name="busco_db" value="insecta" />\n+ </section>\n+ <section name="augustus">\n+ <param name="min_training_models" value="3" />\n+ </section>\n+ <param name="outputs" value="gbk,tbl,gff3,proteins_fa,mrna_transcripts_fa,cds_transcripts_fa,tbl2asn_error,tbl2asn_report,tbl2asn_validation,stats" />\n+ <!-- non deterministic results, so can\'t be more precise here -->\n+ <output name="annot_gbk">\n+ <assert_contents>\n+ <has_text text=" TITLE Direct Submission" />\n+ <has_text text="/locus_tag="FUN_000001"" />\n+ </assert_contents>\n+ </output>\n+ <output name="annot_tbl">\n+ <assert_contents>\n+ <has_text text=">Feature sample" />\n+ <has_text text="gnl|ncbi|FUN_000001-T1_mrna" />\n+ </assert_contents>\n+ </output>\n+ <output name="annot_gff3">\n+ <assert_contents>\n+ <has_text text="##gff-version 3" />\n+ <has_text text="ID=FUN_000001-T1;Parent=FUN_000001;product=hypothetical protein;" />\n+ </assert_contents>\n+ </output>\n+ <output name="fasta_proteins">\n+ <assert_contents>\n+ <has_text text=">FUN_000001-T1 FUN_000001" />\n+ </assert_contents>\n+ </output>\n+ <output name="fasta_transcripts_mrna">\n+ <assert_contents>\n+ <has_text text=">FUN_000001-T1 FUN_000001" />\n+ </assert_contents>\n+ </output>\n+ <output name="fasta_transcripts_cds">\n+ <assert_contents>\n+ <has_text text=">FUN_000001-T1 FUN_000001" />\n+ </assert_contents>\n+ </output>\n+ <assert_stderr>\n+ <has_text text="augustus busco"/>\n+ <has_text text="glimmerhmm busco"/>\n+ <has_text text="snap busco"/>\n+ <has_text text="Running BUSCO to find conserved gene models for training ab-initio predictors"/>\n+ <has_text text="Skipping CodingQuarry as no --rna_bam passed"/>\n+ <has_text text="Running Augustus gene prediction using genus_species parameters"/>\n+ <has_text text="Training Augustus using BUSCO gene models"/>\n+ <not_has_text text="Aligning transcript evidence to genome with minimap2"/>\n+ <not_has_text text="Found 16 alignments, wrote GFF3 and Augustus hints to file"/>\n+ <not_has_text text="Extracting hints from RNA-seq BAM file using bam2hints"/>\n+ <has_text text="Mapping 13 proteins to genome using diamond and exonerate"/>\n+ <has_text text="Found 4 preliminary alignments --> aligning with exonerate"/>\n+ </assert_stderr>\n+ </test>\n </tests>\n <help><![CDATA[\n Funannotate_ predict\n' |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 macros.xml --- a/macros.xml Thu Aug 26 06:55:33 2021 +0000 +++ b/macros.xml Mon Oct 04 19:37:44 2021 +0000 |
| b |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> <macros> <token name="@TOOL_VERSION@">1.8.9</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <xml name="requirements"> <requirement type="package" version="@TOOL_VERSION@">funannotate</requirement> |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/compare/Genus_species.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/compare/Genus_species.gbk Mon Oct 04 19:37:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,4260 @@\n+LOCUS sample 215740 bp DNA linear 28-SEP-2021\n+DEFINITION Genus species.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Genus species\n+ ORGANISM Genus species\n+ Unclassified.\n+REFERENCE 1 (bases 1 to 215740)\n+ AUTHORS Palmer,J.M.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (28-SEP-2021) CFMR, USDA Forest Service, 1 Gifford\n+ Pinchot Drive, Madison, WI 53726, USA\n+COMMENT \'Annotated using 1.8.9\'.\n+FEATURES Location/Qualifiers\n+ source 1..215740\n+ /organism="Genus species"\n+ /mol_type="genomic DNA"\n+ gene complement(1092..1466)\n+ /locus_tag="FUN_000001"\n+ mRNA complement(1092..1466)\n+ /locus_tag="FUN_000001"\n+ /product="hypothetical protein"\n+ CDS complement(1092..1466)\n+ /locus_tag="FUN_000001"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUN_000001-T1"\n+ /translation="MSSFLLVIFILLALRTSESSETGNPLANEPDPLYMKLVDPMVAG\n+ ESPKRMIKDQKDVGLKSTSSSEELRKLPKTRGRQKRFIRNPNYVKANEFYDKMLSSEY\n+ VSKRYKDLPPPHPGFGADQPPA"\n+ gene 2126..3863\n+ /locus_tag="FUN_000002"\n+ mRNA join(2126..2199,2258..3224,3284..3490,3549..3863)\n+ /locus_tag="FUN_000002"\n+ /product="hypothetical protein"\n+ CDS join(2126..2199,2258..3224,3284..3490,3549..3863)\n+ /locus_tag="FUN_000002"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUN_000002-T1"\n+ /translation="MPPTINNSAVNSAAEKRPQRQTERKSEIICRVKYGNNLPDIPFD\n+ LKFLQYPFDSHRFVQYNPTSLERNFKYDVLTEHDLGVTVDLINRELYQADSMTLLDPA\n+ DEKLLEEETLTPTDSVRSRQHSRTVSWLRKSEYISTEQTRFQPQNLENIEAKVGYNVK\n+ KSLREETLYLDREAQIKAIEKTFSDTKSEITKHYSKPNVVPVEVLPIFPDFTNWKFPC\n+ AQVIFDSDPAPAGKNVPAQLEEMSQAMIRGVMDESGEQFVAYFLPTEQTLEKRRTDFI\n+ NGELYKEEEEYEYKIAREYNWNVKTKASKGYEENYFFVMRQDGIYYNELETRVRLNKR\n+ RVKVGQQPNNTKLVVKHRPLDSMEHRMQRYRERQLEVPGEEEEIVEEVREEEQMQIIG\n+ ETEKTSEDAAVGAQAASGADSPAQDLDLAPALGPAAAQSLVLGLVAAPDHAQIRRQDP\n+ RNPDPDRDRYHVPDPVPSPALGRVLGRDPSPVPDHVRAPDLALGRDRPAGLAVARLLV\n+ QDPALEAPQMND"\n+ gene complement(4883..5802)\n+ /locus_tag="FUN_000003"\n+ mRNA complement(join(4883..5539,5797..5802))\n+ /locus_tag="FUN_000003"\n+ /product="hypothetical protein"\n+ CDS complement(join(4883..5539,5797..5802))\n+ /locus_tag="FUN_000003"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUN_000003-T1"\n+ /translation="MYDQEPYKCHLCSKTFRMKGSLRIHLKVVHMMGVPCSNPNPNPN\n+ PSPTPASTTSAVTATPKLSICDRIRHTEPGALGNGNNSTCTASQPYALSGALSMLQQS\n+ PSSPESGTATPKLWECDVCSKSFTTKYFLKKHKRLHTGEMPYTCEICARTFTFQQSYH\n+ KHLLYHSEVKPHVCGVCGRAFKELSTLHNHQRIHSGEKPFKCEVCGEYRSNPLISRPL\n+ FC"\n+ gene complement(8696..10557)\n+ /locus_tag="FUN_000004"\n+ mRNA complement(join(8696..10462,10549..10557))\n+ /locus_tag="FUN_000004"\n+ /product="hypothetical protein"\n+ CDS complement(join(8696..10462,10549..10557))\n+ /locus_tag="FUN_000004"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUN_000004-T'..b'1 agcttttggc actgctcaac gacaatgtcg tcgattgact gcgaaagcag tgcctcctgc\n+ 4501 tcaggatcca caatggagct gctgttgatg gcagctattt cggcgctcgc tggtgaaggc\n+ 4561 tgagtatgcg agtcgttgcc ctccaggaac gcctttatca gctgctccgg tgtctgggcc\n+ 4621 tcctcggtgg gacatcgatg ggtcctttga ctgaccttgt acctgaacgt cttttggcag\n+ 4681 agctcgcact tgtagggcat cactcccgtg tggatgcgcg tgtggacaag gaaagagact\n+ 4741 cgctgccgga aacacttgcc tgtggacgag tccgaaatac gaaaaggtta gacatggagt\n+ 4801 gacccggaaa agaaggtata cctctccttc atttaaagta aatagggcaa atcgcaatgg\n+ 4861 agtatgctca tttataagct ggctaacaaa ataaggggcg gctaattaag gggtttgatc\n+ 4921 gatactcacc gcagacttcg cacttgaagg gcttttcgcc gctgtgaatc ctctggtggt\n+ 4981 tatgcagcgt agacagttcc ttgaaggcgc gtccacaaac cccgcagaca tggggcttta\n+ 5041 cctcgctgtg gtagagcaaa tgcttgtggt acgactgctg gaaggtgaag gtcctggcgc\n+ 5101 agatctcgca tgtgtacggc atctcgccgg tgtggagccg cttgtgcttc ttcagaaagt\n+ 5161 acttggtggt gaaggacttg ctgcacacat cgcactccca cagcttcggg gtggccgtgc\n+ 5221 ccgactccgg cgaactgggg gactgctgga gcatgctcag cgccccactc agcgcgtatg\n+ 5281 gctgggatgc ggtgcacgtg gagttatttc cgttgccaag ggctccaggc tctgtgtgtc\n+ 5341 gaatgcgatc gcaaatgctc agcttgggcg tggcagtaac tgcactggtg gtagaagcgg\n+ 5401 gtgtaggact gggattagga tttggattgg gattggagca gggcacgccc atcatgtgca\n+ 5461 ctactttcag gtggattcga agggagccct tcattcggaa cgtcttggag cagagatggc\n+ 5521 acttgtaggg ctcctggtcc tgtataaagc aataatcgga atttcactta tatttatcaa\n+ 5581 ttcatcaata tgccctcatg gccaaatatt ccattacatt accgtctgtc tctcagtttc\n+ 5641 aaatttatgc acaaaaatca ttcactttca ttcactatat cacaaagttg ccatggtttt\n+ 5701 aaattgatca aaaacaaatt aatatctatc atatatatac atagtcatat gaacagttga\n+ 5761 aaaattaatt gaaaataatg ggaacgatat acgtacatac atcagttgtt tttaaaatat\n+ 5821 aagggtatat agatttcttt cttgttgttg ttgattttaa ttacgtcaaa cttttgtttc\n+ 5881 agattcaatg taaatggtct agctttttaa gtatgatttt tttttgctgc cagtgagcat\n+ 5941 agaaaaaaaa aatcaaaatc gatataagaa tatgcgaaag tgcattacga aactctttag\n+ 6001 ataatagcac ttaatatatg tacatagcca atagttaccg gttccttctg ttggggttcc\n+ 6061 ttttgcttgg gttctccctc cgcattttcg tggactaagc ggacgtgcat gtccctcagc\n+ 6121 tcggtattcc ggaaactgaa ctcgcaaatg tcgcagtggg cgggcggggt ggtccgcaca\n+ 6181 ggcggtgggg ttgggacgac gggcttggac ctggttcgct tggccctccg tttgggagga\n+ 6241 gctgcggcaa ggaagccccg ggacgaggcg ggttggccat tcgctggact ctcgtttccc\n+ 6301 tcctgagcca tcagacttgt gtgcgagaac aggtggatgg tgagcttgtc cagccccagg\n+ 6361 aagagctcct tgcagttggc aaagggacag gccagtgggc cgttggccgc cttgatcagc\n+ 6421 ctctgctgca gtgcgtcaat actgccgaaa ctgggcaccg cgcagagcgg acacagcacc\n+ 6481 gaggtggaac acatttcgcc agtgcactca atcgaatctt atgcaaatgc ttcacctcct\n+ 6541 attgggatta tcctcctgtt cggtctgtga tcatctattc aggagtccat tcccagactg\n+ 6601 cctagtcttt ctgctttcaa aattttctaa aaatatcagc aagtgaagat ttttgaaaac\n+ 6661 tttgggccca gcaatctgac ttctcggcac cgatgccagc taacgaaata atgaaaaata\n+ 6721 atgaaatgcc cggcgcggat cgtcgaatcg tcaagaagac tttcggaaac actcgcagca\n+ 6781 ccgaaatccc atctctcgaa caaggcagtc tcttttctcc gtgtctctgg gtagctcatt\n+ 6841 tcgaaatata gctctgagca cggctatata ctatatgtat gtagaattat ttctggccga\n+ 6901 tatatgttgc actggcggcc atatagcctt cgttctagtc tttgtaacgc acgatgcgca\n+ 6961 ggagcaattc gctgagatga ccacatgcga tttgcgggac ttatctagag atctatcatt\n+ 7021 atcgccagat tggtttaata attggctttt ccgccaatat ccaattggaa tatggttggt\n+ 7081 tactgcaatt gtcgctccat tttttaagca ctccataaaa agtaaacaca ttaatatgta\n+ 7141 ctcttattgg agatttcttc tttcgatttt agtttcggac cagtgaaaat cattcgtttc\n+ 7201 attttcgtaa ataagaactg agaaaatatt attattatat atatttcttt attaggaaaa\n+ 7261 tacgaagatt gagtatttca gattgaatta gcatatccgt ctaaatctta atgctgtaat\n+ 7321 gagcttactt gagatctgat caaaaccaat acaaaaccca caccaaaggt ggtagctaat\n+ 7381 atacatattt tgtgtaatac ttttgtagag tatttactat tcagcgattt aaacaagcaa\n+ 7441 tcgcctagac acacacattt gtccgcctat gtgtatgtgc accgagctat acccccactg\n+ 7501 aatcgctgtg tgctattttt atggccgcga tgctctcttg ttttgacccg cttgggcaac\n+//\n' |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/compare/Other_beast.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/compare/Other_beast.gbk Mon Oct 04 19:37:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,4148 @@\n+LOCUS sample 215740 bp DNA linear 21-JUL-2021\n+DEFINITION Other beast.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Other beast\n+ ORGANISM Other beast\n+ Unclassified.\n+REFERENCE 1 (bases 1 to 215740)\n+ AUTHORS Palmer,J.M.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (21-JUL-2021) CFMR, USDA Forest Service, 1 Gifford\n+ Pinchot Drive, Madison, WI 53726, USA\n+COMMENT \'Annotated using 1.8.7\'.\n+FEATURES Location/Qualifiers\n+ source 1..215740\n+ /organism="Other beast"\n+ /mol_type="genomic DNA"\n+ gene complement(1092..1466)\n+ /locus_tag="FUNC_000001"\n+ mRNA complement(1092..1466)\n+ /locus_tag="FUNC_000001"\n+ /product="hypothetical protein"\n+ CDS complement(1092..1466)\n+ /locus_tag="FUNC_000001"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUNC_000001-T1"\n+ /translation="MSSFLLVIFILLALRTSESSETGNPLANEPDPLYMKLVDPMVAG\n+ ESPKRMIKDQKDVGLKSTSSSEELRKLPKTRGRQKRFIRNPNYVKANEFYDKMLSSEY\n+ VSKRYKDLPPPHPGFGADQPPA"\n+ gene complement(2565..3142)\n+ /locus_tag="FUNC_000002"\n+ mRNA complement(join(2565..2686,2883..3004,3138..3142))\n+ /locus_tag="FUNC_000002"\n+ /product="hypothetical protein"\n+ CDS complement(join(2565..2686,2883..3004,3138..3142))\n+ /locus_tag="FUNC_000002"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUNC_000002-T1"\n+ /translation="MPLYGVSPASALWAGSRRQTVRRSRPSHHESWPATSPPAGRAQS\n+ LLPKRLLDVVTDLGLDVLQVLGLEARLLGGDVLGFAQP"\n+ gene complement(4248..5802)\n+ /locus_tag="FUNC_000003"\n+ mRNA complement(join(4248..4742,4937..5539,5797..5802))\n+ /locus_tag="FUNC_000003"\n+ /product="hypothetical protein"\n+ CDS complement(join(4248..4742,4937..5539,5797..5802))\n+ /locus_tag="FUNC_000003"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUNC_000003-T1"\n+ /translation="MYDQEPYKCHLCSKTFRMKGSLRIHLKVVHMMGVPCSNPNPNPN\n+ PSPTPASTTSAVTATPKLSICDRIRHTEPGALGNGNNSTCTASQPYALSGALSMLQQS\n+ PSSPESGTATPKLWECDVCSKSFTTKYFLKKHKRLHTGEMPYTCEICARTFTFQQSYH\n+ KHLLYHSEVKPHVCGVCGRAFKELSTLHNHQRIHSGEKPFKCERVSFLVHTRIHTGVM\n+ PYKCELCQKTFRYKVSQRTHRCPTEEAQTPEQLIKAFLEGNDSHTQPSPASAEIAAIN\n+ SSSIVDPEQEALLSQSIDDIVVEQCQKLGICGVEPREEGQLISLQPVAVVHFSGNGSP\n+ LQQLQNLRIYSPQQTELPSSDGEVFQRFLMDAT"\n+ gene complement(7691..10664)\n+ /locus_tag="FUNC_000004"\n+ mRNA complement(join(7691..8385,8707..10499,10657..10664))\n+ /locus_tag="FUNC_000004"\n+ /product="hypothetical protein"\n+ CDS complement(join(7691..8385,8707..10499,10657..10664))\n+ /locus_tag="FUNC_000004"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUNC_000004-T1"\n+ /translation="MSNKREIDELTSRIKSAKTTLVEWTEAMEDGNKGYQLIEKYYLD\n+ DQQKARELNIKRQLLQADIDKRRKQVVLLYDEQMTLEKNLERTACLYRSAHAERRQMV\n+ ETWKSAVNQMTQREHDIQRSEIECAELAQKAQQTAQTYKEYDNQLTEVIENNRQVELA\n+ IESLNEESSDMKNQIQILIDATLLKEREIDGLRRELENLSNRVHLQRMDNRSQMKKRD\n+ EKAKELENFASVME'..b'1 agcttttggc actgctcaac gacaatgtcg tcgattgact gcgaaagcag tgcctcctgc\n+ 4501 tcaggatcca caatggagct gctgttgatg gcagctattt cggcgctcgc tggtgaaggc\n+ 4561 tgagtatgcg agtcgttgcc ctccaggaac gcctttatca gctgctccgg tgtctgggcc\n+ 4621 tcctcggtgg gacatcgatg ggtcctttga ctgaccttgt acctgaacgt cttttggcag\n+ 4681 agctcgcact tgtagggcat cactcccgtg tggatgcgcg tgtggacaag gaaagagact\n+ 4741 cgctgccgga aacacttgcc tgtggacgag tccgaaatac gaaaaggtta gacatggagt\n+ 4801 gacccggaaa agaaggtata cctctccttc atttaaagta aatagggcaa atcgcaatgg\n+ 4861 agtatgctca tttataagct ggctaacaaa ataaggggcg gctaattaag gggtttgatc\n+ 4921 gatactcacc gcagacttcg cacttgaagg gcttttcgcc gctgtgaatc ctctggtggt\n+ 4981 tatgcagcgt agacagttcc ttgaaggcgc gtccacaaac cccgcagaca tggggcttta\n+ 5041 cctcgctgtg gtagagcaaa tgcttgtggt acgactgctg gaaggtgaag gtcctggcgc\n+ 5101 agatctcgca tgtgtacggc atctcgccgg tgtggagccg cttgtgcttc ttcagaaagt\n+ 5161 acttggtggt gaaggacttg ctgcacacat cgcactccca cagcttcggg gtggccgtgc\n+ 5221 ccgactccgg cgaactgggg gactgctgga gcatgctcag cgccccactc agcgcgtatg\n+ 5281 gctgggatgc ggtgcacgtg gagttatttc cgttgccaag ggctccaggc tctgtgtgtc\n+ 5341 gaatgcgatc gcaaatgctc agcttgggcg tggcagtaac tgcactggtg gtagaagcgg\n+ 5401 gtgtaggact gggattagga tttggattgg gattggagca gggcacgccc atcatgtgca\n+ 5461 ctactttcag gtggattcga agggagccct tcattcggaa cgtcttggag cagagatggc\n+ 5521 acttgtaggg ctcctggtcc tgtataaagc aataatcgga atttcactta tatttatcaa\n+ 5581 ttcatcaata tgccctcatg gccaaatatt ccattacatt accgtctgtc tctcagtttc\n+ 5641 aaatttatgc acaaaaatca ttcactttca ttcactatat cacaaagttg ccatggtttt\n+ 5701 aaattgatca aaaacaaatt aatatctatc atatatatac atagtcatat gaacagttga\n+ 5761 aaaattaatt gaaaataatg ggaacgatat acgtacatac atcagttgtt tttaaaatat\n+ 5821 aagggtatat agatttcttt cttgttgttg ttgattttaa ttacgtcaaa cttttgtttc\n+ 5881 agattcaatg taaatggtct agctttttaa gtatgatttt tttttgctgc cagtgagcat\n+ 5941 agaaaaaaaa aatcaaaatc gatataagaa tatgcgaaag tgcattacga aactctttag\n+ 6001 ataatagcac ttaatatatg tacatagcca atagttaccg gttccttctg ttggggttcc\n+ 6061 ttttgcttgg gttctccctc cgcattttcg tggactaagc ggacgtgcat gtccctcagc\n+ 6121 tcggtattcc ggaaactgaa ctcgcaaatg tcgcagtggg cgggcggggt ggtccgcaca\n+ 6181 ggcggtgggg ttgggacgac gggcttggac ctggttcgct tggccctccg tttgggagga\n+ 6241 gctgcggcaa ggaagccccg ggacgaggcg ggttggccat tcgctggact ctcgtttccc\n+ 6301 tcctgagcca tcagacttgt gtgcgagaac aggtggatgg tgagcttgtc cagccccagg\n+ 6361 aagagctcct tgcagttggc aaagggacag gccagtgggc cgttggccgc cttgatcagc\n+ 6421 ctctgctgca gtgcgtcaat actgccgaaa ctgggcaccg cgcagagcgg acacagcacc\n+ 6481 gaggtggaac acatttcgcc agtgcactca atcgaatctt atgcaaatgc ttcacctcct\n+ 6541 attgggatta tcctcctgtt cggtctgtga tcatctattc aggagtccat tcccagactg\n+ 6601 cctagtcttt ctgctttcaa aattttctaa aaatatcagc aagtgaagat ttttgaaaac\n+ 6661 tttgggccca gcaatctgac ttctcggcac cgatgccagc taacgaaata atgaaaaata\n+ 6721 atgaaatgcc cggcgcggat cgtcgaatcg tcaagaagac tttcggaaac actcgcagca\n+ 6781 ccgaaatccc atctctcgaa caaggcagtc tcttttctcc gtgtctctgg gtagctcatt\n+ 6841 tcgaaatata gctctgagca cggctatata ctatatgtat gtagaattat ttctggccga\n+ 6901 tatatgttgc actggcggcc atatagcctt cgttctagtc tttgtaacgc acgatgcgca\n+ 6961 ggagcaattc gctgagatga ccacatgcga tttgcgggac ttatctagag atctatcatt\n+ 7021 atcgccagat tggtttaata attggctttt ccgccaatat ccaattggaa tatggttggt\n+ 7081 tactgcaatt gtcgctccat tttttaagca ctccataaaa agtaaacaca ttaatatgta\n+ 7141 ctcttattgg agatttcttc tttcgatttt agtttcggac cagtgaaaat cattcgtttc\n+ 7201 attttcgtaa ataagaactg agaaaatatt attattatat atatttcttt attaggaaaa\n+ 7261 tacgaagatt gagtatttca gattgaatta gcatatccgt ctaaatctta atgctgtaat\n+ 7321 gagcttactt gagatctgat caaaaccaat acaaaaccca caccaaaggt ggtagctaat\n+ 7381 atacatattt tgtgtaatac ttttgtagag tatttactat tcagcgattt aaacaagcaa\n+ 7441 tcgcctagac acacacattt gtccgcctat gtgtatgtgc accgagctat acccccactg\n+ 7501 aatcgctgtg tgctattttt atggccgcga tgctctcttg ttttgacccg cttgggcaac\n+//\n' |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/compare/Other_species.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/compare/Other_species.gbk Mon Oct 04 19:37:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,4259 @@\n+LOCUS sample 215740 bp DNA linear 22-JUL-2021\n+DEFINITION Other species.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Other species\n+ ORGANISM Other species\n+ Unclassified.\n+REFERENCE 1 (bases 1 to 215740)\n+ AUTHORS Palmer,J.M.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (22-JUL-2021) CFMR, USDA Forest Service, 1 Gifford\n+ Pinchot Drive, Madison, WI 53726, USA\n+COMMENT \'Annotated using 1.8.7\'.\n+FEATURES Location/Qualifiers\n+ source 1..215740\n+ /organism="Other species"\n+ /mol_type="genomic DNA"\n+ gene <2331..3254\n+ /locus_tag="FUNB_000001"\n+ mRNA <2331..3254\n+ /locus_tag="FUNB_000001"\n+ /product="hypothetical protein"\n+ CDS <2331..3254\n+ /locus_tag="FUNB_000001"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUNB_000001-T1"\n+ /translation="YPFDSHRFVQYNPTSLERNFKYDVLTEHDLGVTVDLINRELYQA\n+ DSMTLLDPADEKLLEEETLTPTDSVRSRQHSRTVSWLRKSEYISTEQTRFQPQNLENI\n+ EAKVGYNVKKSLREETLYLDREAQIKAIEKTFSDTKSEITKHYSKPNVVPVEVLPIFP\n+ DFTNWKFPCAQVIFDSDPAPAGKNVPAQLEEMSQAMIRGVMDESGEQFVAYFLPTEQT\n+ LEKRRTDFINGELYKEEEEYEYKIAREYNWNVKTKASKGYEENYFFVMRQDGIYYNEL\n+ ETRVRLNKRRVKVGQQPNNTKLVSIFMRIHL"\n+ gene complement(4883..5802)\n+ /locus_tag="FUNB_000002"\n+ mRNA complement(join(4883..5539,5797..5802))\n+ /locus_tag="FUNB_000002"\n+ /product="hypothetical protein"\n+ CDS complement(join(4883..5539,5797..5802))\n+ /locus_tag="FUNB_000002"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUNB_000002-T1"\n+ /translation="MYDQEPYKCHLCSKTFRMKGSLRIHLKVVHMMGVPCSNPNPNPN\n+ PSPTPASTTSAVTATPKLSICDRIRHTEPGALGNGNNSTCTASQPYALSGALSMLQQS\n+ PSSPESGTATPKLWECDVCSKSFTTKYFLKKHKRLHTGEMPYTCEICARTFTFQQSYH\n+ KHLLYHSEVKPHVCGVCGRAFKELSTLHNHQRIHSGEKPFKCEVCGEYRSNPLISRPL\n+ FC"\n+ gene complement(8696..10557)\n+ /locus_tag="FUNB_000003"\n+ mRNA complement(join(8696..10462,10549..10557))\n+ /locus_tag="FUNB_000003"\n+ /product="hypothetical protein"\n+ CDS complement(join(8696..10462,10549..10557))\n+ /locus_tag="FUNB_000003"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUNB_000003-T1"\n+ /translation="MIHSAKTTLVEWTEAMEDGNKGYQLIEKYYLDDQQKARELNIKR\n+ QLLQADIDKRRKQVVLLYDEQMTLEKNLERTACLYRSAHAERRQMVETWKSAVNQMTQ\n+ REHDIQRSEIECAELAQKAQQTAQTYKEYDNQLTEVIENNRQVELAIESLNEESSDMK\n+ NQIQILIDATLLKEREIDGLRRELENLSNRVHLQRMDNRSQMKKRDEKAKELENFASV\n+ MEKVNARLKSVQNKALNAEQRLQILEEMMQAEETALRNLDKEQEKVNEMLYRTQRQVI\n+ ELQDEEKVLKVQNDSLNSNLAAINRNQQQVNNELKRQTEIHYSLSFKCLEAERRLAEI\n+ KGLADDPEVEATNMARLNTLEQEYEKLQRLIATTEAQNKKLNYNMNNLVVQYNADEKE\n+ LEMVRFKIKEAQVYCEGTVKRLRQIRYENSELIVDLNMVKMRCSDLEVGIGGCEQGTY\n+ DLEQHRLAFRRAIKDRTVELRSQEDVLLLKKKHLNEELSTLRADLGERKKQIEAMKAR\n+ FELTAQLLGKNEDGSIMTSTQLKVVSAQERQMLADEGDALNKKVLKAEKEVVALENTL\n+ RQFDKSNDNYRKTFRSVDENSKGEL"\n+ gene complement(14247..15214)\n+ /locus_tag="FUNB_000004"\n+ mRNA complement(join(14247..14648,15209..15214))\n+ /locu'..b'1 agcttttggc actgctcaac gacaatgtcg tcgattgact gcgaaagcag tgcctcctgc\n+ 4501 tcaggatcca caatggagct gctgttgatg gcagctattt cggcgctcgc tggtgaaggc\n+ 4561 tgagtatgcg agtcgttgcc ctccaggaac gcctttatca gctgctccgg tgtctgggcc\n+ 4621 tcctcggtgg gacatcgatg ggtcctttga ctgaccttgt acctgaacgt cttttggcag\n+ 4681 agctcgcact tgtagggcat cactcccgtg tggatgcgcg tgtggacaag gaaagagact\n+ 4741 cgctgccgga aacacttgcc tgtggacgag tccgaaatac gaaaaggtta gacatggagt\n+ 4801 gacccggaaa agaaggtata cctctccttc atttaaagta aatagggcaa atcgcaatgg\n+ 4861 agtatgctca tttataagct ggctaacaaa ataaggggcg gctaattaag gggtttgatc\n+ 4921 gatactcacc gcagacttcg cacttgaagg gcttttcgcc gctgtgaatc ctctggtggt\n+ 4981 tatgcagcgt agacagttcc ttgaaggcgc gtccacaaac cccgcagaca tggggcttta\n+ 5041 cctcgctgtg gtagagcaaa tgcttgtggt acgactgctg gaaggtgaag gtcctggcgc\n+ 5101 agatctcgca tgtgtacggc atctcgccgg tgtggagccg cttgtgcttc ttcagaaagt\n+ 5161 acttggtggt gaaggacttg ctgcacacat cgcactccca cagcttcggg gtggccgtgc\n+ 5221 ccgactccgg cgaactgggg gactgctgga gcatgctcag cgccccactc agcgcgtatg\n+ 5281 gctgggatgc ggtgcacgtg gagttatttc cgttgccaag ggctccaggc tctgtgtgtc\n+ 5341 gaatgcgatc gcaaatgctc agcttgggcg tggcagtaac tgcactggtg gtagaagcgg\n+ 5401 gtgtaggact gggattagga tttggattgg gattggagca gggcacgccc atcatgtgca\n+ 5461 ctactttcag gtggattcga agggagccct tcattcggaa cgtcttggag cagagatggc\n+ 5521 acttgtaggg ctcctggtcc tgtataaagc aataatcgga atttcactta tatttatcaa\n+ 5581 ttcatcaata tgccctcatg gccaaatatt ccattacatt accgtctgtc tctcagtttc\n+ 5641 aaatttatgc acaaaaatca ttcactttca ttcactatat cacaaagttg ccatggtttt\n+ 5701 aaattgatca aaaacaaatt aatatctatc atatatatac atagtcatat gaacagttga\n+ 5761 aaaattaatt gaaaataatg ggaacgatat acgtacatac atcagttgtt tttaaaatat\n+ 5821 aagggtatat agatttcttt cttgttgttg ttgattttaa ttacgtcaaa cttttgtttc\n+ 5881 agattcaatg taaatggtct agctttttaa gtatgatttt tttttgctgc cagtgagcat\n+ 5941 agaaaaaaaa aatcaaaatc gatataagaa tatgcgaaag tgcattacga aactctttag\n+ 6001 ataatagcac ttaatatatg tacatagcca atagttaccg gttccttctg ttggggttcc\n+ 6061 ttttgcttgg gttctccctc cgcattttcg tggactaagc ggacgtgcat gtccctcagc\n+ 6121 tcggtattcc ggaaactgaa ctcgcaaatg tcgcagtggg cgggcggggt ggtccgcaca\n+ 6181 ggcggtgggg ttgggacgac gggcttggac ctggttcgct tggccctccg tttgggagga\n+ 6241 gctgcggcaa ggaagccccg ggacgaggcg ggttggccat tcgctggact ctcgtttccc\n+ 6301 tcctgagcca tcagacttgt gtgcgagaac aggtggatgg tgagcttgtc cagccccagg\n+ 6361 aagagctcct tgcagttggc aaagggacag gccagtgggc cgttggccgc cttgatcagc\n+ 6421 ctctgctgca gtgcgtcaat actgccgaaa ctgggcaccg cgcagagcgg acacagcacc\n+ 6481 gaggtggaac acatttcgcc agtgcactca atcgaatctt atgcaaatgc ttcacctcct\n+ 6541 attgggatta tcctcctgtt cggtctgtga tcatctattc aggagtccat tcccagactg\n+ 6601 cctagtcttt ctgctttcaa aattttctaa aaatatcagc aagtgaagat ttttgaaaac\n+ 6661 tttgggccca gcaatctgac ttctcggcac cgatgccagc taacgaaata atgaaaaata\n+ 6721 atgaaatgcc cggcgcggat cgtcgaatcg tcaagaagac tttcggaaac actcgcagca\n+ 6781 ccgaaatccc atctctcgaa caaggcagtc tcttttctcc gtgtctctgg gtagctcatt\n+ 6841 tcgaaatata gctctgagca cggctatata ctatatgtat gtagaattat ttctggccga\n+ 6901 tatatgttgc actggcggcc atatagcctt cgttctagtc tttgtaacgc acgatgcgca\n+ 6961 ggagcaattc gctgagatga ccacatgcga tttgcgggac ttatctagag atctatcatt\n+ 7021 atcgccagat tggtttaata attggctttt ccgccaatat ccaattggaa tatggttggt\n+ 7081 tactgcaatt gtcgctccat tttttaagca ctccataaaa agtaaacaca ttaatatgta\n+ 7141 ctcttattgg agatttcttc tttcgatttt agtttcggac cagtgaaaat cattcgtttc\n+ 7201 attttcgtaa ataagaactg agaaaatatt attattatat atatttcttt attaggaaaa\n+ 7261 tacgaagatt gagtatttca gattgaatta gcatatccgt ctaaatctta atgctgtaat\n+ 7321 gagcttactt gagatctgat caaaaccaat acaaaaccca caccaaaggt ggtagctaat\n+ 7381 atacatattt tgtgtaatac ttttgtagag tatttactat tcagcgattt aaacaagcaa\n+ 7441 tcgcctagac acacacattt gtccgcctat gtgtatgtgc accgagctat acccccactg\n+ 7501 aatcgctgtg tgctattttt atggccgcga tgctctcttg ttttgacccg cttgggcaac\n+//\n' |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/compare/Yet_another.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/compare/Yet_another.gbk Mon Oct 04 19:37:44 2021 +0000 |
| b |
| b'@@ -0,0 +1,4148 @@\n+LOCUS sample 215740 bp DNA linear 21-JUL-2021\n+DEFINITION Yet another.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Yet another\n+ ORGANISM Yet another\n+ Unclassified.\n+REFERENCE 1 (bases 1 to 215740)\n+ AUTHORS Palmer,J.M.\n+ TITLE Direct Submission\n+ JOURNAL Submitted (21-JUL-2021) CFMR, USDA Forest Service, 1 Gifford\n+ Pinchot Drive, Madison, WI 53726, USA\n+COMMENT \'Annotated using 1.8.7\'.\n+FEATURES Location/Qualifiers\n+ source 1..215740\n+ /organism="Yet another"\n+ /mol_type="genomic DNA"\n+ gene complement(1092..1466)\n+ /locus_tag="FUND_000001"\n+ mRNA complement(1092..1466)\n+ /locus_tag="FUND_000001"\n+ /product="hypothetical protein"\n+ CDS complement(1092..1466)\n+ /locus_tag="FUND_000001"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUND_000001-T1"\n+ /translation="MSSFLLVIFILLALRTSESSETGNPLANEPDPLYMKLVDPMVAG\n+ ESPKRMIKDQKDVGLKSTSSSEELRKLPKTRGRQKRFIRNPNYVKANEFYDKMLSSEY\n+ VSKRYKDLPPPHPGFGADQPPA"\n+ gene complement(2565..3142)\n+ /locus_tag="FUND_000002"\n+ mRNA complement(join(2565..2686,2883..3004,3138..3142))\n+ /locus_tag="FUND_000002"\n+ /product="hypothetical protein"\n+ CDS complement(join(2565..2686,2883..3004,3138..3142))\n+ /locus_tag="FUND_000002"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUND_000002-T1"\n+ /translation="MPLYGVSPASALWAGSRRQTVRRSRPSHHESWPATSPPAGRAQS\n+ LLPKRLLDVVTDLGLDVLQVLGLEARLLGGDVLGFAQP"\n+ gene complement(4248..5802)\n+ /locus_tag="FUND_000003"\n+ mRNA complement(join(4248..4742,4937..5539,5797..5802))\n+ /locus_tag="FUND_000003"\n+ /product="hypothetical protein"\n+ CDS complement(join(4248..4742,4937..5539,5797..5802))\n+ /locus_tag="FUND_000003"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUND_000003-T1"\n+ /translation="MYDQEPYKCHLCSKTFRMKGSLRIHLKVVHMMGVPCSNPNPNPN\n+ PSPTPASTTSAVTATPKLSICDRIRHTEPGALGNGNNSTCTASQPYALSGALSMLQQS\n+ PSSPESGTATPKLWECDVCSKSFTTKYFLKKHKRLHTGEMPYTCEICARTFTFQQSYH\n+ KHLLYHSEVKPHVCGVCGRAFKELSTLHNHQRIHSGEKPFKCERVSFLVHTRIHTGVM\n+ PYKCELCQKTFRYKVSQRTHRCPTEEAQTPEQLIKAFLEGNDSHTQPSPASAEIAAIN\n+ SSSIVDPEQEALLSQSIDDIVVEQCQKLGICGVEPREEGQLISLQPVAVVHFSGNGSP\n+ LQQLQNLRIYSPQQTELPSSDGEVFQRFLMDAT"\n+ gene complement(7691..10664)\n+ /locus_tag="FUND_000004"\n+ mRNA complement(join(7691..8385,8707..10499,10657..10664))\n+ /locus_tag="FUND_000004"\n+ /product="hypothetical protein"\n+ CDS complement(join(7691..8385,8707..10499,10657..10664))\n+ /locus_tag="FUND_000004"\n+ /codon_start=1\n+ /product="hypothetical protein"\n+ /protein_id="ncbi:FUND_000004-T1"\n+ /translation="MSNKREIDELTSRIKSAKTTLVEWTEAMEDGNKGYQLIEKYYLD\n+ DQQKARELNIKRQLLQADIDKRRKQVVLLYDEQMTLEKNLERTACLYRSAHAERRQMV\n+ ETWKSAVNQMTQREHDIQRSEIECAELAQKAQQTAQTYKEYDNQLTEVIENNRQVELA\n+ IESLNEESSDMKNQIQILIDATLLKEREIDGLRRELENLSNRVHLQRMDNRSQMKKRD\n+ EKAKELENFASVME'..b'1 agcttttggc actgctcaac gacaatgtcg tcgattgact gcgaaagcag tgcctcctgc\n+ 4501 tcaggatcca caatggagct gctgttgatg gcagctattt cggcgctcgc tggtgaaggc\n+ 4561 tgagtatgcg agtcgttgcc ctccaggaac gcctttatca gctgctccgg tgtctgggcc\n+ 4621 tcctcggtgg gacatcgatg ggtcctttga ctgaccttgt acctgaacgt cttttggcag\n+ 4681 agctcgcact tgtagggcat cactcccgtg tggatgcgcg tgtggacaag gaaagagact\n+ 4741 cgctgccgga aacacttgcc tgtggacgag tccgaaatac gaaaaggtta gacatggagt\n+ 4801 gacccggaaa agaaggtata cctctccttc atttaaagta aatagggcaa atcgcaatgg\n+ 4861 agtatgctca tttataagct ggctaacaaa ataaggggcg gctaattaag gggtttgatc\n+ 4921 gatactcacc gcagacttcg cacttgaagg gcttttcgcc gctgtgaatc ctctggtggt\n+ 4981 tatgcagcgt agacagttcc ttgaaggcgc gtccacaaac cccgcagaca tggggcttta\n+ 5041 cctcgctgtg gtagagcaaa tgcttgtggt acgactgctg gaaggtgaag gtcctggcgc\n+ 5101 agatctcgca tgtgtacggc atctcgccgg tgtggagccg cttgtgcttc ttcagaaagt\n+ 5161 acttggtggt gaaggacttg ctgcacacat cgcactccca cagcttcggg gtggccgtgc\n+ 5221 ccgactccgg cgaactgggg gactgctgga gcatgctcag cgccccactc agcgcgtatg\n+ 5281 gctgggatgc ggtgcacgtg gagttatttc cgttgccaag ggctccaggc tctgtgtgtc\n+ 5341 gaatgcgatc gcaaatgctc agcttgggcg tggcagtaac tgcactggtg gtagaagcgg\n+ 5401 gtgtaggact gggattagga tttggattgg gattggagca gggcacgccc atcatgtgca\n+ 5461 ctactttcag gtggattcga agggagccct tcattcggaa cgtcttggag cagagatggc\n+ 5521 acttgtaggg ctcctggtcc tgtataaagc aataatcgga atttcactta tatttatcaa\n+ 5581 ttcatcaata tgccctcatg gccaaatatt ccattacatt accgtctgtc tctcagtttc\n+ 5641 aaatttatgc acaaaaatca ttcactttca ttcactatat cacaaagttg ccatggtttt\n+ 5701 aaattgatca aaaacaaatt aatatctatc atatatatac atagtcatat gaacagttga\n+ 5761 aaaattaatt gaaaataatg ggaacgatat acgtacatac atcagttgtt tttaaaatat\n+ 5821 aagggtatat agatttcttt cttgttgttg ttgattttaa ttacgtcaaa cttttgtttc\n+ 5881 agattcaatg taaatggtct agctttttaa gtatgatttt tttttgctgc cagtgagcat\n+ 5941 agaaaaaaaa aatcaaaatc gatataagaa tatgcgaaag tgcattacga aactctttag\n+ 6001 ataatagcac ttaatatatg tacatagcca atagttaccg gttccttctg ttggggttcc\n+ 6061 ttttgcttgg gttctccctc cgcattttcg tggactaagc ggacgtgcat gtccctcagc\n+ 6121 tcggtattcc ggaaactgaa ctcgcaaatg tcgcagtggg cgggcggggt ggtccgcaca\n+ 6181 ggcggtgggg ttgggacgac gggcttggac ctggttcgct tggccctccg tttgggagga\n+ 6241 gctgcggcaa ggaagccccg ggacgaggcg ggttggccat tcgctggact ctcgtttccc\n+ 6301 tcctgagcca tcagacttgt gtgcgagaac aggtggatgg tgagcttgtc cagccccagg\n+ 6361 aagagctcct tgcagttggc aaagggacag gccagtgggc cgttggccgc cttgatcagc\n+ 6421 ctctgctgca gtgcgtcaat actgccgaaa ctgggcaccg cgcagagcgg acacagcacc\n+ 6481 gaggtggaac acatttcgcc agtgcactca atcgaatctt atgcaaatgc ttcacctcct\n+ 6541 attgggatta tcctcctgtt cggtctgtga tcatctattc aggagtccat tcccagactg\n+ 6601 cctagtcttt ctgctttcaa aattttctaa aaatatcagc aagtgaagat ttttgaaaac\n+ 6661 tttgggccca gcaatctgac ttctcggcac cgatgccagc taacgaaata atgaaaaata\n+ 6721 atgaaatgcc cggcgcggat cgtcgaatcg tcaagaagac tttcggaaac actcgcagca\n+ 6781 ccgaaatccc atctctcgaa caaggcagtc tcttttctcc gtgtctctgg gtagctcatt\n+ 6841 tcgaaatata gctctgagca cggctatata ctatatgtat gtagaattat ttctggccga\n+ 6901 tatatgttgc actggcggcc atatagcctt cgttctagtc tttgtaacgc acgatgcgca\n+ 6961 ggagcaattc gctgagatga ccacatgcga tttgcgggac ttatctagag atctatcatt\n+ 7021 atcgccagat tggtttaata attggctttt ccgccaatat ccaattggaa tatggttggt\n+ 7081 tactgcaatt gtcgctccat tttttaagca ctccataaaa agtaaacaca ttaatatgta\n+ 7141 ctcttattgg agatttcttc tttcgatttt agtttcggac cagtgaaaat cattcgtttc\n+ 7201 attttcgtaa ataagaactg agaaaatatt attattatat atatttcttt attaggaaaa\n+ 7261 tacgaagatt gagtatttca gattgaatta gcatatccgt ctaaatctta atgctgtaat\n+ 7321 gagcttactt gagatctgat caaaaccaat acaaaaccca caccaaaggt ggtagctaat\n+ 7381 atacatattt tgtgtaatac ttttgtagag tatttactat tcagcgattt aaacaagcaa\n+ 7441 tcgcctagac acacacattt gtccgcctat gtgtatgtgc accgagctat acccccactg\n+ 7501 aatcgctgtg tgctattttt atggccgcga tgctctcttg ttttgacccg cttgggcaac\n+//\n' |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/Pfam-A.clans.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_db/Pfam-A.clans.tsv Mon Oct 04 19:37:44 2021 +0000 |
| b |
| @@ -0,0 +1,31 @@ +PF00001 CL0192 GPCR_A 7tm_1 7 transmembrane receptor (rhodopsin family) +PF00002 CL0192 GPCR_A 7tm_2 7 transmembrane receptor (Secretin family) +PF00003 CL0192 GPCR_A 7tm_3 7 transmembrane sweet-taste receptor of 3 GCPR +PF00004 CL0023 P-loop_NTPase AAA ATPase family associated with various cellular activities (AAA) +PF00005 CL0023 P-loop_NTPase ABC_tran ABC transporter +PF00006 CL0023 P-loop_NTPase ATP-synt_ab ATP synthase alpha/beta family, nucleotide-binding domain +PF00007 CL0079 Cystine-knot Cys_knot Cystine-knot domain +PF00008 CL0001 EGF EGF EGF-like domain +PF00009 CL0023 P-loop_NTPase GTP_EFTU Elongation factor Tu GTP binding domain +PF00010 HLH Helix-loop-helix DNA-binding domain +PF00011 CL0190 HSP20 HSP20 Hsp20/alpha crystallin family +PF00012 CL0108 Actin_ATPase HSP70 Hsp70 protein +PF00013 CL0007 KH KH_1 KH domain +PF00014 Kunitz_BPTI Kunitz/Bovine pancreatic trypsin inhibitor domain +PF00015 MCPsignal Methyl-accepting chemotaxis protein (MCP) signalling domain +PF00016 RuBisCO_large Ribulose bisphosphate carboxylase large chain, catalytic domain +PF00017 CL0541 SH2-like SH2 SH2 domain +PF00018 CL0010 SH3 SH3_1 SH3 domain +PF00019 CL0079 Cystine-knot TGF_beta Transforming growth factor beta like domain +PF00020 CL0607 TNF_receptor TNFR_c6 TNFR/NGFR cysteine-rich region +PF00021 CL0117 uPAR_Ly6_toxin UPAR_LY6 u-PAR/Ly-6 domain +PF00022 CL0108 Actin_ATPase Actin Actin +PF00023 CL0465 Ank Ank Ankyrin repeat +PF00024 CL0168 PAN PAN_1 PAN domain +PF00025 CL0023 P-loop_NTPase Arf ADP-ribosylation factor family +PF00026 CL0129 Peptidase_AA Asp Eukaryotic aspartyl protease +PF00027 CL0029 Cupin cNMP_binding Cyclic nucleotide-binding domain +PF00028 CL0159 E-set Cadherin Cadherin domain +PF00029 CL0375 Transporter Connexin Connexin +PF00030 CL0333 gCrystallin Crystall Beta/Gamma crystallin +PF00031 CL0121 Cystatin Cystatin Cystatin domain |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/Pfam-A.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_db/Pfam-A.hmm Mon Oct 04 19:37:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,2268 @@\n+HMMER3/f [3.1b2 | February 2015]\n+NAME 1-cysPrx_C\n+ACC PF10417.11\n+DESC C-terminal domain of 1-Cys peroxiredoxin\n+LENG 40\n+ALPH amino\n+RF no\n+MM no\n+CONS yes\n+CS yes\n+MAP yes\n+DATE Wed Feb 24 18:37:46 2021\n+NSEQ 40\n+EFFN 17.426758\n+CKSUM 4086680297\n+GA 21.10 21.10;\n+TC 21.10 21.10;\n+NC 21.00 21.00;\n+BM hmmbuild HMM.ann SEED.ann\n+SM hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq\n+STATS LOCAL MSV -7.5463 0.71948\n+STATS LOCAL VITERBI -7.8624 0.71948\n+STATS LOCAL FORWARD -4.3303 0.71948\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 2.28046 4.31208 2.83393 2.63913 3.90855 2.69988 3.89812 3.33401 2.56310 2.85023 3.99954 3.22924 2.52123 2.90328 3.31238 2.94055 2.70512 2.59551 3.49266 3.82715\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00226 6.48754 7.20989 0.61958 0.77255 0.00000 *\n+ 1 0.29666 6.14436 6.78514 6.79783 7.06332 2.55785 7.22049 6.57837 6.66651 6.27638 3.28757 5.91223 5.83978 6.69238 6.58162 2.20136 4.83343 5.59959 8.41086 7.43107 1 A - - H\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00226 6.48754 7.20989 0.61958 0.77255 0.48576 0.95510\n+ 2 4.59591 5.92009 6.57211 5.96147 1.92899 5.81035 6.10135 2.33093 5.75927 0.69439 2.86149 5.97820 6.07717 5.78793 5.72916 5.13924 4.81708 2.59612 3.18569 3.35842 2 l - - H\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00226 6.48754 7.20989 0.61958 0.77255 0.48576 0.95510\n+ 3 4.81290 7.05274 3.71696 4.47757 6.60126 5.41623 3.72993 5.92180 2.06538 3.59487 6.10993 4.89014 5.75663 0.42291 2.54802 4.76779 4.95656 5.56452 7.24472 6.08615 3 Q - - H\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00226 6.48754 7.20989 0.61958 0.77255 0.48576 0.95510\n+ 4 2.64100 5.28125 5.84007 3.33362 1.80025 5.06896 2.72827 3.71332 5.01717 1.75203 2.65498 5.22280 5.43290 5.15329 5.03455 4.37913 1.80041 2.31249 5.90246 2.63298 4 l - - H\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00226 6.48754 7.20989 0.61958 0.77255 0.48576 0.95510\n+ 5 1.41804 5.70097 4.57246 4.01393 4.89018 2.99141 3.06166 4.26400 3.98607 3.95402 4.82703 3.11439 5.16775 4.30619 4.38279 2.19082 1.83510 1.66601 6.29409 3.75702 5 a - - H\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00226 6.48754 7.20989 0.61958 0.77255 0.48576 0.95510\n+ 6 2.40940 6.27006 0.95419 1.88136 5.61364 4.53669 4.72417 5.09838 3.04943 4.57453 3.59812 4.00473 4.93049 3.33824 2.90687 3.72620 2.65150 4.65993 3.45464 5.29359 6 d - - H\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.5847'..b'.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01335 4.71894 5.44129 0.61958 0.77255 0.48576 0.95510\n+ 442 2.29864 4.36166 2.78326 3.38999 2.53742 2.77187 4.12835 1.90087 3.31519 2.56018 3.47681 3.70473 4.21526 3.57901 3.58783 3.10825 3.02383 2.10914 4.97533 3.76638 497 i - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01335 4.71894 5.44129 0.61958 0.77255 0.48576 0.95510\n+ 443 1.63203 4.34013 4.06646 3.49075 2.53230 3.86648 4.15865 2.76897 3.39829 2.04499 2.63095 2.72733 4.24075 3.64956 3.64097 3.14318 3.03596 2.57834 4.93886 3.73074 498 a - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01335 4.71894 5.44129 0.61958 0.77255 0.48576 0.95510\n+ 444 3.45776 4.79585 5.18920 4.63265 3.52372 4.70258 5.10103 1.90217 4.47095 0.76832 3.34020 4.80189 4.96861 4.60775 4.56613 4.05504 2.50816 2.41399 5.48117 4.38492 499 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01335 4.71894 5.44129 0.61958 0.77255 0.48576 0.95510\n+ 445 2.36957 4.45811 5.03009 4.44127 2.41688 4.36160 4.72344 1.58595 4.26807 1.49345 3.37957 4.49747 4.67797 4.39767 4.31200 3.68800 3.35368 1.84206 5.17229 4.01590 500 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01335 4.71894 5.44129 0.61958 0.77255 0.48576 0.95510\n+ 446 2.96533 4.42430 4.42687 3.84923 3.41907 4.08405 4.39794 2.61936 3.71705 1.40335 1.95988 2.61322 4.43548 3.93974 3.89559 3.38106 3.19904 2.03697 5.04359 3.86701 501 l - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01335 4.71894 5.44129 0.61958 0.77255 0.48576 0.95510\n+ 447 2.78421 4.21512 4.43112 3.83593 2.56381 3.91375 4.21971 2.14171 3.68350 2.40586 3.33147 3.96427 4.28054 3.87190 2.63279 2.49740 3.01625 2.02770 2.95875 2.66709 502 v - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01335 4.71894 5.44129 0.61958 0.77255 0.48576 0.95510\n+ 448 2.82824 5.21690 3.11861 2.17918 2.94314 3.60476 3.77516 3.98203 1.59578 3.49916 4.27124 3.09125 3.99567 2.88856 2.31346 2.30812 3.05474 3.59349 5.65674 4.29044 503 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01335 4.71894 5.44129 0.61958 0.77255 0.48576 0.95510\n+ 449 3.39753 5.46518 3.96355 3.19882 4.85160 4.06610 3.96064 4.17905 1.03571 1.93276 4.52854 3.58771 4.40326 3.09886 1.88259 3.41029 3.55223 3.89272 5.74795 4.58563 504 k - - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00900 4.71460 * 0.61958 0.77255 0.00000 *\n+//\n' |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/Pfam-A.hmm.h3f |
| b |
| Binary file test-data/funannotate_db/Pfam-A.hmm.h3f has changed |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/Pfam-A.hmm.h3i |
| b |
| Binary file test-data/funannotate_db/Pfam-A.hmm.h3i has changed |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/Pfam-A.hmm.h3m |
| b |
| Binary file test-data/funannotate_db/Pfam-A.hmm.h3m has changed |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/Pfam-A.hmm.h3p |
| b |
| Binary file test-data/funannotate_db/Pfam-A.hmm.h3p has changed |
| b |
| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/dbCAN.hmm --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_db/dbCAN.hmm Mon Oct 04 19:37:44 2021 +0000 |
| [ |
| b'@@ -0,0 +1,613 @@\n+HMMER3/b [3.0 | March 2010]\n+NAME CBM10\n+LENG 28\n+ALPH amino\n+RF no\n+CS no\n+MAP yes\n+DATE Thu Apr 21 15:04:19 2011\n+NSEQ 84\n+EFFN 8.697876\n+CKSUM 1939305542\n+STATS LOCAL MSV -7.3395 0.71998\n+STATS LOCAL VITERBI -7.4498 0.71998\n+STATS LOCAL FORWARD -3.9737 0.71998\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 3.06033 2.42663 2.85747 2.77283 4.58046 2.24214 4.56942 3.29197 3.49682 3.34028 4.33944 2.39813 3.09771 2.95262 3.60586 2.44839 2.84569 3.24117 2.72301 3.28669\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.59367 5.66823 0.81137 0.61958 0.77255 0.00000 *\n+ 1 2.74340 3.47729 3.44643 2.64352 4.17985 3.79353 4.02282 3.57300 2.87097 3.22136 2.03109 3.38316 4.18747 1.79120 3.30841 2.03216 2.98385 3.28775 5.51287 4.21451 1 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00925 5.08381 5.80616 0.61958 0.77255 0.72961 0.65797\n+ 2 3.21366 0.33490 5.23672 5.17809 5.69922 3.92522 5.89105 5.22956 5.14397 4.94899 5.73770 3.11988 4.78715 5.32569 5.20447 2.46009 3.79312 4.43668 7.07761 5.95722 2 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00690 5.37599 6.09834 0.61958 0.77255 0.73167 0.65606\n+ 3 3.46517 6.03524 2.03286 2.67508 5.36194 2.25828 4.36563 4.86858 2.77875 4.33291 5.09631 1.07839 4.52524 2.62719 3.73072 2.75509 3.71412 4.41890 6.46315 5.00841 3 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.04091 5.49877 3.32435 0.61958 0.77255 0.52775 0.89143\n+ 4 2.51597 5.24536 3.21395 3.79383 4.81190 3.30725 4.89534 4.21717 3.89295 3.90352 4.76570 4.13904 4.73005 4.17210 4.26805 3.51068 1.58681 3.86875 0.87084 4.95297 4 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00570 5.56595 6.28829 0.61958 0.77255 0.68571 0.70065\n+ 5 1.88947 5.00491 4.00042 3.04471 4.13869 4.17114 3.84034 3.52228 3.40249 3.22374 4.10809 3.86994 4.55537 3.71667 3.77844 2.67165 2.19530 3.28758 3.58338 1.27239 5 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00552 5.59725 6.31960 0.61958 0.77255 0.60266 0.79264\n+ 6 3.27926 5.74099 2.79040 2.94678 5.08062 1.27592 4.24831 3.41153 3.01359 4.05572 4.81107 3.21498 2.15563 2.32440 3.50951 2.31938 3.51838 4.13470 6.20511 4.79969 6 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.00538 5.62391 6.34625 0.61958 0.77255 0.69965 0.68669\n+ 7 2.98451 5.68149 2.03356 2.71108 5.01893 3.09684 4.15179 4.49988 2.89056 3.98355 4.72438 1.82442 4.35665 2.68802 3.38251 2.74393 1.71463 4.06807 3.52699 3.90983 '..b' 4.13890 203 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01622 4.52558 5.24792 0.61958 0.77255 0.61781 0.77462\n+ 156 3.23629 4.53295 5.17116 4.60062 2.56767 4.55401 4.94436 1.53611 4.45009 1.93006 2.67230 4.68873 4.82232 4.56190 4.49974 3.89871 3.47038 1.24322 5.32187 4.18538 204 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01622 4.52558 5.24792 0.61958 0.77255 0.61781 0.77462\n+ 157 3.35666 5.86974 0.68984 2.46426 4.92782 3.56196 2.78368 4.75794 3.22196 4.22981 5.12544 3.04989 4.21061 3.34715 3.81641 3.23366 3.66181 4.32892 6.19564 4.65728 205 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01622 4.52558 5.24792 0.61958 0.77255 0.61781 0.77462\n+ 158 2.67298 5.45036 2.13159 2.39143 4.78238 2.86513 3.84529 4.27738 2.69136 3.76387 4.54115 1.53088 3.99325 2.24761 3.21918 2.86652 3.18624 3.84376 5.91068 4.46667 206 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01622 4.52558 5.24792 0.61958 0.77255 0.61781 0.77462\n+ 159 3.47622 4.69232 5.49800 5.03902 4.03274 5.04172 5.78958 1.10648 4.96863 2.46343 3.77576 5.20399 5.28896 5.22948 5.14151 4.47780 3.74214 0.89149 6.13647 4.91519 207 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01622 4.52558 5.24792 0.61958 0.77255 0.61781 0.77462\n+ 160 2.97740 5.38053 3.16559 1.47840 4.78122 3.66390 3.76082 4.20817 1.84043 3.64747 4.43358 3.13556 4.05699 2.52986 2.01786 2.93673 3.18400 3.80690 5.72537 4.41283 208 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01622 4.52558 5.24792 0.61958 0.77255 0.61781 0.77462\n+ 161 3.57702 4.81880 5.48209 4.93951 3.50997 4.99824 5.42819 1.75624 4.81911 0.87415 3.27296 5.12067 5.15674 4.87874 4.88006 4.38284 3.80904 1.60841 5.63134 4.57121 209 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01622 4.52558 5.24792 0.61958 0.77255 0.61781 0.77462\n+ 162 2.76975 4.18299 4.46129 3.86923 2.59055 3.91437 4.21294 2.01754 3.71166 2.30234 3.27364 3.97872 4.27520 3.88975 3.81544 3.21651 2.25828 2.00412 4.76988 2.10687 210 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.21940 4.52558 1.68107 0.61958 0.77255 0.61781 0.77462\n+ 163 2.75776 4.82375 2.92091 2.81848 4.73679 1.07105 4.24317 4.29296 3.20401 3.89127 4.73515 1.86580 4.00371 3.46690 3.61880 2.84293 3.19250 3.75461 5.98100 4.66726 211 - -\n+ 2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494 3.29354 2.67741 2.69355 4.24690 2.90347 2.73739 3.18146 2.89801 2.37887 2.77519 2.98518 4.58477 3.61503\n+ 0.01339 4.31957 * 0.61958 0.77255 0.00000 *\n+//\n' |
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| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/dbCAN.hmm.h3i |
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| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/dbCAN.hmm.h3p |
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| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/go.obo --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_db/go.obo Mon Oct 04 19:37:44 2021 +0000 |
| [ |
| @@ -0,0 +1,34 @@ +format-version: 1.2 +data-version: releases/2021-08-18 +subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3." +subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" +subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" +subsetdef: goslim_agr "AGR slim" +subsetdef: goslim_aspergillus "Aspergillus GO slim" +subsetdef: goslim_candida "Candida GO slim" +subsetdef: goslim_chembl "ChEMBL protein targets summary" +subsetdef: goslim_drosophila "Drosophila GO slim" +subsetdef: goslim_flybase_ribbon "FlyBase Drosophila GO ribbon slim" +subsetdef: goslim_generic "Generic GO slim" +subsetdef: goslim_metagenomics "Metagenomics GO slim" +subsetdef: goslim_mouse "Mouse GO slim" +subsetdef: goslim_pir "PIR GO slim" +subsetdef: goslim_plant "Plant GO slim" +subsetdef: goslim_pombe "Fission yeast GO slim" +subsetdef: goslim_synapse "synapse GO slim" +subsetdef: goslim_yeast "Yeast GO slim" +synonymtypedef: syngo_official_label "label approved by the SynGO project" +synonymtypedef: systematic_synonym "Systematic synonym" EXACT +default-namespace: gene_ontology +ontology: go +property_value: http://purl.org/dc/elements/1.1/description "The Gene Ontology (GO) provides a framework and set of concepts for describing the functions of gene products from all organisms." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Gene Ontology" xsd:string +property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/ +property_value: owl:versionInfo "2021-08-18" xsd:string + +[Term] +id: GO:0000001 +name: mitochondrion inheritance +namespace: biological_process +def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764] +synonym: "mitochondrial inheritance" EXACT [] |
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| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/interpro.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_db/interpro.tsv Mon Oct 04 19:37:44 2021 +0000 |
| [ |
| @@ -0,0 +1,49 @@ +ENTRY_AC ENTRY_TYPE ENTRY_NAME +IPR000126 Active_site Serine proteases, V8 family, serine active site +IPR000138 Active_site Hydroxymethylglutaryl-CoA lyase, active site +IPR000169 Active_site Cysteine peptidase, cysteine active site +IPR000180 Active_site Membrane dipeptidase, active site +IPR000189 Active_site Prokaryotic transglycosylase, active site +IPR000590 Active_site Hydroxymethylglutaryl-coenzyme A synthase, active site +IPR001252 Active_site Malate dehydrogenase, active site +IPR001345 Active_site Phosphoglycerate/bisphosphoglycerate mutase, active site +IPR001497 Active_site Methylated-DNA-[protein]-cysteine S-methyltransferase, active site +IPR001555 Active_site Phosphoribosylglycinamide formyltransferase, active site +IPR001579 Active_site Glycosyl hydrolases family 18 (GH18) active site +IPR001586 Active_site Beta-lactamase, class-C active site +IPR001969 Active_site Aspartic peptidase, active site +IPR002071 Active_site Thermonuclease active site +IPR002137 Active_site Beta-lactamase, class-D active site +IPR002168 Active_site Lipase, GDXG, putative histidine active site +IPR002471 Active_site Peptidase S9, serine active site +IPR004164 Active_site Coenzyme A transferase active site +IPR006650 Active_site Adenosine/AMP deaminase active site +IPR008255 Active_site Pyridine nucleotide-disulphide oxidoreductase, class-II, active site +IPR008259 Active_site FMN-dependent alpha-hydroxy acid dehydrogenase, active site +IPR008261 Active_site Iodothyronine deiodinase, active site +IPR008263 Active_site Glycoside hydrolase, family 16, active site +IPR008265 Active_site Lipase, GDSL, active site +IPR008266 Active_site Tyrosine-protein kinase, active site +IPR008268 Active_site Peptidase S16, active site +IPR008270 Active_site Glycosyl hydrolases family 25, active site +IPR008271 Active_site Serine/threonine-protein kinase, active site +IPR008272 Active_site 4-hydroxybenzoyl-CoA thioesterase, active site +IPR011767 Active_site Glutaredoxin active site +IPR012999 Active_site Pyridine nucleotide-disulphide oxidoreductase, class I, active site +IPR013808 Active_site Transglutaminase, active site +IPR016129 Active_site Peptidase family C14A, His active site +IPR016130 Active_site Protein-tyrosine phosphatase, active site +IPR017440 Active_site ATP-citrate lyase/succinyl-CoA ligase, active site +IPR017950 Active_site Urease active site +IPR018040 Active_site Pectinesterase, Tyr active site +IPR018053 Active_site Glycoside hydrolase, family 32, active site +IPR018057 Active_site Deoxyribonuclease I, active site +IPR018085 Active_site Uracil-DNA glycosylase, active site +IPR018088 Active_site Chalcone/stilbene synthase, active site +IPR018089 Active_site Orotidine 5'-phosphate decarboxylase, active site +IPR018114 Active_site Serine proteases, trypsin family, histidine active site +IPR018117 Active_site DNA methylase, C-5 cytosine-specific, active site +IPR018120 Active_site Glycoside hydrolase family 1, active site +IPR018129 Active_site Phosphoenolpyruvate carboxylase, Lys active site +IPR018148 Active_site Methylglyoxal synthase, active site +IPR018177 Active_site L-lactate dehydrogenase, active site |
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| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/merops.dmnd |
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| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/merops.formatted.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_db/merops.formatted.fa Mon Oct 04 19:37:44 2021 +0000 |
| b |
| @@ -0,0 +1,49 @@ +>MER0000002 S01A +IVNGEEAVPGSWPWQVSLQDKTGFHFCGGSLINENWVVTAAHCGVTTSDVVVAGEFDQGS +SSEKIQKLKIAKVFKNSKYNSLTINNDITLLKLSTAASFSQTVSAVCLPSASDDFAAGTT +CVTTGWGLTRYTNANTPDRLQQASLPLLSNTNCKKYWGTKIKDAMICAGASGVSSCMGDS +GGPLVCKKNGAWTLVGIVSWGSSTCSTSTPGVYARVTALVNWVQQTLAAN +>MER0000004 S01A +IVNGEDAVPGSWPWQVSLQDSTGFHFCGGSLISEDWVVTAAHCGVTTSDVVVAGEFDQGL +ETEDTQVLKIGKVFKNPKFSILTVRNDITLLKLATPAQFSETVSAVCLPSADEDFPAGML +CATTGWGKTKYNALKTPDKLQQATLPIVSNTDCRKYWGSRVTDVMICAGASGVSSCMGDS +GGPLVCQKNGAWTLAGIVSWGSSTCSTSTPAVYARVTALMPWVQETLAAN +>MER0000009 S01A +VVGGEVAKNGSAPYQVSLQVPGWGHNCGGSLLNDRWVLTAAHCLVGHAPGDLMVLVGTNS +LKEGGELLKVDKLLYHSRYNLPRFHNDIGLVRLEQPVQFSELVQSVEYSEKAVPANATVR +LTGWGRTSANGPSPTLLQSLNVVTLSNEDCNKKGGDPGYTDVGHLCTLTKTGEGACNGDS +GGPLVYEGKLVGVVNFGVPCALGYPDGFARVSYYHDWVRTTMANN +>MER0000012 S01A +YILTAAHCVSNEDVNHVITPIAAERFTIRAGSNDRFSGGVLVQVAEVIVHEEYGNFLNDV +ALLRLESPLILSASIQPIDLPTVDTPADVDVVISGWGRIKHQGDLPRYLQYNTLKSITRQ +QCEELIDFGFEGELCLLHQVDNGACNGDSGGP +>MER0000013 S01A +ITNGYPAYEGKVPYIVGLLFSGNGNWWCGGSIIGNTWVLTAAHCTNGASGVTINYGASIR +TQPQYTHWVGSGDIIQHHHYNSGNLHNDISLIRTPHVDFWSLVNKVELPSYNDRYQDYAG +WWAVASGWGGTYDGSPLPDWLQSVDVQIISQSDCSRTWSLHDNMICINTDGGKSTCGGDS +GGPLVTHDGNRLVGVTSFGSAAGCQSGAPAVFSRVTGYLDWIRDNTGIS +>MER0000015 S01A +ITNGQDAVMGQFPYQVGLSLNLGNFKSAWCGGSLIGNEWVLTAAHCTDGVKSVTVFLGAT +YRTEAEVKYTVKPNDILIHPGWNNKTLKNDISLVKIPETAYTALIQPVELPALASSYPSF +AGDEVIASGWGRISDSASGVTNYLQWARLEVISNAVCARTYGSTITSSNLCVKTPGGVST +CKGDSGGPLVLASSGVQVGLTSFGSILGCEKGFPAAFTRVTSYLEWINEHTGIS +>MER0000020 S01A +IVGGYNCEENSVPYQVSLNSGYHFCGGSLINEQWVVSAGHCYKSRIQVRLGEHNIEVLEG +NEQFINAAKIIRHPQYDRKTLNNDIMLIKLSSRAVINARVSTISLPTAPPATGTKCLISG +WGNTASSGADYPDELQCLDAPVLSQAKCEASYPGKITSNMFCVGFLEGGKDSCQGDSGGP +VVCNGQLQGVVSWGDGCAQKNKPGVYTKVYNYVKWIKNTIAAN +>MER0000021 S01A +IVGGYICEENSVPYQVSLNSGYHFCGGSLISEQWVVSAGHCYKSRIQVRLGEHNIEVLEG +NEQFINAAKIIRHPKYNSRTLDNDILLIKLSSPAVINSRVSAISLPTAPPAAGTESLISG +WGNTLSSGADYPDELQCLDAPVLSQAECEASYPGKITNNMFCVGFLEGGKDSCQGDSGGP +VVSNGELQGIVSWGYGCAQKNRPGVYTKVYNYVDWIKDTIAAN +>MER0000022 S01A +IVGGYTCEENSLPYQVSLNSGSHFCGGSLISEQWVVSAAHCYKTRIQVRLGEHNIKVLEG +NEQFINAAKIIRHPKYNRDTLDNDIMLIKLSSPAVINARVSTISLPTAPPAAGTECLISG +WGNTLSFGADYPDELKCLDAPVLREAECKASCPGKITNSMFCVGFLEGGKDSWKRDSGGP +VVCNGQLQGVVSWGHGCAWKNRPGVYTKVYNYVDWIKDTIAAN +>MER0000024 S01A +IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEG +NEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISG +WGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGP +VVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN |
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| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/ncbi_cleaned_gene_products.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/funannotate_db/ncbi_cleaned_gene_products.txt Mon Oct 04 19:37:44 2021 +0000 |
| b |
| @@ -0,0 +1,54 @@ +#version 1.70 +#Date 06-15-2021 +#Name Description +1-Oct mitochondrial intermediate peptidase +1AMINOCYCLOPROPANE1CARBOXYLATE Probable 1-aminocyclopropane-1-carboxylate deaminase +2ABA Protein phosphatase PP2A 55 kDa regulatory subunit +2ABD Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoform +2E4.130 Regulator of nonsense transcripts 1 +2E4.130_0 Regulator of nonsense transcripts 1 +2E4.130_1 Regulator of nonsense transcripts 1 +2MBCD 2-methylacyl-CoA dehydrogenase, mitochondrial +2METHYLACONITATE Aconitate/2-methylaconitate hydratase +4CL 4-coumarate--CoA ligase +4CL1 4-coumarate--CoA ligase 1 +4CL2 4-coumarate--CoA ligase 2 +4CL3 4-coumarate--CoA ligase 3 +4CLL1 4-coumarate--CoA ligase-like 1 +4CLL2 4-coumarate--CoA ligase-like 2 +4CLL3 4-coumarate--CoA ligase-like 3 +4CLL7 4-coumarate--CoA ligase-like 7 +4CLL7_0 4-coumarate--CoA ligase-like 7 +4CLL7_1 4-coumarate--CoA ligase-like 7 +4CLL7_2 4-coumarate--CoA ligase-like 7 +4CLL9 4-coumarate--CoA ligase-like 9 +4COUMARATECOA 4-coumarateCoA ligase-like 6 +4EBP 4E-binding protein THOR +4EHP Eukaryotic translation initiation factor 4E type 2 +4HYDROXYPHENYLPYRUVATE 4-hydroxyphenylpyruvate dioxygenase +6-PGD 6-phosphogluconate dehydrogenase, decarboxylating +6GAL Endo-beta-1 6-galactanase +6HN3M 6-hydroxynicotinate 3-monooxygenase +6PGD 6-phosphogluconate dehydrogenase, decarboxylating +6PGL phosphogluconolactonase +6PGL4 6-phosphogluconolactonase 4 +20H10.080 NADH-ubiquinone oxidoreductase 21 subunit +26S 26s proteasome regulatory subunit 6B +26S_PRC 26S proteasome regulatory complex protein +40S 40s ribosomal protein SA +60S 60s acidic ribosomal protein P2 +A1 mating type regulatory protein, silenced copy at HMR locus +A1CF APOB1 complementation factor +A2 mating type regulatory protein, silenced copy at HMR locus +A4GALT Lactosylceramide 4-alpha-galactosyltransferase +A4GNT Alpha-1,4-N-acetylglucosaminyltransferase +A4LEA 4-alpha-L-fucosyltransferase +AAA1 Asc-type amino acid transporter 1 +AAC ADP,ATP carrier protein +AAC1 ADP/ATP carrier protein AAC1 +AAC2 ADP,ATP carrier protein 2 +AAC3 ADP/ATP carrier protein AAC3 +AACC7 Aminoglycoside N(3)-acetyltransferase VII +AACS Acetoacetyl-CoA synthetase +AACS_0 Acetoacetyl-CoA synthetase +AACS_1 Acetoacetyl-CoA synthetase |
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| diff -r 40b87aef5241 -r 1a59958c1f76 test-data/funannotate_db/uniprot.dmnd |
| b |
| Binary file test-data/funannotate_db/uniprot.dmnd has changed |