| Previous changeset 0:07a74537acd5 (2024-02-14) Next changeset 2:47f9f4d13d2c (2024-03-18) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 4d89bfa697ebee8a7f87b233e33c7b34649a8ee8 |
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modified:
compleasm.xml macros.xml |
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added:
test-data/test-db/busco_downloads/lineages/eukaryota_odb10/lengths_cutoff test-data/test-db/busco_downloads/lineages/eukaryota_odb10/links_to_ODB10.txt test-data/test-db/busco_downloads/lineages/eukaryota_odb10/scores_cutoff test-data/test-db/busco_downloads/lineages/file_versions.tsv |
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removed:
test-data/test-db/busco_downloads/file_versions.tsv test-data/test-db/busco_downloads/lineages/eukaryota_odb10/hmms/39650at2759.hmm |
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| diff -r 07a74537acd5 -r 79413aecc398 compleasm.xml --- a/compleasm.xml Wed Feb 14 14:31:44 2024 +0000 +++ b/compleasm.xml Tue Mar 12 09:59:05 2024 +0000 |
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| @@ -7,11 +7,16 @@ <requirement type="package" version="@TOOL_VERSION@">compleasm</requirement> </requirements> <command><![CDATA[ + + mkdir -p galaxy_db && + cp -r '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/' && + compleasm run -a '$input' - -o galaxy + -o galaxy_output --mode $mode - -l '$busco_database' + -L 'galaxy_db' + -l '$lineage_dataset' #if str($specified_contigs) != '': --specified_contigs '$specified_contigs' @@ -44,21 +49,25 @@ <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false"> <options from_data_table="busco_database"/> </param> + + <param name="lineage_dataset" type="select" label="Lineage"> + <expand macro="lineages"/> + </param> </inputs> <outputs> - <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy/*_odb10/full_table_busco_format.tsv"> + <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy_output/*_odb10/full_table_busco_format.tsv"> <filter>outputs and 'full_table_busco' in outputs</filter> </data> - <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy/*_odb10/full_table.tsv"> + <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy_output/*_odb10/full_table.tsv"> <filter>outputs and 'full_table' in outputs</filter> </data> - <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy/*_odb10/miniprot_output.gff"> + <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy_output/*_odb10/miniprot_output.gff"> <filter>outputs and 'miniprot' in outputs</filter> </data> - <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy/*_odb10/translated_protein.fasta"> + <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta"> <filter>outputs and 'translated_protein' in outputs</filter> - </data> + </data> </outputs> <tests> @@ -66,7 +75,8 @@ <param name="input" value="small_genome.fasta"/> <param name="mode" value="busco"/> <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/> - <param name="busco_database" value="eukaryota"/> + <param name="busco_database" value="eukaryota_odb10"/> + <param name="lineage_dataset" value="eukaryota_odb10"/> <output name="full_table_busco"> <assert_contents> <has_text text="Busco id"/> |
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| diff -r 07a74537acd5 -r 79413aecc398 macros.xml --- a/macros.xml Wed Feb 14 14:31:44 2024 +0000 +++ b/macros.xml Tue Mar 12 09:59:05 2024 +0000 |
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| b'@@ -1,6 +1,6 @@\n <macros>\n <token name="@TOOL_VERSION@">0.2.5</token>\n- <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@VERSION_SUFFIX@">1</token>\n \n <xml name="citation">\n <citations>\n@@ -8,4 +8,173 @@\n </citations>\n </xml>\n \n+ <xml name="lineages">\n+ <option value="acidobacteria_odb10">Acidobacteria</option>\n+ <option value="aconoidasida_odb10">Aconoidasida</option>\n+ <option value="actinobacteria_class_odb10">Actinobacteria class</option>\n+ <option value="actinobacteria_phylum_odb10">Actinobacteria phylum</option>\n+ <option value="actinopterygii_odb10">Actinopterygii</option>\n+ <option value="agaricales_odb10">Agaricales</option>\n+ <option value="agaricomycetes_odb10">Agaricomycetes</option>\n+ <option value="alphaproteobacteria_odb10">Alphaproteobacteria</option>\n+ <option value="alteromonadales_odb10">Alteromonadales</option>\n+ <option value="alveolata_odb10">Alveolata</option>\n+ <option value="apicomplexa_odb10">Apicomplexa</option>\n+ <option value="aquificae_odb10">Aquificae</option>\n+ <option value="arachnida_odb10">Arachnida</option>\n+ <option value="archaea_odb10">Archaea</option>\n+ <option value="arthropoda_odb10">Arthropoda</option>\n+ <option value="ascomycota_odb10">Ascomycota</option>\n+ <option value="aves_odb10">Aves</option>\n+ <option value="bacillales_odb10">Bacillales</option>\n+ <option value="bacilli_odb10">Bacilli</option>\n+ <option value="bacteria_odb10">Bacteria</option>\n+ <option value="bacteroidales_odb10">Bacteroidales</option>\n+ <option value="bacteroidetes-chlorobi_group_odb10">Bacteroidetes-chlorobi group</option>\n+ <option value="bacteroidetes_odb10">Bacteroidetes</option>\n+ <option value="bacteroidia_odb10">Bacteroidia</option>\n+ <option value="basidiomycota_odb10">Basidiomycota</option>\n+ <option value="betaproteobacteria_odb10">Betaproteobacteria</option>\n+ <option value="boletales_odb10">Boletales</option>\n+ <option value="brassicales_odb10">Brassicales</option>\n+ <option value="burkholderiales_odb10">Burkholderiales</option>\n+ <option value="campylobacterales_odb10">Campylobacterales</option>\n+ <option value="capnodiales_odb10">Capnodiales</option>\n+ <option value="carnivora_odb10">Carnivora</option>\n+ <option value="cellvibrionales_odb10">Cellvibrionales</option>\n+ <option value="cetartiodactyla_odb10">Cetartiodactyla</option>\n+ <option value="chaetothyriales_odb10">Chaetothyriales</option>\n+ <option value="chlamydiae_odb10">Chlamydiae</option>\n+ <option value="chlorobi_odb10">Chlorobi</option>\n+ <option value="chloroflexi_odb10">Chloroflexi</option>\n+ <option value="chlorophyta_odb10">Chlorophyta</option>\n+ <option value="chromatiales_odb10">Chromatiales</option>\n+ <option value="chroococcales_odb10">Chroococcales</option>\n+ <option value="clostridia_odb10">Clostridia</option>\n+ <option value="clostridiales_odb10">Clostridiales</option>\n+ <option value="coccidia_odb10">Coccidia</option>\n+ <option value="coriobacteriales_odb10">Coriobacteriales</option>\n+ <option value="coriobacteriia_odb10">Coriobacteriia</option>\n+ <option value="corynebacteriales_odb10">Corynebacteriales</option>\n+ <option value="cyanobacteria_odb10">Cyanobacteria</option>\n+ <option value="cyprinodontiformes_odb10">Cyprinodontiformes</option>\n+ <option value="cytophagales_odb10">Cytophagales</option>\n+ <option value="cytophagia_odb10">Cytophagia</option>\n+ <option value="delta-epsilon-subdivisions_odb10">Delta-epsilon-subdivisions</option>\n+ <option value="deltaproteobacteria_odb10">Deltaproteobacteria</option>\n+ <option value="desulfobacterales_odb10">Desulfobacterales</option>\n+ <option value="desu'..b'plasmatales_odb10">Mycoplasmatales</option>\n+ <option value="natrialbales_odb10">Natrialbales</option>\n+ <option value="neisseriales_odb10">Neisseriales</option>\n+ <option value="nematoda_odb10">Nematoda</option>\n+ <option value="nitrosomonadales_odb10">Nitrosomonadales</option>\n+ <option value="nostocales_odb10">Nostocales</option>\n+ <option value="oceanospirillales_odb10">Oceanospirillales</option>\n+ <option value="onygenales_odb10">Onygenales</option>\n+ <option value="oscillatoriales_odb10">Oscillatoriales</option>\n+ <option value="passeriformes_odb10">Passeriformes</option>\n+ <option value="pasteurellales_odb10">Pasteurellales</option>\n+ <option value="planctomycetes_odb10">Planctomycetes</option>\n+ <option value="plasmodium_odb10">Plasmodium</option>\n+ <option value="pleosporales_odb10">Pleosporales</option>\n+ <option value="poales_odb10">Poales</option>\n+ <option value="polyporales_odb10">Polyporales</option>\n+ <option value="primates_odb10">Primates</option>\n+ <option value="propionibacteriales_odb10">Propionibacteriales</option>\n+ <option value="proteobacteria_odb10">Proteobacteria</option>\n+ <option value="pseudomonadales_odb10">Pseudomonadales</option>\n+ <option value="rhizobiales_odb10">Rhizobiales</option>\n+ <option value="rhizobium-agrobacterium_group_odb10">Rhizobium-agrobacterium group</option>\n+ <option value="rhodobacterales_odb10">Rhodobacterales</option>\n+ <option value="rhodospirillales_odb10">Rhodospirillales</option>\n+ <option value="rickettsiales_odb10">Rickettsiales</option>\n+ <option value="saccharomycetes_odb10">Saccharomycetes</option>\n+ <option value="sauropsida_odb10">Sauropsida</option>\n+ <option value="selenomonadales_odb10">Selenomonadales</option>\n+ <option value="solanales_odb10">Solanales</option>\n+ <option value="sordariomycetes_odb10">Sordariomycetes</option>\n+ <option value="sphingobacteriia_odb10">Sphingobacteriia</option>\n+ <option value="sphingomonadales_odb10">Sphingomonadales</option>\n+ <option value="spirochaetales_odb10">Spirochaetales</option>\n+ <option value="spirochaetes_odb10">Spirochaetes</option>\n+ <option value="spirochaetia_odb10">Spirochaetia</option>\n+ <option value="stramenopiles_odb10">Stramenopiles</option>\n+ <option value="streptomycetales_odb10">Streptomycetales</option>\n+ <option value="streptosporangiales_odb10">Streptosporangiales</option>\n+ <option value="sulfolobales_odb10">Sulfolobales</option>\n+ <option value="synechococcales_odb10">Synechococcales</option>\n+ <option value="synergistetes_odb10">Synergistetes</option>\n+ <option value="tenericutes_odb10">Tenericutes</option>\n+ <option value="tetrapoda_odb10">Tetrapoda</option>\n+ <option value="thaumarchaeota_odb10">Thaumarchaeota</option>\n+ <option value="thermoanaerobacterales_odb10">Thermoanaerobacterales</option>\n+ <option value="thermoplasmata_odb10">Thermoplasmata</option>\n+ <option value="thermoproteales_odb10">Thermoproteales</option>\n+ <option value="thermoprotei_odb10">Thermoprotei</option>\n+ <option value="thermotogae_odb10">Thermotogae</option>\n+ <option value="thiotrichales_odb10">Thiotrichales</option>\n+ <option value="tissierellales_odb10">Tissierellales</option>\n+ <option value="tissierellia_odb10">Tissierellia</option>\n+ <option value="tremellomycetes_odb10">Tremellomycetes</option>\n+ <option value="verrucomicrobia_odb10">Verrucomicrobia</option>\n+ <option value="vertebrata_odb10">Vertebrata</option>\n+ <option value="vibrionales_odb10">Vibrionales</option>\n+ <option value="viridiplantae_odb10">Viridiplantae</option>\n+ <option value="xanthomonadales_odb10">Xanthomonadales</option>\n+ </xml>\n+\n </macros>\n' |
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| diff -r 07a74537acd5 -r 79413aecc398 test-data/test-db/busco_downloads/file_versions.tsv --- a/test-data/test-db/busco_downloads/file_versions.tsv Wed Feb 14 14:31:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,213 +0,0 @@\n-acidobacteria_odb10\t2024-01-08\t13046d110cf6d038af269ee6e0681bdc\tProkaryota\tlineages\n-aconoidasida_odb10\t2024-01-08\t47b6ece13859b681466c79f4e6c6d1ad\tEukaryota\tlineages\n-actinobacteria_class_odb10\t2024-01-08\t0a326071854e20d1977a13a5e3a5f84f\tProkaryota\tlineages\n-actinobacteria_phylum_odb10\t2024-01-08\teaa25a3d973f580d4cf59b7251309e5a\tProkaryota\tlineages\n-actinopterygii_odb10\t2024-01-08\t6b042870822559fcacf129fdedea8927\tEukaryota\tlineages\n-agaricales_odb10\t2024-01-08\t1bf1c632dab6ae5b4ff0be6fad8ff8cf\tEukaryota\tlineages\n-agaricomycetes_odb10\t2024-01-08\t717f3e2543617972c9a45bbd4ac975b6\tEukaryota\tlineages\n-alphaproteobacteria_odb10\t2024-01-08\t22db70ba9f321e8b8f4eed0b2be41b6f\tProkaryota\tlineages\n-alteromonadales_odb10\t2024-01-08\t0a959f97971c349fdd69bc37e7796514\tProkaryota\tlineages\n-alveolata_odb10\t2024-01-08\tcbd2ddb6b18efb2b4ca218a74688aacf\tEukaryota\tlineages\n-apicomplexa_odb10\t2024-01-08\te27eb839243c4a4280e4187108b48596\tEukaryota\tlineages\n-aquificae_odb10\t2024-01-08\t0285bccb18097979aef7badd2b554378\tProkaryota\tlineages\n-arachnida_odb10\t2024-01-08\t625818d0544cd760356af0b8e9a5a412\tEukaryota\tlineages\n-archaea_odb10\t2024-01-08\t3eb26c670c520c0f3b32bff46fce03d7\tProkaryota\tlineages\n-arthropoda_odb10\t2024-01-08\t915ae2790da249b81eceeb1cea2ad922\tEukaryota\tlineages\n-ascomycota_odb10\t2024-01-08\t694c2ad193a01cd6e95487a3ddcbcce8\tEukaryota\tlineages\n-aves_odb10\t2024-01-08\teea0b7e8122b1f528c97c142e9ddfd82\tEukaryota\tlineages\n-bacillales_odb10\t2024-01-08\te2fb5d46b90c76f849d9ec9c49ae79ca\tProkaryota\tlineages\n-bacilli_odb10\t2024-01-08\te8dc4ad8c6e26e2dfc47e155736896bd\tProkaryota\tlineages\n-bacteria_odb10\t2024-01-08\tbff9523df89980699c01e8f31e490496\tProkaryota\tlineages\n-bacteroidales_odb10\t2024-01-08\t60e4d09d2526ad90561bc0ad4c67f783\tProkaryota\tlineages\n-bacteroidetes-chlorobi_group_odb10\t2024-01-08\t4d2ae5165b8aec5f42f42d79e98bc05d\tProkaryota\tlineages\n-bacteroidetes_odb10\t2024-01-08\t81eddd495a27b2c15b661eb2f018b01b\tProkaryota\tlineages\n-bacteroidia_odb10\t2024-01-08\t1756db675bfee79e3a3a6e9946003038\tProkaryota\tlineages\n-basidiomycota_odb10\t2024-01-08\t55ee0a0b2ca18812393fd43faf4f1897\tEukaryota\tlineages\n-betaproteobacteria_odb10\t2024-01-08\t040cf23dfcfc0fa632bd48fde213b61f\tProkaryota\tlineages\n-boletales_odb10\t2024-01-08\t7a7b1635d171d069a5525ee24faf8c83\tEukaryota\tlineages\n-brassicales_odb10\t2024-01-08\t7f96488b36e2f391dd594a099b31ea24\tEukaryota\tlineages\n-burkholderiales_odb10\t2024-01-08\tb41288c7ab665a79a592214850af3dcf\tProkaryota\tlineages\n-campylobacterales_odb10\t2024-01-08\t950fa5f90829dfbfe879e71f22d8a6f1\tProkaryota\tlineages\n-capnodiales_odb10\t2024-01-08\ta1601671360646aa38c968520f81a9bc\tEukaryota\tlineages\n-carnivora_odb10\t2024-01-08\ta81b85b7d90b046315b8cb1bea8605c1\tEukaryota\tlineages\n-cellvibrionales_odb10\t2024-01-08\t4284a714433698dfcf38b7297bc6ef4b\tProkaryota\tlineages\n-cetartiodactyla_odb10\t2024-01-08\t7d348bed34a92a77c86adb4194a4d0cc\tEukaryota\tlineages\n-chaetothyriales_odb10\t2024-01-08\t721a498d4da22ab75c48a705cb7ffafe\tEukaryota\tlineages\n-chlamydiae_odb10\t2024-01-08\tf9a0d5d18b525f5b25ffd28cbc79511a\tProkaryota\tlineages\n-chlorobi_odb10\t2024-01-08\t1accab3fc927c6e614d96d3b76eb7d41\tProkaryota\tlineages\n-chloroflexi_odb10\t2024-01-08\t9633d49879fba7efe9d59e9ec1f6fb70\tProkaryota\tlineages\n-chlorophyta_odb10\t2024-01-08\t7dbcc25dd421be9fbb0f0ae0d7095284\tEukaryota\tlineages\n-chromatiales_odb10\t2024-01-08\t113389b263ee38c451831b513a56ae85\tProkaryota\tlineages\n-chroococcales_odb10\t2024-01-08\t319aa6d9e5ce2606aecfc0bce4419eb8\tProkaryota\tlineages\n-clostridiales_odb10\t2024-01-08\t9b90a303dc2395f6197c1d64f03fbfc0\tProkaryota\tlineages\n-clostridia_odb10\t2024-01-08\t7eeb8a01b7c4643aa9fbbd1fd03c887f\tProkaryota\tlineages\n-coccidia_odb10\t2024-01-08\tec804a941baabf38053a0f8b8c7021dd\tEukaryota\tlineages\n-coriobacteriales_odb10\t2024-01-08\t18776c9d1cf45a170a71a57e6b0bf32c\tProkaryota\tlineages\n-coriobacteriia_odb10\t2024-01-08\t6837d15f63527b8b9ad624f9e4a26daf\tProkaryota\tlineages\n-corynebacteriales_odb10\t2024-01-08\taf866d8ea389f71092f9344fb9603f5c\tProkaryota\tlineages\n-cyanobacteria_odb10\t2024-01'..b'6c7a944c1f36dc22353a62e663065b\tProkaryota\tlineages\n-thermoplasmata_odb10\t2024-01-08\tf3ec5b6d8fa79c4c6caa37e6b0c09776\tProkaryota\tlineages\n-thermoproteales_odb10\t2024-01-08\tc92700b9bc1018ba50741c453632a758\tProkaryota\tlineages\n-thermoprotei_odb10\t2024-01-08\te9c08ac322b0c8e4d1c052e6738ad85d\tProkaryota\tlineages\n-thermotogae_odb10\t2024-01-08\t546306dabbd386be2d9940a2c0d0deb1\tProkaryota\tlineages\n-thiotrichales_odb10\t2024-01-08\t7871f11be31cf3dfb0f57e8a1f5b31f1\tProkaryota\tlineages\n-tissierellales_odb10\t2024-01-08\td5651b1b2e07433fc212881bd1482b72\tProkaryota\tlineages\n-tissierellia_odb10\t2024-01-08\tf56b85fda5d5cb55322a8cbd452dd365\tProkaryota\tlineages\n-tree.archaea_odb10.nwk\t2019-12-16\t23a9602460ca3ba12a4382964c40add4\tProkaryota\tplacement_files\n-tree.bacteria_odb10.nwk\t2019-12-16\t3cbe2d6292e02ee78b92b42ec7c13bf5\tProkaryota\tplacement_files\n-tree.eukaryota_odb10.nwk\t2019-12-16\tcb0d434ee9d87f5d6babd1832a3fa419\tEukaryota\tplacement_files\n-tree_metadata.archaea_odb10.txt\t2019-12-16\t1cc8a1284c883d9a5a8e33e70a81a743\tProkaryota\tplacement_files\n-tree_metadata.bacteria_odb10.txt\t2019-12-16\t04a34d1dbcc0814bd0f5acee1d2a9c3f\tProkaryota\tplacement_files\n-tree_metadata.eukaryota_odb10.txt\t2019-12-16\t589ac2a41cb79863d4b0b061e472afea\tEukaryota\tplacement_files\n-tremellomycetes_odb10\t2024-01-08\ta0bfe1ffe4313753173cd341ddcc4c07\tEukaryota\tlineages\n-verrucomicrobia_odb10\t2024-01-08\t1c380e10eaac2482a9485fe14b7bad47\tProkaryota\tlineages\n-vertebrata_odb10\t2024-01-08\td292737afaec0ac95bde4f4a8d2ea814\tEukaryota\tlineages\n-vibrionales_odb10\t2024-01-08\te9ec5827bed867a01d07d7d03aaddc4c\tProkaryota\tlineages\n-viridiplantae_odb10\t2024-01-08\t90d6ce27fde83f1e4aba1d6a8f523673\tEukaryota\tlineages\n-xanthomonadales_odb10\t2024-01-08\t47dd98a24916b28b52500e9a036eb8a8\tProkaryota\tlineages\n-alphaherpesvirinae_odb10\t2024-01-08\t44433a26b31aa50e4314a013eb2d1ff4\tVirus\tlineages\n-baculoviridae_odb10\t2024-01-08\t78a612f186cb5b88ec8c030661e46487\tVirus\tlineages\n-rudiviridae_odb10\t2024-01-08\tafad43502a74667304b97a39459700b4\tVirus\tlineages\n-betaherpesvirinae_odb10\t2024-01-08\t1fd9d15097a377d712c6458451bf65af\tVirus\tlineages\n-herpesviridae_odb10\t2024-01-08\t79856510300f9379e518cc8180ad14fb\tVirus\tlineages\n-poxviridae_odb10\t2024-01-08\t4cb2e71a92b2088a0a0b1f4ff20f94ef\tVirus\tlineages\n-tevenvirinae_odb10\t2024-01-08\tfac34fac2c70199fcbe69c0a7a663d71\tVirus\tlineages\n-aviadenovirus_odb10\t2024-01-08\tf9c946051627e87ff717ad466d6c5966\tVirus\tlineages\n-enquatrovirus_odb10\t2024-01-08\tf6c05f3de730a09cc7eaf58bcc50636c\tVirus\tlineages\n-teseptimavirus_odb10\t2024-01-08\t18d63d8e679c6fc6086d906d6b917f05\tVirus\tlineages\n-bclasvirinae_odb10\t2024-01-08\t51a9dce485c577e575d411d10c566820\tVirus\tlineages\n-fromanvirus_odb10\t2024-01-08\t48f5b7b57afa387315c9e006410f55b9\tVirus\tlineages\n-skunavirus_odb10\t2024-01-08\t68fbb8404853ae930651c3af1baa7b49\tVirus\tlineages\n-betabaculovirus_odb10\t2024-01-08\taab73c1e308f8a1cec4f4529b06ee3d4\tVirus\tlineages\n-pahexavirus_odb10\t2024-01-08\t3b1410a4b594471e05c0b4d466e3173b\tVirus\tlineages\n-alphabaculovirus_odb10\t2024-01-08\tec04ed01eab6001f35c1a6ebfc70180f\tVirus\tlineages\n-tunavirinae_odb10\t2024-01-08\tfe8a69addddcbc43732a4504aff538e2\tVirus\tlineages\n-simplexvirus_odb10\t2024-01-08\tfffd2907f63fe04c78fabd61d2f56919\tVirus\tlineages\n-gammaherpesvirinae_odb10\t2024-01-08\tda764ed072f3fb78cae2ff7e90868a9f\tVirus\tlineages\n-varicellovirus_odb10\t2024-01-08\t43c79da0fb65e9d5941d71458cf844ad\tVirus\tlineages\n-cheoctovirus_odb10\t2024-01-08\t74dacf2a763c2a462356ded5e79921db\tVirus\tlineages\n-guernseyvirinae_odb10\t2024-01-08\t484f59b9efc120c118fae2e6c178ffaa\tVirus\tlineages\n-tequatrovirus_odb10\t2024-01-08\t67a3c9d25ded118212840dfd87c37d96\tVirus\tlineages\n-chordopoxvirinae_odb10\t2024-01-08\tc5ff51b8e86771a94400c0df8f8eb383\tVirus\tlineages\n-peduovirus_odb10\t2024-01-08\t660b6c8dae78bf76bddd9ba1be2c8bd9\tVirus\tlineages\n-iridoviridae_odb10\t2024-01-08\t3b3e67bb85d616fd874b26479d6abaea\tVirus\tlineages\n-spounavirinae_odb10\t2024-01-08\t286365f43fe02aad53b89555d36cd6b0\tVirus\tlineages\n-virus_datasets.txt\t2020-11-26\ta7d1e4d4bb6327d01efde3bcc8658cb3\tNaN\tinformation\n' |
| b |
| diff -r 07a74537acd5 -r 79413aecc398 test-data/test-db/busco_downloads/lineages/eukaryota_odb10/hmms/39650at2759.hmm --- a/test-data/test-db/busco_downloads/lineages/eukaryota_odb10/hmms/39650at2759.hmm Wed Feb 14 14:31:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,4663 +0,0 @@\n-HMMER3/f [3.1b2 | February 2015]\n-NAME 39650at2759\n-LENG 1547\n-ALPH amino\n-RF no\n-MM no\n-CONS yes\n-CS no\n-MAP yes\n-DATE Fri Apr 12 16:08:02 2019\n-NSEQ 70\n-EFFN 0.798950\n-CKSUM 1890963858\n-STATS LOCAL MSV -13.5314 0.69473\n-STATS LOCAL VITERBI -14.3147 0.69473\n-STATS LOCAL FORWARD -7.5604 0.69473\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 2.57898 4.17942 2.94856 2.66427 3.22674 3.11185 3.73362 2.73129 2.65473 2.37386 3.54788 3.11965 3.40753 3.08322 2.90804 2.73302 2.89739 2.57776 4.43213 3.33559\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- 0.06070 4.05726 3.17963 0.61958 0.77255 0.00000 *\n- 1 2.71832 5.18605 1.80493 2.01185 4.48353 3.31150 3.45612 3.75868 2.44483 3.47158 4.25745 2.49475 3.74115 2.76597 2.92078 2.60241 2.96567 3.55515 5.63628 4.21371 1 d - - -\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- 0.02694 4.02349 4.74584 0.61958 0.77255 0.52159 0.90036\n- 2 2.39190 4.90176 2.80572 2.06203 4.17694 3.35433 3.50579 3.43463 2.25507 3.11198 3.96367 2.85659 3.77641 2.62320 2.72271 2.45219 2.77997 3.14373 5.37787 4.01624 2 e - - -\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- 0.02694 4.02349 4.74584 0.61958 0.77255 0.52159 0.90036\n- 3 2.79774 4.24400 4.21858 3.64357 3.25252 3.95152 4.27372 1.63123 3.51728 1.78812 2.86269 3.90072 4.28421 3.76187 3.41904 3.25028 2.93756 1.89531 4.94238 3.76922 3 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- 0.02694 4.02349 4.74584 0.61958 0.77255 0.52159 0.90036\n- 4 2.97417 5.53478 1.15022 1.92938 4.81351 3.23099 3.78931 4.33384 2.81996 3.83953 4.70285 2.69498 3.77178 2.86491 3.41650 2.85589 3.26726 3.91282 6.00507 4.49409 4 d - - -\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- 0.02694 4.02349 4.74584 0.61958 0.77255 0.52159 0.90036\n- 5 2.42258 4.87271 2.86530 2.06744 4.14761 3.26692 3.59776 3.52148 2.36680 3.02606 3.94929 2.87654 3.78739 2.67506 2.61017 2.29357 2.76403 3.22808 5.36390 4.01234 5 e - - -\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- 0.02694 4.02349 4.74584 0.61958 0.77255 0.52159 0.90036\n- 6 2.49612 4.77994 3.04122 2.47051 4.02992 3.33809 3.61341 3.29125 1.94818 2.98279 3.51049 2.90160 3.82287 2.75171 2.40544 2.56258 2.84113 3.08274 5.27115 3.95883 6 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- 0.02694 4.02349 4.74584 0.61958 0.77255 0.50029 0.93231\n- 7 2.51306 4.10913 4.01190 3.43337 2.50729 3.71171 3.83672 2.47276 3.31729 1.90208 2.64865 3.65722 4.07281 3.4'..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- 0.02730 4.01014 4.73249 0.61958 0.77255 0.52810 0.89092\n- 1540 2.59038 5.00372 2.87751 2.32026 4.31516 2.96380 3.12596 3.75560 1.98801 3.28016 4.06420 2.73076 3.79765 2.57891 2.50571 2.49139 2.87013 3.37858 5.44388 4.08840 1561 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- 0.02730 4.01014 4.73249 0.61958 0.77255 0.52810 0.89092\n- 1541 2.43697 4.76730 2.96983 2.31440 3.86713 3.00779 3.60680 3.42332 2.37146 2.94774 3.65763 2.93573 3.79382 2.39028 2.76490 2.50934 2.64197 3.10181 5.27162 3.94037 1562 e - - -\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- 0.02730 4.01014 4.73249 0.61958 0.77255 0.52810 0.89092\n- 1542 2.57269 4.18933 3.96143 3.30105 3.34352 3.78842 4.11669 1.94742 3.26027 2.07683 3.25391 3.69087 3.90516 3.57055 3.54913 3.07688 2.87281 1.62438 4.91626 3.71148 1563 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- 0.02730 4.01014 4.73249 0.61958 0.77255 0.52810 0.89092\n- 1543 2.75120 5.04797 3.17466 2.55276 4.40986 3.53720 3.58981 3.60454 1.52013 3.29762 4.12152 2.98355 3.91279 2.55261 2.03797 2.76756 3.01732 3.45602 5.41824 4.15943 1564 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- 0.02730 4.01014 4.73249 0.61958 0.77255 0.52810 0.89092\n- 1544 2.39304 4.83066 2.80787 2.23884 4.08699 3.23642 3.40769 3.43340 2.36918 3.03275 3.70928 2.90480 3.77987 2.64015 2.57650 2.48453 2.71894 3.03585 5.32066 3.97283 1565 e - - -\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- 0.02730 4.01014 4.73249 0.61958 0.77255 0.52810 0.89092\n- 1545 2.39842 4.94270 2.62230 2.16343 4.23035 3.36688 3.42468 3.67747 2.33595 3.19184 4.00176 2.56248 3.71725 2.69236 2.68822 2.47419 2.67611 3.30273 4.98557 4.03802 1566 e - - -\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- 0.02730 4.01014 4.73249 0.61958 0.77255 0.52810 0.89092\n- 1546 2.61857 4.98240 2.59482 2.19255 4.26523 3.25717 3.06009 3.71518 2.36297 3.10815 4.04640 2.25275 3.77771 2.71827 2.85649 2.53437 2.75433 3.34133 5.45023 3.92401 1567 e - - -\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- 0.02730 4.01014 4.73249 0.61958 0.77255 0.52810 0.89092\n- 1547 2.76349 4.24570 4.10775 3.53005 2.71500 3.86680 4.14630 2.38186 3.27248 1.49147 2.36786 3.79651 4.20073 3.63996 3.56628 3.15686 2.92448 2.28437 4.80710 3.62382 1568 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- 0.01846 4.00130 * 0.61958 0.77255 0.00000 *\n-//\n' |