| Previous changeset 6:4ff81ce331f9 (2024-07-22) Next changeset 8:b9a4fd399d63 (2025-02-13) |
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Commit message:
planemo upload for repository https://gitlab.pasteur.fr/galaxy-team/galaxy-tools/-/tree/master/tools/defense-finder commit 8623294c7e90dca09b4613bfe466ff741f83b97a |
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modified:
defense_finder.xml macros.xml test-data/inputs/df_test_prot.faa test-data/outputs/nt/defense_finder_genes.tsv test-data/outputs/nt/defense_finder_hmmer.tsv test-data/outputs/nt/defense_finder_systems.tsv test-data/outputs/prot/defense_finder_genes.tsv test-data/outputs/prot/defense_finder_genes_with_antidefense.tsv test-data/outputs/prot/defense_finder_hmmer.tsv test-data/outputs/prot/defense_finder_hmmer_with_antidefense.tsv test-data/outputs/prot/defense_finder_systems.tsv test-data/outputs/prot/defense_finder_systems_with_antidefense.tsv tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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added:
test-data/defense-finder.2.loc tool-data/defense-finder.2.loc.sample |
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removed:
test-data/defense-finder.loc tool-data/defense-finder.loc.sample |
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| diff -r 4ff81ce331f9 -r f5b9109b889a defense_finder.xml --- a/defense_finder.xml Mon Jul 22 11:12:44 2024 +0000 +++ b/defense_finder.xml Thu Feb 13 15:46:29 2025 +0000 |
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| @@ -30,12 +30,7 @@ <option value="unordered">Unordered</option> </param> <param argument="--no-cut-ga" type="boolean" truevalue="--no-cut-ga" falsevalue="" label="Run macsyfinder in no-cut-ga mode" help="By default MSF try to applied a threshold per profile by using the hmmer -cut-ga option. This is possible only if the GA bit score is present in the profile otherwise MSF switch to use the --e-value-search (-E in hmmsearch). If this option is set the --e-value-search option is used for all profiles regardless the presence of the a GA bit score in the profiles."/> - <param name="models" argument="--models-dir" type="select" label="Select the DefenseFinder models version to search against" help=""> - <options from_data_table="defense-finder"> - <filter type="static_value" column="1" value="defense-finder-models"/> - <validator type="no_options" message="No dataset available for the selected input dataset"/> - </options> - </param> + <expand macro="models"/> <param argument="--coverage" type="float" value="0.4" min="0" max="1" label="Coverage" help="Minimal percentage of coverage for each profiles"/> <param argument="--preserve-raw" type="boolean" truevalue="--preserve-raw" falsevalue="" label="Preserve raw MacsyFinder outputs" help="Preserve raw MacsyFinder outputs alongside Defense Finder results inside the output directory"/> <param argument="--antidefensefinder" type="boolean" truevalue="--antidefensefinder" falsevalue="" label="AntiDefenseFinder" help="Also run AntiDefenseFinder models to find antidefense systems"/> @@ -51,14 +46,14 @@ <tests> <test> <param name="genome" value="inputs/df_test_prot.faa"/> - <param name="models" value="defense-finder-models_1.3.0"/> + <param name="models" value="defense-finder-models_2.0.2"/> <output name="genes" compare="contains" file="outputs/prot/defense_finder_genes.tsv"/> <output name="hmmer" compare="contains" file="outputs/prot/defense_finder_hmmer.tsv"/> <output name="systems" compare="contains" file="outputs/prot/defense_finder_systems.tsv"/> </test> <test> <param name="genome" value="inputs/df_test_prot.faa"/> - <param name="models" value="defense-finder-models_1.3.0"/> + <param name="models" value="defense-finder-models_2.0.2"/> <param name="antidefensefinder" value="--antidefensefinder" /> <output name="genes" compare="contains" file="outputs/prot/defense_finder_genes_with_antidefense.tsv"/> <output name="hmmer" compare="contains" file="outputs/prot/defense_finder_hmmer_with_antidefense.tsv"/> @@ -67,7 +62,7 @@ <test> <param name="genome" value="inputs/df_test_nt.fna"/> - <param name="models" value="defense-finder-models_1.3.0"/> + <param name="models" value="defense-finder-models_2.0.2"/> <output name="genes" compare="contains" file="outputs/nt/defense_finder_genes.tsv"/> <output name="hmmer" compare="contains" file="outputs/nt/defense_finder_hmmer.tsv"/> <output name="systems" compare="contains" file="outputs/nt/defense_finder_systems.tsv"/> @@ -99,6 +94,6 @@ guaranteed! --help Show this message and exit. - ]]></help> + ]]> </help> <expand macro="citations"/> </tool> |
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| diff -r 4ff81ce331f9 -r f5b9109b889a macros.xml --- a/macros.xml Mon Jul 22 11:12:44 2024 +0000 +++ b/macros.xml Thu Feb 13 15:46:29 2025 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.3.0</token> + <token name="@TOOL_VERSION@">2.0.0</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0085</edam_topic> @@ -15,6 +15,20 @@ <yield/> </requirements> </xml> + <token name="@COMPATIBILITY_SPEC@"><![CDATA[(.*2\.0\.0.*$)]]></token> + <!-- <xml name="hidden_version"> + <param name="version" type="hidden" value="@TOOL_VERSION@" /> + </xml> --> + <xml name="models"> + <param name="models" argument="--models-dir" type="select" label="Select the DefenseFinder models version to search against" help=""> + <options from_data_table="defense-finder"> + <filter type="static_value" column="1" value="defense-finder-models"/> + <filter type="regexp" value="@COMPATIBILITY_SPEC@" column="4" /> + <validator type="no_options" message="No dataset available for the selected input dataset"/> + </options> + </param> + </xml> + <xml name="citations"> <citations> <citation type="doi">10.1038/s41467-022-30269-9</citation> |
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| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/defense-finder.2.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/defense-finder.2.loc Thu Feb 13 15:46:29 2025 +0000 |
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| @@ -0,0 +1,6 @@ +# <unique_build_id> <dbkey> <name> <version> <soft compatibility version> <description> <file_base_path> + +defense-finder-models_1.2.3 defense-finder-models version 1.2.3 1.2.3 1.2.0,1.2.2,2.0.0 MacSyFinder models allowing for a systematic search of anti-phage systems ${__HERE__}/defense-finder/defense-finder-models_1.2.3 +defense-finder-models_1.2.4 defense-finder-models version 1.2.4 1.2.4 1.2.0,1.2.2,2.0.0 MacSyFinder models allowing for a systematic search of anti-phage systems ${__HERE__}/defense-finder/defense-finder-models_1.2.4 +defense-finder-models_1.3.0 defense-finder-models version 1.3.0 1.3.0 1.3.0,2.0.0 MacSyFinder models allowing for a systematic search of anti-phage systems ${__HERE__}/defense-finder/defense-finder-models_1.3.0 +defense-finder-models_2.0.2 defense-finder-models version 2.0.2 2.0.2 2.0.0 MacSyFinder models allowing for a systematic search of anti-phage systems ${__HERE__}/defense-finder/defense-finder-models_2.0.2 \ No newline at end of file |
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| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/defense-finder.loc --- a/test-data/defense-finder.loc Mon Jul 22 11:12:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -# <unique_build_id> <dbkey> <name> <version> <description> <file_base_path> - -defense-finder-models_1.2.3 defense-finder-models Defense Finder models (version 1.2.3) 1.2.3 MacSyFinder models allowing for a systematic search of anti-phage systems ${__HERE__}/defense-finder/defense-finder-models_1.2.3 -defense-finder-models_1.2.4 defense-finder-models Defense Finder models (version 1.2.4) 1.2.4 MacSyFinder models allowing for a systematic search of anti-phage systems ${__HERE__}/defense-finder/defense-finder-models_1.2.4 -defense-finder-models_1.3.0 defense-finder-models Defense Finder models (version 1.3.0) 1.3.0 MacSyFinder models allowing for a systematic search of anti-phage systems ${__HERE__}/defense-finder/defense-finder-models_1.3.0 \ No newline at end of file |
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| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/inputs/df_test_prot.faa --- a/test-data/inputs/df_test_prot.faa Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/inputs/df_test_prot.faa Thu Feb 13 15:46:29 2025 +0000 |
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| b'@@ -1,20845 +1,12960 @@\n->PSAE004.0722.00032.C001_06398 D ATG TAA 6874359 6874574 Valid IOMTU133_RS31560 216 @WP_060853310.1@ IOMTU133_RS31560 1 6874359 6874574 | helix-turn-helix domain-containing protein (translation)\n-MDDRWLSVDEIADYLGVAKDTIYTWVTSKGMPGHKVGRFWKFKKEDVDAWVRDGGAAASS\n-DDFDDKEPRNA\n->PSAE004.0722.00032.C001_06399 D ATG TGA 6874567 6876609 Valid IOMTU133_RS31565 2043 @WP_197671914.1@ IOMTU133_RS31565 1 6874567 6876609 | N-6 DNA methylase (translation)\n-MPKQRSVQDNNDMSALDQEAQAPESVLEEGKVFDYITGKPVKDSDKEQVRQRIARAIIHE\n-YGIAAEDMEPDFKVKVLGKNRKLDIAIFKPGQAHTVDNLYRAVVVEKEPKLGTKGAYRMR\n-DPEEARKDFEVLETVMAEVESCDYGLWTNGLEFFFFKKEVTRFDTKFKPIGDWPLGDDTF\n-SVEGRSMGRMRRADPVMLRTAFRRCHNYIHGNEGMPKDAAFWQFLYLIFCKMYDEQQPNE\n-ARGFYVGPFEPFDPAGQKAIRLRIKPLFERVKKKYSGLFKGNEEITLSDRALAFIVSELA\n-RYDFGRTDVDAKGAAYQEIVGTNLRGDRGQYFTPRGAISLVVKMLAPKEHERVLDSSCGT\n-GGFLVETLNYLNKVFHEEKRIKAGDENTEEFVSIRDRLAHFAANNLFGADFDPFLVRAAQ\n-MNVMMAGNSLGHLYHMNSLEFPAGHLPGVPAAKAAIPLGTIDVLMTNPPFGSDIPVTEKT\n-ILEQYELARRWERQGDGFVMTNAIKPAVSPEVLFIERCVKWLKPGGRAGIVLPDGILGNP\n-GDEFIRYWILRHCWVLASIDLPVESFIVEANVNILTSLLFLKRKPAEVIQAEDLGQKKDY\n-PVFMAVAEKVGFDRRGNTLYKRHPDGEEILVDVSHEEKVRIGGGLQVRTLHRKERILDDD\n-LPEIAKAYAEFRAQHPEPSK\n->PSAE004.0722.00032.C001_06400 D ATG TGA 6876606 6877943 Valid IOMTU133_RS31570 1338 @WP_060853311.1@ IOMTU133_RS31570 1 6876606 6877943 | AAA family ATPase (translation)\n-MITRLEATRYRCFERLGVDVGDFRVLVGANGSGKTTLLDLPVLLGDLLRANNVSAPFMDR\n-RPELPPRAGSLSELVFAGRGSDFSLAVEARLPEAVQSKVLEGLFASKRTERSRQALQEDR\n-RQWPTHIRYEIGLRIGADQSLLVAYEYLFLFPEADGPDRRQAGFHGATAASKKLWHLTLK\n-REIGYESEFKPETPHAKAVKVGLPETLLAMPRVLFESEAGYPAARWLHTLLTTDAVFLEP\n-NWSAMRQASPPGQPKFITANGRNIPWLALELKREGAPEAAPADYRSERYADWIAHVQTAL\n-PQVTDIEVREREDDHHTYFVVSYRGDFKVPSAGLSEGTLRILTLTLLPYLSKQPAIVVTE\n-EPENGIHPRAIEAVLQSLSSMYDSQVWVSSHSPVVLARAKLDQLLCARLASEGGVEMVAG\n-TDHPRLQEWRGGIDLGSLFAAGVLG\n->PSAE004.0722.00032.C001_06401 D ATG TGA 6877940 6878596 Valid IOMTU133_RS31575 657 @WP_060853312.1@ IOMTU133_RS31575 1 6877940 6878596 | hypothetical protein (translation)\n-MMNKRPCVILVADSNMAATFRGYFKRERWHLSLGCAPFEINTDVGADLLVDEGGNDPGVY\n-TKGHELLRPYQNSHQRALVVLDCEWEGSPGKDAIVAHITANLVASGWAEDAVKVIAIEPE\n-LENWLWQDKPQVVDALGYQGTKPLRQHLADSGQWPIDVAKPPRPKETAEWVLKQAKKPRS\n-SAIYQKLAEHISIRGCTDAAFAEMHAAFLAWFPLEVPA\n->PSAE004.0722.00032.C001_06402 D ATG TGA 6878593 6879984 Valid IOMTU133_RS31580 1392 @WP_060853313.1@ IOMTU133_RS31580 1 6878593 6879984 | hypothetical protein (translation)\n-MTAVKLKIVRAAWLDEGGRRLDCNPYMSGALEARDTLKRLAARKDKLRDVTLGMFDSGRE\n-SRNWVDDPRFGVRYMGSSAITLADLSSLPLISNKQVARNPKLLIKEGWSLITRSGTIGRM\n-AYVRREMAGLACSEDVLRVVPDPERIAPGYLYAFLSSRYGVPLVVSGTYGAIIQHIEPEH\n-IADLPVPRFDAQTEAAVAEKVDAAARARSEAVELLQEARNRLHLRLGLSAPTPVSVLTKP\n-DVTSVSSDTFRDRGDGYYYSARNAESRRAFDAAGGNRALGEVAEVFIPGIFKRLYASDPQ\n-FGSPYITGGDVFELAPVSDKFLMKRVAAEYGLLLKKGMIVVQEAGQLGGLIGRSVMVGSY\n-LDGFSCSNNMIRIVPEDDIDGGYLFTLLSSEHGVRLLSREAAGSSIPHTDEQRVKRIQVP\n-WPARKDREDIGAPAIRARELRDQACAWEQEARDMLEAKVLGGE\n->PSAE004.0722.00032.C001_06403 D ATG TGA 6879986 6884149 Valid IOMTU133_RS31585 4164 @WP_060853314.1@ IOMTU133_RS31585 1 6879986 6884149 | serine/threonine protein kinase (translation)\n-MAKVIPVGQPVNDAERSAIAYLRDRLPDNFVLLHNFEIERQGERFEIDIALLTPHALYLI\n-DVKGTRGTIDVYGNKWYPEGRAPYPSPLGKLRGHARTVKGLVTQANPGRNELDGIYVDAA\n-ILLTAPDAHLNDREQLDADRAVKLKDAERYFKDAKRIPARFSKNILQQQGLILHALKVVK\n-PASTMKRFGHWQVKEKLGGAEAYTEFRAENAFAGGTARLRVYQADPYQPEEVRKAQVNRI\n-ANAYRALSKLPLHPNIVAARDFFPTDDDKTFILILDDAPGQALTVHMARPQLALTLDQKW\n-RVAKDLLAALAHAHHHGVVHRNLTPGAILIGQDGTTRITDFDFAKPGGDRSRTIASDIVD\n-LVEKAYVAPEAFREPGAASSASDIFSAGVILYELFTGERPFAGEPTTVWDREGEFLFKPS\n-TLRPELNEAFDAWLQNLCAFDEHQRLTASAALVALNALLQPVAQATNQAPEEPKPEVFEV\n-DDAQTDYLNLAAGHRLTHKFIVEKKLGRGSFGVVYKVIDTLGDVARTVKLIVSDRHSTLE\n-RLKKEYRHLVQIPEHPHVVRVLDADVIPGRDIPFLVFEYVEGADVGDMIHDRLLSPEDAL\n-ELGKQVIEGLVHLHAQGFHHCDIKPRNLLWTQKGAKIIDFNVSVRADDKESRGGGSRRYL\n-PPDFDPEVIPHNGERADRDLYALGLTLYEALTARYPWDTTEPPINKPAPDPRELSGYADL\n-APELVNVVLKAVASHRAERFHSAIDFRDALADVRHARRIQDVRLAAMVTAVSSGQPALTE\n-SAANTNAFVSHLLTLYSQSRRSNAGTRGMDALGFSAYVDTALDRALLPAVLQGEFRLVLI\n-SGNAGDGKTAFLQRLEKEVETRGGAVNRGLANGSELDLDGKRYLINYDGSQDEGNKDNNQ\n-VLLDFLAPFKGNDAASWR'..b'VGSGAFLVAACRALGDALVTAWHTHDQLPPIPLDEDEVLLARRLVAQRCLYGVDKNPMAADLAKLSLWLATLARDHPFTFLDHSIRAGDSLVGLSRRQIEDFHWKPEPHPTFGQEIIGRRLKAETAVRREILEAGDDLDPRLKAQKLATADEALELVRLVGDLVIAAFFGADKDKARDLKRDALRAELTHKLQAGNLMNLPDAPALDLRGGAKPLVPFHWEIEFPEVFQRDGKGFDAILGNPPFAGKNTLIQGTRDGYLDWLKVLHPESHGNADLVAHFFRRAFDLLRPDGCFGLIATNTIGQGDTRSTGLRWIRTHGGSIYWARKRYKWPGEAAVIVSVINGIRGAWSEDVELDGKQVPTITAYLFHAGSDEDPKRLEANANKSFQGSIVLGMGFTFDDTDTKSVASPIAEMYRLIQHDPRNSERIFPYIGGDEVNESPTHAHHRYVVNFEDFPLRRDDLGETWTGADESRRKKWLCMGIVPADYPGPVAMDWPDLLDIVERKVKPERDAQNRKALRERWWQYAEKRPGLVTALRALERVLIIARTSKHFALSWSSPVFVYSENLVVITLETPAGFAVMQSSVQEVWMKFTSSTLEDRQGYRPSDCFETFPFPDC\n+>CATH005.0523.00001.002P_06696\tC\tATG\tTGA\t471443\t471838\t131\tNA\tTHSYN_RS36595\tWP_100917962.1\thypothetical_protein\n+MASTALNDYVNFPHVAQVCRIERAVTELTSGKQRDETVFAVTSLPPQLADPPRLLQLNRGHWGIENRSHYVRDVTFDEDRSRVRVGHGPAIMASLRNFAIALARLHGFTNIASALRAFAHQPRRALAAIGV\n+>CATH005.0523.00001.002P_06697\tC\tATG\tTAA\t471870\t473204\t444\tNA\tTHSYN_RS33255\tWP_216644545.1\tISAs1_family_transposase\n+MAEIPCQSCRPASELLRRLEVRLILPGERDAWDALVEAHHYLGLRSLFGKTLRYVATLDGCWLALLGWQAAALKCAARDAWIGWPRVLHYQRLHLLANNARFLILPATGRVPNLASRILALNLRRLSDDWLRVHGHRLLLAETFVDPTRFTGACYRAANWQVVGTTRGFARCNGRYTPHGEPKQALVYPLHPRARALLCAPVLPAPWSTPMQSVTLTTAQMQDLQQRLRALPDRRRPRGKRHPQATVLSIGLAAVLAGNRGYTALAEWAARLTQAQLKRLHARYNPRTERFEPPSEPTLRRVLQASDVAAIDATLSDWLLGLVAADDAVAVDGKALRGAVRPDGTQVHLLSAFLQDQGVTVAQREIPAKTNEIPELKPLLAPLDLTGRVVTADALHTQRETARFLVEEKQAHYFFTVKENQPTLYADLSALTEAHFPPLHHDPR\n+>CATH005.0523.00001.002P_06698\tC\tATG\tTAG\t473273\t473545\t90\tNA\tTHSYN_RS33260\tWP_100923305.1\thypothetical_protein\n+MSTDPAIRDHQAWLGYLQPDGLVVSPAALVDLQVILPRDSREEQQRFLECVTAGTIGTADPVPVIADLPGFLHSFLEWPDTLAGLRRVHP\n+>CATH005.0523.00001.002P_06700\tC\tATG\tTGA\t476959\t480759\t1266\tNA\tTHSYN_RS33270\tWP_100923306.1\tEAL_domain-containing_protein\n+MTKDVATIAADAPLSVALDQMTTRRIRSVLVHDGGALVGIVTGHDLITAAARGTAFVTPVAALMSYPVLRLPAHTPLASAYGRMRRTGLRHLVVTGRDGTPAGIVSETDFFQHLSAAQLTSALTVADIMDLSPATLGPEATLAQVLMAVATAPSDCAVVTRGAQPLVIVTEGSLLARLRAGADLLATRLIDQSDKVVTLNTVAASASLAEARALFRSRKVHTLAVVHPDGALAGVLALRGLIGAALPDRGDGRAGVPSTTAPSRVRLRQFQRAVQQSPVSVIITDTEGTIEYVNPRFCEVTGYREDEVLGRNPRLLKSGAQDATFYQALWRAISAGRVWKGELCNRRRDTSLYWEAATISPVRDDRGDIVNFVAVKEDITARKRAERALRESESKYRGLIASLSGEYLLYRREPAGPMTYLSPSVEHMTGYTPAELEGPWISHLTDHPLNQSALETSRRALEGARQEPYDIEIRVKSGDVKRLRVSESPLFNLQGQVVAVQGIAQDVTELHRTRVLLDGRSRVLERLARGRPQAEVLEAITAYIAEAQPGAMPAVYLLDQDGPRLWLGAAPALPAHFNRALDGGAIGPGVGTCASVSDQDPLVVCEDIRSHPDWAALREIILTTELRACWSHPIRGRSGRVLGTFAIYHRESRRPAPREREIIAAAADLAAVVLDYFQAQVALGHAEERERLLLISTTEGVLGVDRLGITTFVNPAAARMLGYLPEELTGTVIHDRIHRPTVGHADSRAAENHPLAHCPLVAPALDGRARHGIRETLYRRDGSAVPVELWSNPVLVDGQLAGAAVTFRDISERLEQEQRIHFLAFHDALTGLPNRNLLRESLDRELARLRRHDTPFALYLLDLDHFKDVNDSLGHPAGDELLQVVAERLRAQLRAEDSVARMGGDEFAIIQSYTGGADGVARLANRLVDALARPIPIRGREIRIGASLGVVMVNDPLDADTLMAQADVALYEAKGRGRNRYALFAPDMARALERELEIVGSLSQAIANGDLHLVYQPQVRIASGALYAVEALVRWHHRRLGALLPGDFVPILERRGTVARLDGWVLRQAARQARDWTRRGCPFGRLAVNLSTLYPDDGQGAATPPDLIRRHGGNPQDLELELTERMLTRETYGIAESIAAIRGAGMGIAIDDFGTGYASLSYLRRFNPRTLKIDRALVADMAGDQGAAEIVKAAIALGRALGLALVAEGVEDSAQADYLVAYGCELAQGYLYGGALEIEAFNERFFADCTPVGEGTGSDQAASDSR\n+>CATH005.0523.00001.002P_06701\tC\tATG\tTAA\t482408\t483508\t366\tNA\tTHSYN_RS33275\tWP_100923307.1\thypothetical_protein\n+MQDDQQDGAPRDLKRTLERLERQARERSVKQQRTAPAAAPTSPAPRTKALRRTNAGVPGPKVIAEANARLERFLRERGIEQFELFPSAEYPTPLTRLPLFPPVQRSTARELAAAADWIALESRWDGGGVYKAGPALTVYDEDTLFGLMNMRQQGMTGPADRLPIPAPPTVALSGLAPGNPVRVHALYCLVSQLESVIQGYTPPRGWGGRAITKRRESMENLAAITLKFQKPKGGDAFHGKPIQLIFIEYVATAEDACYYVQFHPLVSQWLEEYRTFLDFDIRRQLSPLGKAMHRSLASQRSNRTFSIPLTEFFASIGAFGELRDRKREAIPQLQKLITLQFLECFAITGTGRRTPWLLAVTFFRRK\n+>CATH005.0523.00001.002P_06702\tD\tATG\tTAA\t483644\t484801\t385\tNA\tTHSYN_RS33280\tWP_100923308.1\tAAA_family_ATPase\n+MRAKRSIEDLLGRIQGVRDRLKDYNLAPDHVKRDTRLYAMREAAELIGRSDQTIRDAEAEGKLPTPEIGRNGKRIGYTLAQINAARDVLGTRLRRGADEEPVVIGCQSFKGGSGKTTTAVHLTQYLARQGLRVLLVDCDPQASATAIFGYVPEADLSPDETLLPFLEGDRADLAYAVRPTYFDGVFLVPSNLHLYRSEYTLAAGTAKLDRLKDGIDTIAVNFDVVVIDPPPSLGMISLNALYASNALIIPMSLGLLDFYSTVSFIQMLNETLDVIERRVGTVRSKFVKVLMTRVNEVKPVHVQLADHLQASFGTYLMKARMHDSAAVDNAGVMMRTVYELEKTAANRKTLLRAMMLFDLVNAEILTLVRSTWPSHHKALRAQGLM\n' |
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| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/outputs/nt/defense_finder_genes.tsv --- a/test-data/outputs/nt/defense_finder_genes.tsv Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/outputs/nt/defense_finder_genes.tsv Thu Feb 13 15:46:29 2025 +0000 |
| b |
| b'@@ -1,50 +1,51 @@\n replicon\thit_id\tgene_name\thit_pos\tmodel_fqn\tsys_id\tsys_loci\tlocus_num\tsys_wholeness\tsys_score\tsys_occ\thit_gene_ref\thit_status\thit_seq_len\thit_i_eval\thit_score\thit_profile_cov\thit_seq_cov\thit_begin_match\thit_end_match\tcounterpart\tused_in\ttype\tsubtype\tactivity\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_22\tRM_Type_II__Type_II_REases\t22\tdefense-finder-models/RM/RM/RM_Type_II\tKOAN001.0722.00001.C001_RM_Type_II_23\t1\t1\t1.0\t2.0\t1\tRM_Type_II__Type_II_REases\tmandatory\t401\t5.200000000000001e-44\t149.4\t0.996\t0.933\t10\t383\t\t\tRM\tRM_Type_II\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_23\tRM_Type_II__Type_II_MTases\t23\tdefense-finder-models/RM/RM/RM_Type_II\tKOAN001.0722.00001.C001_RM_Type_II_23\t1\t1\t1.0\t2.0\t1\tRM_Type_II__Type_II_MTases\tmandatory\t836\t7.6e-54\t181.4\t0.986\t0.463\t2\t388\t\t\tRM\tRM_Type_II\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_254\tSeptu__PtuB\t254\tdefense-finder-models/DefenseFinder_2/Septu/Septu\tKOAN001.0722.00001.C001_Septu_11\t1\t1\t1.0\t2.0\t1\tSeptu__PtuB\tmandatory\t298\t4.1e-37\t126.6\t0.869\t0.862\t1\t257\t\t\tSeptu\tSeptu\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_255\tSeptu__PtuA\t255\tdefense-finder-models/DefenseFinder_2/Septu/Septu\tKOAN001.0722.00001.C001_Septu_11\t1\t1\t1.0\t2.0\t1\tSeptu__PtuA\tmandatory\t788\t1.3e-76\t257.2\t0.968\t0.503\t363\t758\t\t\tSeptu\tSeptu\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_677\tRM__Type_I_S\t677\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_21\t1\t1\t1.0\t2.5\t1\tRM__Type_I_S\taccessory\t407\t7.000000000000001e-60\t201.4\t0.464\t0.985\t3\t403\t\t\tRM\tRM_Type_I\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_678\tRM__Type_I_MTases\t678\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_21\t1\t1\t1.0\t2.5\t1\tRM__Type_I_MTases\tmandatory\t543\t2.7e-114\t380.9\t0.99\t0.983\t8\t541\t\t\tRM\tRM_Type_I\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_679\tRM__Type_I_REases\t679\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_21\t1\t1\t1.0\t2.5\t1\tRM__Type_I_REases\tmandatory\t1023\t9.7e-91\t303.6\t0.965\t0.943\t1\t965\t\t\tRM\tRM_Type_I\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_680\tAbiZ__AbiZ\t680\tdefense-finder-models/DefenseFinder_1/AbiZ/AbiZ\tKOAN001.0722.00001.C001_AbiZ_5\t1\t1\t1.0\t1.0\t1\tAbiZ__AbiZ\tmandatory\t440\t9.599999999999999e-41\t138.4\t0.923\t0.923\t33\t438\t\t\tAbiZ\tAbiZ\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_1086\tRM_Type_IIG__Type_IIG\t1086\tdefense-finder-models/RM/RM/RM_Type_IIG\tKOAN001.0722.00001.C001_RM_Type_IIG_25\t1\t1\t1.0\t1.0\t1\tRM_Type_IIG__Type_IIG\tmandatory\t676\t3.2e-233\t775.0\t0.705\t0.991\t1\t670\t\t\tRM\tRM_Type_IIG\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_1160\tAbiL__AbiLii\t1160\tdefense-finder-models/DefenseFinder_1/AbiL/AbiL\tKOAN001.0722.00001.C001_AbiL_4\t1\t1\t1.0\t2.0\t1\tAbiL__AbiLii\tmandatory\t213\t5.7e-06\t23.7\t0.475\t0.671\t50\t192\t\t\tAbiL\tAbiL\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_1161\tAbiL__AbiLi2\t1161\tdefense-finder-models/DefenseFinder_1/AbiL/AbiL\tKOAN001.0722.00001.C001_AbiL_4\t1\t1\t1.0\t2.0\t1\tAbiL__AbiLi\tmandatory\t432\t3.5e-41\t139.9\t0.98\t0.981\t1\t424\t\t\tAbiL\tAbiL\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_1167\tSeptu__PtuB\t1167\tdefense-finder-models/DefenseFinder_2/Septu/Septu\tKOAN001.0722.00001.C001_Septu_12\t1\t1\t1.0\t2.0\t1\tSeptu__PtuB\tmandatory\t223\t1.5e-21\t75.7\t0.902\t0.942\t1\t210\t\t\tSeptu\tSeptu\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_1168\tSeptu__PtuA\t1168\tdefense-finder-models/DefenseFinder_2/Septu/Septu\tKOAN001.0722.00001.C001_Septu_12\t1\t1\t1.0\t2.0\t1\tSeptu__PtuA\tmandatory\t412\t8e-57\t192.0\t0.972\t0.976\t4\t405\t\t\tSeptu\tSeptu\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_1740\tGabija__GajA\t1740\tdefense-finder-models/DefenseFinder_1/Gabija/Gabija\tKOAN001.0722.00001.C001_Gabija_6\t1\t1\t1.0\t2.0\t1\tGabija__GajA\tmandatory\t692\t9.500000000000001e-100\t333.2\t0.989\t0.999\t1\t691\t\t\tGabija\tGabija\tDefense\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_1741\tGabija__GajB_1\t1741\tdefense-finder-models/DefenseFinder_1/Gabija/Gabija\tKOAN001.0722.00001.'..b'Type_II\tKOAN001.0722.00001.C001_RM_Type_II_27\t1\t1\t1.0\t2.0\t1\tRM_Type_II__Type_II_REase01\tmandatory\t237\t5.1e-11\t41.3\t0.735\t0.835\t7\t204\t\t\tRM\tRM_Type_II\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_3068\tAbiD__AbiD\t3068\tdefense-finder-models/DefenseFinder/AbiD/AbiD\tKOAN001.0722.00001.C001_AbiD_1\t1\t1\t1.0\t1.0\t1\tAbiD__AbiD\tmandatory\t291\t7e-54\t181.4\t0.885\t0.979\t3\t287\t\t\tAbiD\tAbiD\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_3146\tRetron_VI__HTH\t3146\tdefense-finder-models/DefenseFinder/Retron/Retron_VI\tKOAN001.0722.00001.C001_Retron_VI_11\t1\t1\t1.0\t2.0\t1\tRetron_VI__HTH\tmandatory\t98\t1.4e-25\t87.2\t0.919\t0.939\t3\t94\t\t\tRetron\tRetron_VI\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_3147\tRetron__RT_Tot_10\t3147\tdefense-finder-models/DefenseFinder/Retron/Retron_VI\tKOAN001.0722.00001.C001_Retron_VI_11\t1\t1\t1.0\t2.0\t1\tRetron__RT_Tot_1\tmandatory\t285\t3.8000000000000004e-80\t267.6\t0.778\t0.916\t1\t261\t\t\tRetron\tRetron_VI\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_3309\tAbiH__AbiH\t3309\tdefense-finder-models/DefenseFinder/AbiH/AbiH\tKOAN001.0722.00001.C001_AbiH_2\t1\t1\t1.0\t1.0\t1\tAbiH__AbiH\tmandatory\t408\t2.1e-27\t94.8\t0.992\t0.868\t4\t357\t\t\tAbiH\tAbiH\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_3317\tNLR_like_bNACHT01__NLR_like_bNACHT01\t3317\tdefense-finder-models/DefenseFinder/NLR/NLR_like_bNACHT01\tKOAN001.0722.00001.C001_NLR_like_bNACHT01_9\t1\t1\t1.0\t1.0\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\tmandatory\t657\t3.9e-97\t324.4\t0.905\t0.826\t13\t555\t\t\tNLR\tNLR_like_bNACHT01\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4033\tRM__Type_I_REases_FAM_0.einsi_trimmed\t4033\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_25\t1\t1\t1.0\t3.0\t1\tRM__Type_I_REases_FAM_0.einsi_trimmed\tmandatory\t1087\t1.8e-184\t613.8\t0.972\t0.954\t13\t1049\t\tKOAN001.0722.00001.C001_PrrC_23\tRM\tRM_Type_I\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4034\tCBASS__2TM_5\t4034\tdefense-finder-models/DefenseFinder/Pycsar/Pycsar\tKOAN001.0722.00001.C001_Pycsar_10\t1\t1\t1.0\t1.5\t1\tCBASS__Effector_2TM_S_2TMBeta\taccessory\t173\t1.4e-27\t94.4\t0.931\t0.954\t4\t168\t\t\tPycsar\tPycsar\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4035\tPycsar__AG_cyclase\t4035\tdefense-finder-models/DefenseFinder/Pycsar/Pycsar\tKOAN001.0722.00001.C001_Pycsar_10\t1\t1\t1.0\t1.5\t1\tPycsar__AG_cyclase\tmandatory\t334\t4.4e-31\t106.3\t0.586\t0.545\t11\t192\t\t\tPycsar\tPycsar\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4036\tRM__Type_I_S_51\t4036\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_25\t1\t1\t1.0\t3.0\t1\tRM__Type_I_S_01\tmandatory\t413\t6e-80\t267.0\t0.836\t0.969\t12\t411\t\tKOAN001.0722.00001.C001_PrrC_23\tRM\tRM_Type_I\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4038\tRM__Type_I_MTases_FAM_0\t4038\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_25\t1\t1\t1.0\t3.0\t1\tRM__Type_I_MTases_FAM_0\tmandatory\t501\t7.4e-176\t584.0\t0.996\t0.998\t1\t500\t\tKOAN001.0722.00001.C001_PrrC_23\tRM\tRM_Type_I\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4280\tViperin__pVip\t4280\tdefense-finder-models/DefenseFinder/Viperin/Viperin\tKOAN001.0722.00001.C001_Viperin_19\t1\t1\t1.0\t1.0\t1\tViperin__pVip\tmandatory\t304\t2.9e-108\t359.5\t0.913\t0.921\t24\t303\t\t\tViperin\tViperin\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4361\tRloC__RloC\t4361\tdefense-finder-models/DefenseFinder/RloC/RloC\tKOAN001.0722.00001.C001_RloC_12\t1\t1\t1.0\t1.0\t1\tRloC__RloC\tmandatory\t787\t6.3e-145\t482.8\t0.996\t0.995\t1\t783\t\t\tRloC\tRloC\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4604\tUG19_small__UG19_small\t4604\tdefense-finder-models/DefenseFinder/All_UG/UG19_small\tKOAN001.0722.00001.C001_UG19_small_18\t1\t1\t1.0\t1.5\t1\tUG19_small__UG19_small\tmandatory\t551\t2.8e-261\t866.1\t1.0\t0.998\t1\t550\t\t\tAll_UG\tUG19_small\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4605\tUG19_small__HP\t4605\tdefense-finder-models/DefenseFinder/All_UG/UG19_small\tKOAN001.0722.00001.C001_UG19_small_18\t1\t1\t1.0\t1.5\t1\tUG19_small__HP\taccessory\t213\t2.7e-99\t329.0\t1.0\t0.995\t1\t212\t\t\tAll_UG\tUG19_small\tDefense\n' |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/outputs/nt/defense_finder_hmmer.tsv --- a/test-data/outputs/nt/defense_finder_hmmer.tsv Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/outputs/nt/defense_finder_hmmer.tsv Thu Feb 13 15:46:29 2025 +0000 |
| b |
| b'@@ -1,89 +1,105 @@\n hit_id\treplicon\thit_pos\thit_sequence_length\tgene_name\ti_eval\thit_score\thit_profile_cov\thit_seq_cov\thit_begin_match\thit_end_match\n+KOAN001.0722.00001.C001_3\tKOAN001.0722.00001.C001\t3\t146\tVeles__VlsC1\t3.3000000000000003e-34\t116.2\t0.926\t0.979\t1\t143\n+KOAN001.0722.00001.C001_3\tKOAN001.0722.00001.C001\t3\t146\tVeles__VlsC2\t2.9e-35\t119.6\t0.926\t0.973\t1\t142\n KOAN001.0722.00001.C001_17\tKOAN001.0722.00001.C001\t17\t312\tCARD_NLR__Endonuclease_new\t5.1999999999999994e-51\t171.7\t0.784\t0.888\t3\t279\n-KOAN001.0722.00001.C001_22\tKOAN001.0722.00001.C001\t22\t401\tRM_Type_II__Type_II_REases\t5.2e-44\t149.4\t0.996\t0.933\t10\t383\n+KOAN001.0722.00001.C001_22\tKOAN001.0722.00001.C001\t22\t401\tRM_Type_II__Type_II_REase17\t5.2e-44\t149.4\t0.981\t0.933\t10\t383\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_30\t1.4e-10\t38.3\t0.464\t0.335\t386\t665\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_22\t1.9e-10\t38.5\t0.449\t0.221\t15\t199\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_28\t1.9e-15\t54.4\t0.415\t0.275\t437\t666\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_10\t9.6e-17\t59.0\t0.489\t0.282\t432\t667\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_21\t6.7e-18\t62.7\t0.482\t0.272\t8\t234\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_6\t2.5e-18\t64.1\t0.407\t0.258\t435\t650\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_13\t4.299999999999999e-22\t76.4\t0.634\t0.445\t317\t688\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_15\t2.2999999999999998e-23\t80.8\t0.87\t0.396\t6\t336\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_2\t1.8e-26\t91.2\t0.972\t0.456\t3\t383\n KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tDruantia_II__DruM\t1.8999999999999998e-39\t134.0\t0.891\t0.477\t5\t403\n KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tDISARM_2__drmMII\t6.5e-40\t135.4\t0.987\t0.467\t1\t390\n-KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases\t7.599999999999999e-54\t181.4\t0.986\t0.463\t2\t388\n-KOAN001.0722.00001.C001_85\tKOAN001.0722.00001.C001\t85\t607\tShango__SngC\t2.2999999999999998e-23\t80.8\t0.535\t0.59\t9\t366\n-KOAN001.0722.00001.C001_85\tKOAN001.0722.00001.C001\t85\t607\tPsyrTA__PsyrT\t6e-26\t88.8\t0.594\t0.69\t13\t431\n+KOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001\t23\t836\tRM_Type_II__Type_II_MTases_FAM_0\t7.599999999999999e-54\t181.4\t0.986\t0.463\t2\t388\n KOAN001.0722.00001.C001_131\tKOAN001.0722.00001.C001\t131\t552\tRetron_I_A__ATPase_TypeIA\t1.3e-06\t25.8\t0.5\t0.505\t2\t280\n KOAN001.0722.00001.C001_147\tKOAN001.0722.00001.C001\t147\t455\tDEDDh_I_II_III_IV_V_VI_1\t2e-42\t143.1\t0.994\t0.341\t4\t158\n KOAN001.0722.00001.C001_167\tKOAN001.0722.00001.C001\t167\t868\tDodola__DolB\t5e-24\t83.1\t0.429\t0.2\t546\t719\n+KOAN001.0722.00001.C001_217\tKOAN001.0722.00001.C001\t217\t260\tDS-6__DS-6A\t1.3e-43\t147.8\t0.634\t0.958\t7\t255\n KOAN001.0722.00001.C001_238\tKOAN001.0722.00001.C001\t238\t153\tThoeris__ThsB_Global\t9.8e-13\t46.5\t0.596\t0.745\t15\t128\n KOAN001.0722.00001.C001_242\tKOAN001.0722.00001.C001\t242\t780\tGabija__GajB_3\t3.8e-13\t47.5\t0.663\t0.362\t28\t309\n KOAN001.0722.00001.C001_242\tKOAN001.0722.00001.C001\t242\t780\tGabija__GajB_1\t2e-40\t137.1\t0.914\t0.779\t21\t628\n+KOAN001.0722.00001.C001_242\tKOAN001.0722.00001.C001\t242\t780\tUG35__UvrD\t7.3e-97\t323.4\t0.534\t0.567\t10\t451\n KOAN001.0722.00001.C001_242\tKOAN001.0722.00001.C001\t242\t780\tGabija__GajB_2\t2e-108\t361.5\t0.775\t0.841\t4\t659\n KOAN001.0722.00001.C001_249\tKOAN001.0722.00001.C001\t249\t294\tZorya__ZorB\t1.3e-08\t32.6\t0.687\t0.582\t114\t284\n KOAN001.0722.00001.C001_254\tKOAN001.0722.00001.C001\t254\t298\tRetron_I_A__HNH_TIGR02646\t1.2e-21\t75.6\t0.795\t0.745\t37\t258\n KOAN001.0722.00001.C001_254\tKOAN001.0722.00001.C001\t254\t298\tSeptu__PtuB\t4.1e-37\t126.6\t0.869\t0.862\t1\t257\n-KOAN001.0722.00001.C001_255\tKOAN001.0722.00001.C001\t255\t788\tParis_II__AAA'..b'es\t2.9e-41\t139.9\t0.724\t0.507\t157\t410\n+KOAN001.0722.00001.C001_4036\tKOAN001.0722.00001.C001\t4036\t413\tRM__Type_I_S_02\t3.6999999999999995e-22\t77.1\t0.466\t0.528\t15\t232\n+KOAN001.0722.00001.C001_4036\tKOAN001.0722.00001.C001\t4036\t413\tRM__Type_I_S_06\t1.3e-28\t98.3\t0.723\t0.927\t29\t411\n+KOAN001.0722.00001.C001_4036\tKOAN001.0722.00001.C001\t4036\t413\tRM__Type_I_S_03\t7e-36\t122.5\t0.834\t0.947\t19\t409\n+KOAN001.0722.00001.C001_4036\tKOAN001.0722.00001.C001\t4036\t413\tRM__Type_I_S_52\t2.6e-41\t140.2\t0.671\t0.947\t18\t408\n+KOAN001.0722.00001.C001_4036\tKOAN001.0722.00001.C001\t4036\t413\tRM__Type_I_S_04\t9.1e-58\t194.6\t0.767\t0.969\t11\t410\n+KOAN001.0722.00001.C001_4036\tKOAN001.0722.00001.C001\t4036\t413\tRM__Type_I_S_51\t6e-80\t267.0\t0.836\t0.969\t12\t411\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM_Type_II__Type_II_MTases_FAM_28\t6.3e-13\t46.1\t0.447\t0.517\t178\t436\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM_Type_II__Type_II_MTases_FAM_29\t2.2e-14\t51.0\t0.511\t0.605\t160\t462\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM_Type_II__Type_II_MTases_FAM_14\t2.0000000000000002e-20\t70.8\t0.453\t0.507\t173\t426\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM_Type_II__Type_II_MTases_FAM_13\t1.7e-21\t74.5\t0.443\t0.517\t151\t409\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM_Type_II__Type_II_MTases_FAM_6\t4.0999999999999995e-22\t76.6\t0.456\t0.493\t175\t421\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM_Type_II__Type_II_MTases_FAM_33\t2.9e-41\t139.9\t0.488\t0.507\t157\t410\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM__Type_I_MTases_FAM_2\t8.7e-48\t161.4\t0.923\t0.97\t5\t490\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM__Type_I_MTases_FAM_3\t3.6999999999999997e-54\t182.1\t0.711\t0.902\t4\t455\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM__Type_I_MTases_FAM_1\t7.2e-60\t201.0\t0.978\t0.968\t11\t495\n KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tPrrC__EcoprrI\t1.9000000000000002e-109\t365.3\t0.958\t0.996\t1\t499\n-KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM__Type_I_MTases\t7.4e-176\t584.0\t0.996\t0.998\t1\t500\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM__Type_I_MTases_FAM_0\t7.4e-176\t584.0\t0.996\t0.998\t1\t500\n KOAN001.0722.00001.C001_4114\tKOAN001.0722.00001.C001\t4114\t137\tDpd__QueD\t3.5e-12\t44.8\t0.842\t0.839\t1\t115\n-KOAN001.0722.00001.C001_4118\tKOAN001.0722.00001.C001\t4118\t412\tPsyrTA__PsyrT\t1.7e-21\t74.1\t0.479\t0.806\t23\t354\n-KOAN001.0722.00001.C001_4118\tKOAN001.0722.00001.C001\t4118\t412\tShango__SngC\t7.599999999999999e-23\t79.0\t0.507\t0.835\t7\t350\n KOAN001.0722.00001.C001_4154\tKOAN001.0722.00001.C001\t4154\t258\tDEDDh_I_II_III_IV_V_VI_1\t5.7e-39\t131.9\t0.994\t0.605\t10\t165\n KOAN001.0722.00001.C001_4280\tKOAN001.0722.00001.C001\t4280\t304\tViperin__pVip\t2.9e-108\t359.5\t0.913\t0.921\t24\t303\n KOAN001.0722.00001.C001_4361\tKOAN001.0722.00001.C001\t4361\t787\tRloC__RloC\t6.2999999999999994e-145\t482.8\t0.996\t0.995\t1\t783\n-KOAN001.0722.00001.C001_4379\tKOAN001.0722.00001.C001\t4379\t377\tParis_I__AAA_15\t1.5e-09\t36.1\t0.633\t0.645\t18\t260\n-KOAN001.0722.00001.C001_4379\tKOAN001.0722.00001.C001\t4379\t377\tRetron_I_B__ATPase_TOPRIM_COG3593\t1.4e-14\t52.3\t0.544\t0.891\t18\t353\n KOAN001.0722.00001.C001_4420\tKOAN001.0722.00001.C001\t4420\t342\tDodola__DolB\t3.6e-07\t27.7\t0.571\t0.602\t33\t238\n+KOAN001.0722.00001.C001_4503\tKOAN001.0722.00001.C001\t4503\t398\tVeles__VlsB1\t7e-94\t313.0\t0.883\t0.857\t7\t347\n+KOAN001.0722.00001.C001_4503\tKOAN001.0722.00001.C001\t4503\t398\tVeles__VlsB2\t1.1e-97\t325.6\t0.846\t0.852\t7\t345\n KOAN001.0722.00001.C001_4604\tKOAN001.0722.00001.C001\t4604\t551\tRT_I_II_III_IV_V_VI_1\t2.4e-26\t90.4\t0.488\t0.263\t150\t294\n+KOAN001.0722.00001.C001_4604\tKOAN001.0722.00001.C001\t4604\t551\tUG19_small__UG19_small\t2.8e-261\t866.1\t1.0\t0.998\t1\t550\n+KOAN001.0722.00001.C001_4605\tKOAN001.0722.00001.C001\t4605\t213\tUG19_small__HP\t2.7000000000000003e-99\t329.0\t1.0\t0.995\t1\t212\n KOAN001.0722.00001.C001_4697\tKOAN001.0722.00001.C001\t4697\t472\tLamassu-Fam__LmuA_effector_Protease\t2.6e-11\t41.4\t0.431\t0.356\t103\t270\n' |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/outputs/nt/defense_finder_systems.tsv --- a/test-data/outputs/nt/defense_finder_systems.tsv Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/outputs/nt/defense_finder_systems.tsv Thu Feb 13 15:46:29 2025 +0000 |
| b |
| b'@@ -1,28 +1,27 @@\n sys_id\ttype\tsubtype\tactivity\tsys_beg\tsys_end\tprotein_in_syst\tgenes_count\tname_of_profiles_in_sys\n-KOAN001.0722.00001.C001_RM_Type_II_23\tRM\tRM_Type_II\tDefense\tKOAN001.0722.00001.C001_22\tKOAN001.0722.00001.C001_23\tKOAN001.0722.00001.C001_22,KOAN001.0722.00001.C001_23\t2\tRM_Type_II__Type_II_MTases,RM_Type_II__Type_II_REases\n-KOAN001.0722.00001.C001_Septu_11\tSeptu\tSeptu\tDefense\tKOAN001.0722.00001.C001_254\tKOAN001.0722.00001.C001_255\tKOAN001.0722.00001.C001_254,KOAN001.0722.00001.C001_255\t2\tSeptu__PtuA,Septu__PtuB\n-KOAN001.0722.00001.C001_RM_Type_I_21\tRM\tRM_Type_I\tDefense\tKOAN001.0722.00001.C001_677\tKOAN001.0722.00001.C001_679\tKOAN001.0722.00001.C001_677,KOAN001.0722.00001.C001_678,KOAN001.0722.00001.C001_679\t3\tRM__Type_I_MTases,RM__Type_I_REases,RM__Type_I_S\n-KOAN001.0722.00001.C001_AbiZ_5\tAbiZ\tAbiZ\tDefense\tKOAN001.0722.00001.C001_680\tKOAN001.0722.00001.C001_680\tKOAN001.0722.00001.C001_680\t1\tAbiZ__AbiZ\n-KOAN001.0722.00001.C001_RM_Type_IIG_25\tRM\tRM_Type_IIG\tDefense\tKOAN001.0722.00001.C001_1086\tKOAN001.0722.00001.C001_1086\tKOAN001.0722.00001.C001_1086\t1\tRM_Type_IIG__Type_IIG\n-KOAN001.0722.00001.C001_AbiL_4\tAbiL\tAbiL\tDefense\tKOAN001.0722.00001.C001_1160\tKOAN001.0722.00001.C001_1161\tKOAN001.0722.00001.C001_1160,KOAN001.0722.00001.C001_1161\t2\tAbiL__AbiLi2,AbiL__AbiLii\n-KOAN001.0722.00001.C001_Septu_12\tSeptu\tSeptu\tDefense\tKOAN001.0722.00001.C001_1167\tKOAN001.0722.00001.C001_1168\tKOAN001.0722.00001.C001_1167,KOAN001.0722.00001.C001_1168\t2\tSeptu__PtuA,Septu__PtuB\n-KOAN001.0722.00001.C001_Gabija_6\tGabija\tGabija\tDefense\tKOAN001.0722.00001.C001_1740\tKOAN001.0722.00001.C001_1741\tKOAN001.0722.00001.C001_1740,KOAN001.0722.00001.C001_1741\t2\tGabija__GajA,Gabija__GajB_1\n-KOAN001.0722.00001.C001_Wadjet_I_14\tWadjet\tWadjet_I\tDefense\tKOAN001.0722.00001.C001_1742\tKOAN001.0722.00001.C001_1745\tKOAN001.0722.00001.C001_1742,KOAN001.0722.00001.C001_1743,KOAN001.0722.00001.C001_1744,KOAN001.0722.00001.C001_1745\t4\tWadjet__JetA_I,Wadjet__JetB_I,Wadjet__JetC_I,Wadjet__JetD_I\n-KOAN001.0722.00001.C001_NLR_like_bNACHT01_9\tNLR\tNLR_like_bNACHT01\tDefense\tKOAN001.0722.00001.C001_2014\tKOAN001.0722.00001.C001_2014\tKOAN001.0722.00001.C001_2014\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\n-KOAN001.0722.00001.C001_SpbK_15\tSpbK\tSpbK\tDefense\tKOAN001.0722.00001.C001_2040\tKOAN001.0722.00001.C001_2040\tKOAN001.0722.00001.C001_2040\t1\tSpbK__SpbK\n-KOAN001.0722.00001.C001_Dnd_ABCDE_16\tDnd\tDnd_ABCDE\tDefense\tKOAN001.0722.00001.C001_2084\tKOAN001.0722.00001.C001_2091\tKOAN001.0722.00001.C001_2084,KOAN001.0722.00001.C001_2086,KOAN001.0722.00001.C001_2087,KOAN001.0722.00001.C001_2089,KOAN001.0722.00001.C001_2090,KOAN001.0722.00001.C001_2091\t6\tDnd__DndB,Dnd__DndC,Dnd__DndD,Dnd__DndD,Dnd__DndE,Dnd__DndE\n-KOAN001.0722.00001.C001_CAS_Class2-Subtype-II-C_26\tCas\tCAS_Class2-Subtype-II-C\tDefense\tKOAN001.0722.00001.C001_2421\tKOAN001.0722.00001.C001_2423\tKOAN001.0722.00001.C001_2421,KOAN001.0722.00001.C001_2422,KOAN001.0722.00001.C001_2423\t3\tcas1_I_II_III_IV_V_VI_5,cas2_I_II_III_IV_V_VI_6,cas9_II-A_II-B_II-C_1\n-KOAN001.0722.00001.C001_SoFic_20\tSoFIC\tSoFic\tDefense\tKOAN001.0722.00001.C001_2823\tKOAN001.0722.00001.C001_2823\tKOAN001.0722.00001.C001_2823\t1\tSoFic__SoFic\n-KOAN001.0722.00001.C001_AbiE_2\tAbiE\tAbiE\tDefense\tKOAN001.0722.00001.C001_2843\tKOAN001.0722.00001.C001_2844\tKOAN001.0722.00001.C001_2843,KOAN001.0722.00001.C001_2844\t2\tAbiEii__AbiEi_4,AbiEii__AbiEii\n-KOAN001.0722.00001.C001_AbiE_2\tAbiE\tAbiE\tDefense\tKOAN001.0722.00001.C001_2843\tKOAN001.0722.00001.C001_2844\tKOAN001.0722.00001.C001_2843,KOAN001.0722.00001.C001_2844\t2\tAbiEii__AbiEi_4,AbiEii__AbiEii\n-KOAN001.0722.00001.C001_SanaTA_19\tSanaTA\tSanaTA\tDefense\tKOAN001.0722.00001.C001_2843\tKOAN001.0722.00001.C001_2844\tKOAN001.0722.00001.C001_2843,KOAN001.0722.00001.C001_2844\t2\tSanaTA__SanaA,SanaTA__SanaT\n-KOAN001.0722.00001.C001_SanaTA_19\tSanaTA\tSanaTA\tDefense\tKOAN001.0722.00001.C001_2843\tKOAN001.0722.00001.C001_2844\tKOAN001.0722.00001.C001_2843,KOAN001.0722.00001.C001_2844\t2\tSanaTA__SanaA,SanaTA__SanaT\n-KOAN001.0722.00001.C001_RM_Type_II'..b'DndE,Dnd__DndE\n+KOAN001.0722.00001.C001_CAS_Class2-Subtype-II-C_29\tCas\tCAS_Class2-Subtype-II-C\tDefense\tKOAN001.0722.00001.C001_2421\tKOAN001.0722.00001.C001_2423\tKOAN001.0722.00001.C001_2421,KOAN001.0722.00001.C001_2422,KOAN001.0722.00001.C001_2423\t3\tcas1_I_II_III_IV_V_VI_5,cas2_I_II_III_IV_V_VI_6,cas9_II-A_II-B_II-C_1\n+KOAN001.0722.00001.C001_SoFic_16\tSoFIC\tSoFic\tDefense\tKOAN001.0722.00001.C001_2823\tKOAN001.0722.00001.C001_2823\tKOAN001.0722.00001.C001_2823\t1\tSoFic__SoFic\n+KOAN001.0722.00001.C001_SanaTA_13\tSanaTA\tSanaTA\tDefense\tKOAN001.0722.00001.C001_2843\tKOAN001.0722.00001.C001_2844\tKOAN001.0722.00001.C001_2843,KOAN001.0722.00001.C001_2844\t2\tSanaTA__SanaA,SanaTA__SanaT_1\n+KOAN001.0722.00001.C001_RM_Type_II_27\tRM\tRM_Type_II\tDefense\tKOAN001.0722.00001.C001_2943\tKOAN001.0722.00001.C001_2944\tKOAN001.0722.00001.C001_2943,KOAN001.0722.00001.C001_2944\t2\tRM_Type_II__Type_II_MTases_FAM_0,RM_Type_II__Type_II_REase18\n KOAN001.0722.00001.C001_AbiD_1\tAbiD\tAbiD\tDefense\tKOAN001.0722.00001.C001_3068\tKOAN001.0722.00001.C001_3068\tKOAN001.0722.00001.C001_3068\t1\tAbiD__AbiD\n-KOAN001.0722.00001.C001_Retron_VI_18\tRetron\tRetron_VI\tDefense\tKOAN001.0722.00001.C001_3146\tKOAN001.0722.00001.C001_3147\tKOAN001.0722.00001.C001_3146,KOAN001.0722.00001.C001_3147\t2\tRetron_VI__HTH,Retron__RT_Tot\n-KOAN001.0722.00001.C001_AbiH_3\tAbiH\tAbiH\tDefense\tKOAN001.0722.00001.C001_3309\tKOAN001.0722.00001.C001_3309\tKOAN001.0722.00001.C001_3309\t1\tAbiH__AbiH\n-KOAN001.0722.00001.C001_NLR_like_bNACHT01_10\tNLR\tNLR_like_bNACHT01\tDefense\tKOAN001.0722.00001.C001_3317\tKOAN001.0722.00001.C001_3317\tKOAN001.0722.00001.C001_3317\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\n-KOAN001.0722.00001.C001_RM_Type_I_22\tRM\tRM_Type_I\tDefense\tKOAN001.0722.00001.C001_4033\tKOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001_4033,KOAN001.0722.00001.C001_4036,KOAN001.0722.00001.C001_4038\t3\tRM__Type_I_MTases,RM__Type_I_REases,RM__Type_I_S\n-KOAN001.0722.00001.C001_Pycsar_17\tPycsar\tPycsar\tDefense\tKOAN001.0722.00001.C001_4034\tKOAN001.0722.00001.C001_4035\tKOAN001.0722.00001.C001_4034,KOAN001.0722.00001.C001_4035\t2\tCBASS__2TM_5,Pycsar__AG_cyclase\n-KOAN001.0722.00001.C001_Viperin_8\tViperin\tViperin\tDefense\tKOAN001.0722.00001.C001_4280\tKOAN001.0722.00001.C001_4280\tKOAN001.0722.00001.C001_4280\t1\tViperin__pVip\n-KOAN001.0722.00001.C001_RloC_7\tRloC\tRloC\tDefense\tKOAN001.0722.00001.C001_4361\tKOAN001.0722.00001.C001_4361\tKOAN001.0722.00001.C001_4361\t1\tRloC__RloC\n+KOAN001.0722.00001.C001_Retron_VI_11\tRetron\tRetron_VI\tDefense\tKOAN001.0722.00001.C001_3146\tKOAN001.0722.00001.C001_3147\tKOAN001.0722.00001.C001_3146,KOAN001.0722.00001.C001_3147\t2\tRetron_VI__HTH,Retron__RT_Tot_10\n+KOAN001.0722.00001.C001_AbiH_2\tAbiH\tAbiH\tDefense\tKOAN001.0722.00001.C001_3309\tKOAN001.0722.00001.C001_3309\tKOAN001.0722.00001.C001_3309\t1\tAbiH__AbiH\n+KOAN001.0722.00001.C001_NLR_like_bNACHT01_9\tNLR\tNLR_like_bNACHT01\tDefense\tKOAN001.0722.00001.C001_3317\tKOAN001.0722.00001.C001_3317\tKOAN001.0722.00001.C001_3317\t1\tNLR_like_bNACHT01__NLR_like_bNACHT01\n+KOAN001.0722.00001.C001_RM_Type_I_25\tRM\tRM_Type_I\tDefense\tKOAN001.0722.00001.C001_4033\tKOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001_4033,KOAN001.0722.00001.C001_4036,KOAN001.0722.00001.C001_4038\t3\tRM__Type_I_MTases_FAM_0,RM__Type_I_REases_FAM_0.einsi_trimmed,RM__Type_I_S_51\n+KOAN001.0722.00001.C001_Pycsar_10\tPycsar\tPycsar\tDefense\tKOAN001.0722.00001.C001_4034\tKOAN001.0722.00001.C001_4035\tKOAN001.0722.00001.C001_4034,KOAN001.0722.00001.C001_4035\t2\tCBASS__2TM_5,Pycsar__AG_cyclase\n+KOAN001.0722.00001.C001_Viperin_19\tViperin\tViperin\tDefense\tKOAN001.0722.00001.C001_4280\tKOAN001.0722.00001.C001_4280\tKOAN001.0722.00001.C001_4280\t1\tViperin__pVip\n+KOAN001.0722.00001.C001_RloC_12\tRloC\tRloC\tDefense\tKOAN001.0722.00001.C001_4361\tKOAN001.0722.00001.C001_4361\tKOAN001.0722.00001.C001_4361\t1\tRloC__RloC\n+KOAN001.0722.00001.C001_UG19_small_18\tAll_UG\tUG19_small\tDefense\tKOAN001.0722.00001.C001_4604\tKOAN001.0722.00001.C001_4605\tKOAN001.0722.00001.C001_4604,KOAN001.0722.00001.C001_4605\t2\tUG19_small__HP,UG19_small__UG19_small\n' |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/outputs/prot/defense_finder_genes.tsv --- a/test-data/outputs/prot/defense_finder_genes.tsv Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/outputs/prot/defense_finder_genes.tsv Thu Feb 13 15:46:29 2025 +0000 |
| b |
| b'@@ -1,562 +1,161 @@\n replicon\thit_id\tgene_name\thit_pos\tmodel_fqn\tsys_id\tsys_loci\tlocus_num\tsys_wholeness\tsys_score\tsys_occ\thit_gene_ref\thit_status\thit_seq_len\thit_i_eval\thit_score\thit_profile_cov\thit_seq_cov\thit_begin_match\thit_end_match\tcounterpart\tused_in\ttype\tsubtype\tactivity\n-df_test_prot\tPSAE004.0722.00032.C001_06398\tMADS__mad1\t1\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad1\tmandatory\t71\t1.9e-44\t146.8\t0.986\t0.986\t1\t70\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06399\tMADS__mad2\t2\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad2\tmandatory\t680\t0.0\t1469.4\t0.999\t0.987\t10\t680\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06400\tMADS__mad3\t3\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad3\tmandatory\t445\t3.8e-214\t708.9\t1.0\t1.0\t1\t445\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06401\tMADS__mad4\t4\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad4\tmandatory\t218\t6.2e-108\t356.6\t0.991\t0.972\t5\t216\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06402\tMADS__mad5\t5\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad5\tmandatory\t463\t1.2e-174\t578.9\t0.987\t0.991\t4\t462\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06403\tMADS__mad6\t6\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad6\tmandatory\t1387\t0.0\t2841.9\t1.0\t1.0\t1\t1387\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06404\tMADS__mad7\t7\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad7\tmandatory\t557\t0.0\t1125.0\t0.998\t0.998\t1\t556\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06405\tMADS__mad8\t8\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad8\tmandatory\t1853\t0.0\t3835.3\t1.0\t1.0\t1\t1853\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01127\tDpd__QueE\t18\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__QueE\taccessory\t222\t4.3e-122\t403.0\t1.0\t0.995\t2\t222\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01128\tDpd__DpdE\t19\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdE\tmandatory\t1002\t0.0\t1044.8\t0.925\t0.978\t1\t980\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01129\tDpd__DpdF\t20\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdF\tmandatory\t851\t4.5999999999999996e-299\t991.8\t0.995\t0.994\t5\t850\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01130\tDpd__DpdG\t21\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdG\tmandatory\t310\t2e-87\t290.7\t0.997\t0.997\t1\t309\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01131\tDpd__DpdH\t22\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdH\tmandatory\t1031\t0.0\t1143.7\t0.999\t0.997\t1\t1028\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01132\tDpd__DpdI\t23\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdI\tmandatory\t249\t6e-43\t144.7\t0.984\t0.988\t4\t249\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01133\tDpd__DpdJ\t24\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdJ\tmandatory\t1495\t0.0\t1757.1\t0.997\t0.998\t3\t1494\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01134\tDpd__DpdK\t25\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdK\tmandatory\t178\t2.6e-62\t207.0\t0.889\t0.983\t1\t175\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01135\tDpd__DpdD\t26\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdD\tmandatory\t720\t2.6e-282\t935.6\t0.994\t0.999\t1\t719\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01136\tDpd__QueC\t27\tdefense-fin'..b'\n+df_test_prot\tCATH005.0523.00001.002P_06403\tWadjet__JetD_I\t6196\tdefense-finder-models/DefenseFinder/Wadjet/Wadjet_I\tdf_test_prot_Wadjet_I_41\t1\t1\t1.0\t4.0\t1\tWadjet__JetD_I\tmandatory\t395\t9.3e-126\t418.6\t0.972\t0.99\t1\t391\t\tdf_test_prot_Wadjet_40\tWadjet\tWadjet_I\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06404\tRM_Type_III__Type_III_REases_FAM_0.einsi_trimmed\t6197\tdefense-finder-models/RM/RM/RM_Type_III\tdf_test_prot_RM_Type_III_80\t1\t1\t1.0\t2.0\t1\tRM_Type_III__Type_III_REases_FAM_0.einsi_trimmed\tmandatory\t1002\t5.3999999999999994e-251\t834.2\t0.987\t0.99\t1\t992\t\t\tRM\tRM_Type_III\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06406\tRM_Type_III__Type_III_MTases_FAM_0\t6199\tdefense-finder-models/RM/RM/RM_Type_III\tdf_test_prot_RM_Type_III_80\t1\t1\t1.0\t2.0\t1\tRM_Type_III__Type_III_MTases_FAM_0\tmandatory\t633\t4.700000000000001e-180\t599.2\t0.965\t0.981\t1\t621\t\t\tRM\tRM_Type_III\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06602\tGao_RL__RL_D\t6384\tdefense-finder-models/DefenseFinder/Gao_RL/Gao_RL\tdf_test_prot_Gao_RL_14\t1\t1\t1.0\t4.0\t1\tGao_RL__RL_D\tmandatory\t915\t0.0\t1054.8\t1.0\t0.998\t1\t913\t\t\tGao_RL\tGao_RL\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06606\tGao_RL__RL_C\t6388\tdefense-finder-models/DefenseFinder/Gao_RL/Gao_RL\tdf_test_prot_Gao_RL_14\t1\t1\t1.0\t4.0\t1\tGao_RL__RL_C\tmandatory\t1017\t0.0\t1153.2\t0.987\t0.976\t19\t1011\t\t\tGao_RL\tGao_RL\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06607\tGao_RL__RL_B\t6389\tdefense-finder-models/DefenseFinder/Gao_RL/Gao_RL\tdf_test_prot_Gao_RL_14\t1\t1\t1.0\t4.0\t1\tGao_RL__RL_B\tmandatory\t197\t1.5e-54\t182.9\t0.943\t0.934\t12\t195\t\t\tGao_RL\tGao_RL\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06608\tGao_RL__RL_A\t6390\tdefense-finder-models/DefenseFinder/Gao_RL/Gao_RL\tdf_test_prot_Gao_RL_14\t1\t1\t1.0\t4.0\t1\tGao_RL__RL_A\tmandatory\t1039\t5.7e-261\t867.1\t0.997\t0.996\t4\t1038\t\t\tGao_RL\tGao_RL\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06621\tcas10_III-D_3\t6403\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcas10_III-D_1\tmandatory\t614\t6.1e-70\t234.8\t0.956\t0.695\t10\t436\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06624\tcsx19_III-D_4\t6406\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcsx19_III-D_2\tmandatory\t182\t1.5e-06\t26.5\t0.781\t0.813\t28\t175\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06625\tcsm3gr7_III-D_2\t6407\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcsm3gr7_III-D_1\tmandatory\t858\t1.8e-25\t88.4\t0.423\t0.4\t493\t835\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06626\tcasR_III-D_6\t6408\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcasR_III-D_10\taccessory\t638\t7.3e-09\t33.4\t0.521\t0.458\t328\t619\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06627\tcas1_I_II_III_IV_V_VI_10\t6409\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcas1_I_II_III_IV_V_VI_10\taccessory\t1052\t4.1000000000000004e-67\t224.9\t0.993\t0.267\t725\t1005\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06628\tcas2_I_II_III_IV_V_VI_3\t6410\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcas2_I_II_III_IV_V_VI_5\taccessory\t93\t2e-21\t74.5\t0.949\t0.817\t4\t79\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06666\tViperin__pVip\t6445\tdefense-finder-models/DefenseFinder/Viperin/Viperin\tdf_test_prot_Viperin_39\t1\t1\t1.0\t1.0\t1\tViperin__pVip\tmandatory\t284\t2.1999999999999998e-91\t304.5\t0.903\t0.986\t5\t284\t\t\tViperin\tViperin\tDefense\n' |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/outputs/prot/defense_finder_genes_with_antidefense.tsv --- a/test-data/outputs/prot/defense_finder_genes_with_antidefense.tsv Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/outputs/prot/defense_finder_genes_with_antidefense.tsv Thu Feb 13 15:46:29 2025 +0000 |
| b |
| b'@@ -1,564 +1,162 @@\n replicon\thit_id\tgene_name\thit_pos\tmodel_fqn\tsys_id\tsys_loci\tlocus_num\tsys_wholeness\tsys_score\tsys_occ\thit_gene_ref\thit_status\thit_seq_len\thit_i_eval\thit_score\thit_profile_cov\thit_seq_cov\thit_begin_match\thit_end_match\tcounterpart\tused_in\ttype\tsubtype\tactivity\n-df_test_prot\tPSAE004.0722.00032.C001_06398\tMADS__mad1\t1\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad1\tmandatory\t71\t1.9e-44\t146.8\t0.986\t0.986\t1\t70\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06399\tMADS__mad2\t2\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad2\tmandatory\t680\t0.0\t1469.4\t0.999\t0.987\t10\t680\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06400\tMADS__mad3\t3\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad3\tmandatory\t445\t3.8e-214\t708.9\t1.0\t1.0\t1\t445\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06401\tMADS__mad4\t4\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad4\tmandatory\t218\t6.2e-108\t356.6\t0.991\t0.972\t5\t216\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06402\tMADS__mad5\t5\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad5\tmandatory\t463\t1.2e-174\t578.9\t0.987\t0.991\t4\t462\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06403\tMADS__mad6\t6\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad6\tmandatory\t1387\t0.0\t2841.9\t1.0\t1.0\t1\t1387\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06404\tMADS__mad7\t7\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad7\tmandatory\t557\t0.0\t1125.0\t0.998\t0.998\t1\t556\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tPSAE004.0722.00032.C001_06405\tMADS__mad8\t8\tdefense-finder-models/DefenseFinder_5/MADS/MADS\tdf_test_prot_MADS_231\t1\t1\t1.0\t8.0\t1\tMADS__mad8\tmandatory\t1853\t0.0\t3835.3\t1.0\t1.0\t1\t1853\t\t\tMADS\tMADS\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01127\tDpd__QueE\t18\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__QueE\taccessory\t222\t4.3e-122\t403.0\t1.0\t0.995\t2\t222\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01128\tDpd__DpdE\t19\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdE\tmandatory\t1002\t0.0\t1044.8\t0.925\t0.978\t1\t980\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01129\tDpd__DpdF\t20\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdF\tmandatory\t851\t4.5999999999999996e-299\t991.8\t0.995\t0.994\t5\t850\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01130\tDpd__DpdG\t21\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdG\tmandatory\t310\t2e-87\t290.7\t0.997\t0.997\t1\t309\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01131\tDpd__DpdH\t22\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdH\tmandatory\t1031\t0.0\t1143.7\t0.999\t0.997\t1\t1028\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01132\tDpd__DpdI\t23\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdI\tmandatory\t249\t6e-43\t144.7\t0.984\t0.988\t4\t249\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01133\tDpd__DpdJ\t24\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdJ\tmandatory\t1495\t0.0\t1757.1\t0.997\t0.998\t3\t1494\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01134\tDpd__DpdK\t25\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdK\tmandatory\t178\t2.6e-62\t207.0\t0.889\t0.983\t1\t175\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01135\tDpd__DpdD\t26\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.0\t13.0\t1\tDpd__DpdD\tmandatory\t720\t2.6e-282\t935.6\t0.994\t0.999\t1\t719\t\t\tDpd\tDpd\tDefense\n-df_test_prot\tTHCR001.0722.00001.C001_01136\tDpd__QueC\t27\tdefense-fin'..b'\n+df_test_prot\tCATH005.0523.00001.002P_06403\tWadjet__JetD_I\t6196\tdefense-finder-models/DefenseFinder/Wadjet/Wadjet_I\tdf_test_prot_Wadjet_I_41\t1\t1\t1.0\t4.0\t1\tWadjet__JetD_I\tmandatory\t395\t9.3e-126\t418.6\t0.972\t0.99\t1\t391\t\tdf_test_prot_Wadjet_40\tWadjet\tWadjet_I\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06404\tRM_Type_III__Type_III_REases_FAM_0.einsi_trimmed\t6197\tdefense-finder-models/RM/RM/RM_Type_III\tdf_test_prot_RM_Type_III_80\t1\t1\t1.0\t2.0\t1\tRM_Type_III__Type_III_REases_FAM_0.einsi_trimmed\tmandatory\t1002\t5.3999999999999994e-251\t834.2\t0.987\t0.99\t1\t992\t\t\tRM\tRM_Type_III\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06406\tRM_Type_III__Type_III_MTases_FAM_0\t6199\tdefense-finder-models/RM/RM/RM_Type_III\tdf_test_prot_RM_Type_III_80\t1\t1\t1.0\t2.0\t1\tRM_Type_III__Type_III_MTases_FAM_0\tmandatory\t633\t4.700000000000001e-180\t599.2\t0.965\t0.981\t1\t621\t\t\tRM\tRM_Type_III\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06602\tGao_RL__RL_D\t6384\tdefense-finder-models/DefenseFinder/Gao_RL/Gao_RL\tdf_test_prot_Gao_RL_14\t1\t1\t1.0\t4.0\t1\tGao_RL__RL_D\tmandatory\t915\t0.0\t1054.8\t1.0\t0.998\t1\t913\t\t\tGao_RL\tGao_RL\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06606\tGao_RL__RL_C\t6388\tdefense-finder-models/DefenseFinder/Gao_RL/Gao_RL\tdf_test_prot_Gao_RL_14\t1\t1\t1.0\t4.0\t1\tGao_RL__RL_C\tmandatory\t1017\t0.0\t1153.2\t0.987\t0.976\t19\t1011\t\t\tGao_RL\tGao_RL\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06607\tGao_RL__RL_B\t6389\tdefense-finder-models/DefenseFinder/Gao_RL/Gao_RL\tdf_test_prot_Gao_RL_14\t1\t1\t1.0\t4.0\t1\tGao_RL__RL_B\tmandatory\t197\t1.5e-54\t182.9\t0.943\t0.934\t12\t195\t\t\tGao_RL\tGao_RL\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06608\tGao_RL__RL_A\t6390\tdefense-finder-models/DefenseFinder/Gao_RL/Gao_RL\tdf_test_prot_Gao_RL_14\t1\t1\t1.0\t4.0\t1\tGao_RL__RL_A\tmandatory\t1039\t5.7e-261\t867.1\t0.997\t0.996\t4\t1038\t\t\tGao_RL\tGao_RL\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06621\tcas10_III-D_3\t6403\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcas10_III-D_1\tmandatory\t614\t6.1e-70\t234.8\t0.956\t0.695\t10\t436\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06624\tcsx19_III-D_4\t6406\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcsx19_III-D_2\tmandatory\t182\t1.5e-06\t26.5\t0.781\t0.813\t28\t175\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06625\tcsm3gr7_III-D_2\t6407\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcsm3gr7_III-D_1\tmandatory\t858\t1.8e-25\t88.4\t0.423\t0.4\t493\t835\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06626\tcasR_III-D_6\t6408\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcasR_III-D_10\taccessory\t638\t7.3e-09\t33.4\t0.521\t0.458\t328\t619\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06627\tcas1_I_II_III_IV_V_VI_10\t6409\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcas1_I_II_III_IV_V_VI_10\taccessory\t1052\t4.1000000000000004e-67\t224.9\t0.993\t0.267\t725\t1005\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06628\tcas2_I_II_III_IV_V_VI_3\t6410\tCasFinder/CAS_Class1-Subtype-III-D\tdf_test_prot_CAS_Class1-Subtype-III-D_85\t1\t1\t0.6\t6.0\t1\tcas2_I_II_III_IV_V_VI_5\taccessory\t93\t2e-21\t74.5\t0.949\t0.817\t4\t79\t\tdf_test_prot_CAS_Class1-Type-III_90,df_test_prot_CAS_Cluster_94\tCas\tCAS_Class1-Subtype-III-D\tDefense\n+df_test_prot\tCATH005.0523.00001.002P_06666\tViperin__pVip\t6445\tdefense-finder-models/DefenseFinder/Viperin/Viperin\tdf_test_prot_Viperin_39\t1\t1\t1.0\t1.0\t1\tViperin__pVip\tmandatory\t284\t2.1999999999999998e-91\t304.5\t0.903\t0.986\t5\t284\t\t\tViperin\tViperin\tDefense\n' |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/outputs/prot/defense_finder_hmmer.tsv --- a/test-data/outputs/prot/defense_finder_hmmer.tsv Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/outputs/prot/defense_finder_hmmer.tsv Thu Feb 13 15:46:29 2025 +0000 |
| b |
| b'@@ -1,912 +1,639 @@\n hit_id\treplicon\thit_pos\thit_sequence_length\tgene_name\ti_eval\thit_score\thit_profile_cov\thit_seq_cov\thit_begin_match\thit_end_match\n-PSAE004.0722.00032.C001_06398\tdf_test_prot\t1\t71\tMADS__mad1\t1.8999999999999998e-44\t146.8\t0.986\t0.986\t1\t70\n-PSAE004.0722.00032.C001_06399\tdf_test_prot\t2\t680\tRM_Type_II__Type_II_MTases\t4.3e-154\t511.5\t1.415\t0.919\t51\t675\n-PSAE004.0722.00032.C001_06399\tdf_test_prot\t2\t680\tMADS__mad2\t0.0\t1469.4\t0.999\t0.987\t10\t680\n-PSAE004.0722.00032.C001_06400\tdf_test_prot\t3\t445\tParis_II__AAA_21\t4.6e-22\t76.4\t0.993\t0.838\t25\t397\n-PSAE004.0722.00032.C001_06400\tdf_test_prot\t3\t445\tMADS__mad3\t3.8e-214\t708.9\t1.0\t1.0\t1\t445\n-PSAE004.0722.00032.C001_06401\tdf_test_prot\t4\t218\tMADS__mad4\t6.2e-108\t356.6\t0.991\t0.972\t5\t216\n-PSAE004.0722.00032.C001_06402\tdf_test_prot\t5\t463\tMADS__mad5\t1.2e-174\t578.9\t0.987\t0.991\t4\t462\n-PSAE004.0722.00032.C001_06403\tdf_test_prot\t6\t1387\tSspBCDE__SspF\t1.1e-13\t47.6\t0.503\t0.218\t823\t1124\n-PSAE004.0722.00032.C001_06403\tdf_test_prot\t6\t1387\tBREX__pglW\t8.200000000000001e-78\t259.5\t0.522\t0.538\t12\t757\n-PSAE004.0722.00032.C001_06403\tdf_test_prot\t6\t1387\tMADS__mad6\t0.0\t2841.9\t1.0\t1.0\t1\t1387\n-PSAE004.0722.00032.C001_06404\tdf_test_prot\t7\t557\tMADS__mad7\t0.0\t1125.0\t0.998\t0.998\t1\t556\n-PSAE004.0722.00032.C001_06405\tdf_test_prot\t8\t1853\tMADS__mad8\t0.0\t3835.3\t1.0\t1.0\t1\t1853\n-THCR001.0722.00001.C001_01127\tdf_test_prot\t18\t222\tDpd__QueE\t4.3e-122\t403.0\t1.0\t0.995\t2\t222\n-THCR001.0722.00001.C001_01128\tdf_test_prot\t19\t1002\tDpd__DpdE\t0.0\t1044.8\t0.925\t0.978\t1\t980\n-THCR001.0722.00001.C001_01129\tdf_test_prot\t20\t851\tShango__SngC\t2.5e-12\t43.4\t0.486\t0.402\t149\t490\n-THCR001.0722.00001.C001_01129\tdf_test_prot\t20\t851\tPsyrTA__PsyrT\t2.9e-51\t171.7\t0.475\t0.403\t148\t490\n-THCR001.0722.00001.C001_01129\tdf_test_prot\t20\t851\tDpd__DpdF\t4.5999999999999996e-299\t991.8\t0.995\t0.994\t5\t850\n-THCR001.0722.00001.C001_01130\tdf_test_prot\t21\t310\tDpd__DpdG\t2e-87\t290.7\t0.997\t0.997\t1\t309\n-THCR001.0722.00001.C001_01131\tdf_test_prot\t22\t1031\tDpd__DpdH\t0.0\t1143.7\t0.999\t0.997\t1\t1028\n-THCR001.0722.00001.C001_01132\tdf_test_prot\t23\t249\tDpd__DpdI\t6e-43\t144.7\t0.984\t0.988\t4\t249\n-THCR001.0722.00001.C001_01133\tdf_test_prot\t24\t1495\tShango__SngC\t6.7e-25\t85.0\t0.454\t0.302\t180\t631\n-THCR001.0722.00001.C001_01133\tdf_test_prot\t24\t1495\tDpd__DpdJ\t0.0\t1757.1\t0.997\t0.998\t3\t1494\n-THCR001.0722.00001.C001_01134\tdf_test_prot\t25\t178\tDpd__DpdK\t2.6e-62\t207.0\t0.889\t0.983\t1\t175\n-THCR001.0722.00001.C001_01135\tdf_test_prot\t26\t720\tDpd__DpdD\t2.6e-282\t935.6\t0.994\t0.999\t1\t719\n-THCR001.0722.00001.C001_01136\tdf_test_prot\t27\t219\tDpd__QueC\t7e-122\t402.0\t0.986\t0.991\t2\t218\n-THCR001.0722.00001.C001_01137\tdf_test_prot\t28\t399\tDpd__DpdB\t3.1e-62\t207.5\t0.88\t0.932\t17\t388\n-THCR001.0722.00001.C001_01138\tdf_test_prot\t29\t468\tDpd__DpdA\t1.9e-104\t346.9\t0.971\t0.959\t5\t453\n-THCR001.0722.00001.C001_01139\tdf_test_prot\t30\t287\tDpd__DpdC\t1.1e-85\t284.7\t0.906\t0.972\t6\t284\n-THCR001.0722.00001.C001_01140\tdf_test_prot\t31\t120\tDpd__QueD\t9.2e-59\t194.3\t1.0\t1.0\t1\t120\n-THCR001.0722.00001.C001_01142\tdf_test_prot\t32\t186\tDpd__FolE\t2.5e-103\t340.6\t0.989\t0.962\t5\t183\n-STPL001.0722.00001.C001_00362\tdf_test_prot\t42\t732\tBREX__brxHII\t2.8e-96\t320.9\t0.653\t0.732\t20\t555\n-STPL001.0722.00001.C001_00362\tdf_test_prot\t42\t732\tShango__SngC\t1e-115\t385.3\t0.975\t0.945\t30\t721\n-STPL001.0722.00001.C001_00362\tdf_test_prot\t42\t732\tBREX__brxHI\t0.0\t1133.1\t0.993\t0.973\t19\t730\n-STPL001.0722.00001.C001_00363\tdf_test_prot\t43\t449\tShango__SngB\t1.6e-38\t130.0\t0.847\t0.804\t11\t371\n-STPL001.0722.00001.C001_00363\tdf_test_prot\t43\t449\tBREX__brxD\t1.6e-218\t723.1\t0.993\t0.978\t11\t449\n-STPL001.0722.00001.C001_00366\tdf_test_prot\t44\t971\tBREX__pglZ2\t0.0\t1073.1\t0.968\t0.987\t11\t968\n-STPL001.0722.00001.C001_00367\tdf_test_prot\t45\t1302\tBREX__pglY\t0.0\t1774.2\t0.999\t0.999\t2\t1302\n-STPL001.0722.00001.C001_00374\tdf_test_prot\t46\t1202\tRM_Type_II__Type_II_MTases\t3.1e-16\t56.3\t0.585\t0.225\t194\t464\n-STPL001.0722.00001.C001_00374\tdf_test_prot\t46\t1202\tBREX__pglX2\t0.0\t1861.3\t0.93\t0.999\t1\t1201\n-STPL001.0722.00001.C001_00375\tdf_test_prot\t47\t1565\tBREX__pglW\t0.0\t1803.8\t0.968\t0.993\t1\t1554\n-ESCO001.0722.00905.C001_00698\tdf'..b'f_test_prot\t6199\t633\tRM_Type_II__Type_II_MTases_FAM_3\t4.6e-15\t54.3\t0.851\t0.55\t90\t437\n+CATH005.0523.00001.002P_06406\tdf_test_prot\t6199\t633\tRM_Type_II__Type_II_MTases_FAM_1\t1e-17\t63.1\t0.516\t0.278\t87\t262\n+CATH005.0523.00001.002P_06406\tdf_test_prot\t6199\t633\tRM_Type_II__Type_II_MTases_FAM_37\t4.6000000000000003e-35\t119.8\t0.815\t0.583\t57\t425\n+CATH005.0523.00001.002P_06406\tdf_test_prot\t6199\t633\tRM_Type_III__Type_III_MTases_FAM_0\t4.700000000000001e-180\t599.2\t0.965\t0.981\t1\t621\n+CATH005.0523.00001.002P_06429\tdf_test_prot\t6221\t587\tThoeris__ThsB_Global\t5e-05\t21.8\t0.503\t0.16\t442\t535\n+CATH005.0523.00001.002P_06444\tdf_test_prot\t6235\t947\tEleos__LeoA\t5.6e-05\t20.8\t0.411\t0.266\t226\t477\n+CATH005.0523.00001.002P_06530\tdf_test_prot\t6317\t339\tWYL_I_II_III_IV_V_VI_1\t3.7e-10\t38.4\t0.537\t0.531\t152\t331\n+CATH005.0523.00001.002P_06530\tdf_test_prot\t6317\t339\tWYL_I_II_III_IV_V_VI_4\t1.2e-26\t92.3\t0.994\t0.528\t152\t330\n+CATH005.0523.00001.002P_06595\tdf_test_prot\t6377\t267\tThoeris__ThsB_Global\t1.1e-08\t33.7\t0.477\t0.333\t2\t90\n+CATH005.0523.00001.002P_06602\tdf_test_prot\t6384\t915\tGao_RL__RL_D\t0.0\t1054.8\t1.0\t0.998\t1\t913\n+CATH005.0523.00001.002P_06606\tdf_test_prot\t6388\t1017\tRM_Type_II__Type_II_MTases_FAM_27\t1.1000000000000001e-30\t105.1\t0.418\t0.536\t22\t566\n+CATH005.0523.00001.002P_06606\tdf_test_prot\t6388\t1017\tGao_RL__RL_C\t0.0\t1153.2\t0.987\t0.976\t19\t1011\n+CATH005.0523.00001.002P_06607\tdf_test_prot\t6389\t197\tGao_RL__RL_B\t1.5e-54\t182.9\t0.943\t0.934\t12\t195\n+CATH005.0523.00001.002P_06608\tdf_test_prot\t6390\t1039\tHma__HmaC\t5.6e-49\t165.5\t0.676\t0.577\t36\t635\n+CATH005.0523.00001.002P_06608\tdf_test_prot\t6390\t1039\tGao_RL__RL_A\t5.7e-261\t867.1\t0.997\t0.996\t4\t1038\n+CATH005.0523.00001.002P_06617\tdf_test_prot\t6399\t916\tDodola__DolB\t7.900000000000001e-26\t89.5\t0.403\t0.179\t608\t771\n+CATH005.0523.00001.002P_06621\tdf_test_prot\t6403\t614\tcas10_III-D_3\t6.1e-70\t234.8\t0.956\t0.695\t10\t436\n+CATH005.0523.00001.002P_06624\tdf_test_prot\t6406\t182\tcsx19_III-D_4\t1.5e-06\t26.5\t0.781\t0.813\t28\t175\n+CATH005.0523.00001.002P_06625\tdf_test_prot\t6407\t858\tcsm3gr7_III-D_2\t1.8000000000000002e-25\t88.4\t0.423\t0.4\t493\t835\n+CATH005.0523.00001.002P_06626\tdf_test_prot\t6408\t638\tcasR_III-D_6\t7.3e-09\t33.4\t0.521\t0.458\t328\t619\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas6_I_II_III_IV_V_VI_22\t9.7e-07\t27.9\t0.509\t0.054\t221\t277\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_7\t5.2e-28\t96.7\t0.856\t0.266\t730\t1009\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_2\t9.199999999999999e-53\t177.7\t1.0\t0.246\t725\t983\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_8\t1.4e-53\t180.6\t0.814\t0.257\t724\t993\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_1\t1.8e-64\t216.4\t0.997\t0.302\t724\t1041\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tRT_I_II_III_IV_V_VI_1\t2.0000000000000003e-65\t219.2\t0.774\t0.219\t399\t628\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_10\t4.1e-67\t224.9\t0.993\t0.267\t725\t1005\n+CATH005.0523.00001.002P_06628\tdf_test_prot\t6410\t93\tcas2_I_II_III_IV_V_VI_5\t6.1e-18\t63.5\t0.865\t0.828\t4\t80\n+CATH005.0523.00001.002P_06628\tdf_test_prot\t6410\t93\tcas2_I_II_III_IV_V_VI_13\t5.1e-20\t70.0\t0.958\t0.742\t3\t71\n+CATH005.0523.00001.002P_06628\tdf_test_prot\t6410\t93\tcas2_I_II_III_IV_V_VI_3\t2.0000000000000002e-21\t74.5\t0.949\t0.817\t4\t79\n+CATH005.0523.00001.002P_06666\tdf_test_prot\t6445\t284\tViperin__pVip\t2.2e-91\t304.5\t0.903\t0.986\t5\t284\n+CATH005.0523.00001.002P_06688\tdf_test_prot\t6467\t594\tDISARM__drmB\t2.4e-161\t537.0\t0.974\t0.992\t5\t593\n+CATH005.0523.00001.002P_06689\tdf_test_prot\t6468\t1150\tDISARM__drmA\t0.0\t1225.2\t0.81\t0.994\t2\t1144\n+CATH005.0523.00001.002P_06690\tdf_test_prot\t6469\t155\tPD-T4-9__PD-T4-9_C\t6.4e-06\t24.9\t0.679\t0.594\t59\t150\n+CATH005.0523.00001.002P_06692\tdf_test_prot\t6471\t106\tMqsRAC__mqsR\t2.1e-11\t42.8\t0.773\t0.972\t3\t105\n+CATH005.0523.00001.002P_06695\tdf_test_prot\t6474\t1111\tRM_Type_IIG__Type_IIG_5\t4.4e-221\t736.2\t0.752\t0.976\t27\t1110\n+CATH005.0523.00001.002P_06695\tdf_test_prot\t6474\t1111\tDISARM_1__drmMI\t0.0\t1141.1\t0.809\t0.992\t9\t1110\n' |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/outputs/prot/defense_finder_hmmer_with_antidefense.tsv --- a/test-data/outputs/prot/defense_finder_hmmer_with_antidefense.tsv Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/outputs/prot/defense_finder_hmmer_with_antidefense.tsv Thu Feb 13 15:46:29 2025 +0000 |
| b |
| b'@@ -1,914 +1,642 @@\n hit_id\treplicon\thit_pos\thit_sequence_length\tgene_name\ti_eval\thit_score\thit_profile_cov\thit_seq_cov\thit_begin_match\thit_end_match\n-PSAE004.0722.00032.C001_06398\tdf_test_prot\t1\t71\tMADS__mad1\t1.8999999999999998e-44\t146.8\t0.986\t0.986\t1\t70\n-PSAE004.0722.00032.C001_06399\tdf_test_prot\t2\t680\tRM_Type_II__Type_II_MTases\t4.3e-154\t511.5\t1.415\t0.919\t51\t675\n-PSAE004.0722.00032.C001_06399\tdf_test_prot\t2\t680\tMADS__mad2\t0.0\t1469.4\t0.999\t0.987\t10\t680\n-PSAE004.0722.00032.C001_06400\tdf_test_prot\t3\t445\tParis_II__AAA_21\t4.6e-22\t76.4\t0.993\t0.838\t25\t397\n-PSAE004.0722.00032.C001_06400\tdf_test_prot\t3\t445\tMADS__mad3\t3.8e-214\t708.9\t1.0\t1.0\t1\t445\n-PSAE004.0722.00032.C001_06401\tdf_test_prot\t4\t218\tMADS__mad4\t6.2e-108\t356.6\t0.991\t0.972\t5\t216\n-PSAE004.0722.00032.C001_06402\tdf_test_prot\t5\t463\tMADS__mad5\t1.2e-174\t578.9\t0.987\t0.991\t4\t462\n-PSAE004.0722.00032.C001_06403\tdf_test_prot\t6\t1387\tSspBCDE__SspF\t1.1e-13\t47.6\t0.503\t0.218\t823\t1124\n-PSAE004.0722.00032.C001_06403\tdf_test_prot\t6\t1387\tBREX__pglW\t8.200000000000001e-78\t259.5\t0.522\t0.538\t12\t757\n-PSAE004.0722.00032.C001_06403\tdf_test_prot\t6\t1387\tMADS__mad6\t0.0\t2841.9\t1.0\t1.0\t1\t1387\n-PSAE004.0722.00032.C001_06404\tdf_test_prot\t7\t557\tMADS__mad7\t0.0\t1125.0\t0.998\t0.998\t1\t556\n-PSAE004.0722.00032.C001_06405\tdf_test_prot\t8\t1853\tMADS__mad8\t0.0\t3835.3\t1.0\t1.0\t1\t1853\n-THCR001.0722.00001.C001_01127\tdf_test_prot\t18\t222\tDpd__QueE\t4.3e-122\t403.0\t1.0\t0.995\t2\t222\n-THCR001.0722.00001.C001_01128\tdf_test_prot\t19\t1002\tDpd__DpdE\t0.0\t1044.8\t0.925\t0.978\t1\t980\n-THCR001.0722.00001.C001_01129\tdf_test_prot\t20\t851\tShango__SngC\t2.5e-12\t43.4\t0.486\t0.402\t149\t490\n-THCR001.0722.00001.C001_01129\tdf_test_prot\t20\t851\tPsyrTA__PsyrT\t2.9e-51\t171.7\t0.475\t0.403\t148\t490\n-THCR001.0722.00001.C001_01129\tdf_test_prot\t20\t851\tDpd__DpdF\t4.5999999999999996e-299\t991.8\t0.995\t0.994\t5\t850\n-THCR001.0722.00001.C001_01130\tdf_test_prot\t21\t310\tDpd__DpdG\t2e-87\t290.7\t0.997\t0.997\t1\t309\n-THCR001.0722.00001.C001_01131\tdf_test_prot\t22\t1031\tDpd__DpdH\t0.0\t1143.7\t0.999\t0.997\t1\t1028\n-THCR001.0722.00001.C001_01132\tdf_test_prot\t23\t249\tDpd__DpdI\t6e-43\t144.7\t0.984\t0.988\t4\t249\n-THCR001.0722.00001.C001_01133\tdf_test_prot\t24\t1495\tShango__SngC\t6.7e-25\t85.0\t0.454\t0.302\t180\t631\n-THCR001.0722.00001.C001_01133\tdf_test_prot\t24\t1495\tDpd__DpdJ\t0.0\t1757.1\t0.997\t0.998\t3\t1494\n-THCR001.0722.00001.C001_01134\tdf_test_prot\t25\t178\tDpd__DpdK\t2.6e-62\t207.0\t0.889\t0.983\t1\t175\n-THCR001.0722.00001.C001_01135\tdf_test_prot\t26\t720\tDpd__DpdD\t2.6e-282\t935.6\t0.994\t0.999\t1\t719\n-THCR001.0722.00001.C001_01136\tdf_test_prot\t27\t219\tDpd__QueC\t7e-122\t402.0\t0.986\t0.991\t2\t218\n-THCR001.0722.00001.C001_01137\tdf_test_prot\t28\t399\tDpd__DpdB\t3.1e-62\t207.5\t0.88\t0.932\t17\t388\n-THCR001.0722.00001.C001_01138\tdf_test_prot\t29\t468\tDpd__DpdA\t1.9e-104\t346.9\t0.971\t0.959\t5\t453\n-THCR001.0722.00001.C001_01139\tdf_test_prot\t30\t287\tDpd__DpdC\t1.1e-85\t284.7\t0.906\t0.972\t6\t284\n-THCR001.0722.00001.C001_01140\tdf_test_prot\t31\t120\tDpd__QueD\t9.2e-59\t194.3\t1.0\t1.0\t1\t120\n-THCR001.0722.00001.C001_01142\tdf_test_prot\t32\t186\tDpd__FolE\t2.5e-103\t340.6\t0.989\t0.962\t5\t183\n-STPL001.0722.00001.C001_00362\tdf_test_prot\t42\t732\tBREX__brxHII\t2.8e-96\t320.9\t0.653\t0.732\t20\t555\n-STPL001.0722.00001.C001_00362\tdf_test_prot\t42\t732\tShango__SngC\t1e-115\t385.3\t0.975\t0.945\t30\t721\n-STPL001.0722.00001.C001_00362\tdf_test_prot\t42\t732\tBREX__brxHI\t0.0\t1133.1\t0.993\t0.973\t19\t730\n-STPL001.0722.00001.C001_00363\tdf_test_prot\t43\t449\tShango__SngB\t1.6e-38\t130.0\t0.847\t0.804\t11\t371\n-STPL001.0722.00001.C001_00363\tdf_test_prot\t43\t449\tBREX__brxD\t1.6e-218\t723.1\t0.993\t0.978\t11\t449\n-STPL001.0722.00001.C001_00366\tdf_test_prot\t44\t971\tBREX__pglZ2\t0.0\t1073.1\t0.968\t0.987\t11\t968\n-STPL001.0722.00001.C001_00367\tdf_test_prot\t45\t1302\tBREX__pglY\t0.0\t1774.2\t0.999\t0.999\t2\t1302\n-STPL001.0722.00001.C001_00374\tdf_test_prot\t46\t1202\tRM_Type_II__Type_II_MTases\t3.1e-16\t56.3\t0.585\t0.225\t194\t464\n-STPL001.0722.00001.C001_00374\tdf_test_prot\t46\t1202\tBREX__pglX2\t0.0\t1861.3\t0.93\t0.999\t1\t1201\n-STPL001.0722.00001.C001_00375\tdf_test_prot\t47\t1565\tBREX__pglW\t0.0\t1803.8\t0.968\t0.993\t1\t1554\n-ESCO001.0722.00905.C001_00698\tdf'..b'f_test_prot\t6199\t633\tRM_Type_II__Type_II_MTases_FAM_3\t4.6e-15\t54.3\t0.851\t0.55\t90\t437\n+CATH005.0523.00001.002P_06406\tdf_test_prot\t6199\t633\tRM_Type_II__Type_II_MTases_FAM_1\t1e-17\t63.1\t0.516\t0.278\t87\t262\n+CATH005.0523.00001.002P_06406\tdf_test_prot\t6199\t633\tRM_Type_II__Type_II_MTases_FAM_37\t4.6000000000000003e-35\t119.8\t0.815\t0.583\t57\t425\n+CATH005.0523.00001.002P_06406\tdf_test_prot\t6199\t633\tRM_Type_III__Type_III_MTases_FAM_0\t4.700000000000001e-180\t599.2\t0.965\t0.981\t1\t621\n+CATH005.0523.00001.002P_06429\tdf_test_prot\t6221\t587\tThoeris__ThsB_Global\t5e-05\t21.8\t0.503\t0.16\t442\t535\n+CATH005.0523.00001.002P_06444\tdf_test_prot\t6235\t947\tEleos__LeoA\t5.6e-05\t20.8\t0.411\t0.266\t226\t477\n+CATH005.0523.00001.002P_06530\tdf_test_prot\t6317\t339\tWYL_I_II_III_IV_V_VI_1\t3.7e-10\t38.4\t0.537\t0.531\t152\t331\n+CATH005.0523.00001.002P_06530\tdf_test_prot\t6317\t339\tWYL_I_II_III_IV_V_VI_4\t1.2e-26\t92.3\t0.994\t0.528\t152\t330\n+CATH005.0523.00001.002P_06595\tdf_test_prot\t6377\t267\tThoeris__ThsB_Global\t1.1e-08\t33.7\t0.477\t0.333\t2\t90\n+CATH005.0523.00001.002P_06602\tdf_test_prot\t6384\t915\tGao_RL__RL_D\t0.0\t1054.8\t1.0\t0.998\t1\t913\n+CATH005.0523.00001.002P_06606\tdf_test_prot\t6388\t1017\tRM_Type_II__Type_II_MTases_FAM_27\t1.1000000000000001e-30\t105.1\t0.418\t0.536\t22\t566\n+CATH005.0523.00001.002P_06606\tdf_test_prot\t6388\t1017\tGao_RL__RL_C\t0.0\t1153.2\t0.987\t0.976\t19\t1011\n+CATH005.0523.00001.002P_06607\tdf_test_prot\t6389\t197\tGao_RL__RL_B\t1.5e-54\t182.9\t0.943\t0.934\t12\t195\n+CATH005.0523.00001.002P_06608\tdf_test_prot\t6390\t1039\tHma__HmaC\t5.6e-49\t165.5\t0.676\t0.577\t36\t635\n+CATH005.0523.00001.002P_06608\tdf_test_prot\t6390\t1039\tGao_RL__RL_A\t5.7e-261\t867.1\t0.997\t0.996\t4\t1038\n+CATH005.0523.00001.002P_06617\tdf_test_prot\t6399\t916\tDodola__DolB\t7.900000000000001e-26\t89.5\t0.403\t0.179\t608\t771\n+CATH005.0523.00001.002P_06621\tdf_test_prot\t6403\t614\tcas10_III-D_3\t6.1e-70\t234.8\t0.956\t0.695\t10\t436\n+CATH005.0523.00001.002P_06624\tdf_test_prot\t6406\t182\tcsx19_III-D_4\t1.5e-06\t26.5\t0.781\t0.813\t28\t175\n+CATH005.0523.00001.002P_06625\tdf_test_prot\t6407\t858\tcsm3gr7_III-D_2\t1.8000000000000002e-25\t88.4\t0.423\t0.4\t493\t835\n+CATH005.0523.00001.002P_06626\tdf_test_prot\t6408\t638\tcasR_III-D_6\t7.3e-09\t33.4\t0.521\t0.458\t328\t619\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas6_I_II_III_IV_V_VI_22\t9.7e-07\t27.9\t0.509\t0.054\t221\t277\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_7\t5.2e-28\t96.7\t0.856\t0.266\t730\t1009\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_2\t9.199999999999999e-53\t177.7\t1.0\t0.246\t725\t983\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_8\t1.4e-53\t180.6\t0.814\t0.257\t724\t993\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_1\t1.8e-64\t216.4\t0.997\t0.302\t724\t1041\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tRT_I_II_III_IV_V_VI_1\t2.0000000000000003e-65\t219.2\t0.774\t0.219\t399\t628\n+CATH005.0523.00001.002P_06627\tdf_test_prot\t6409\t1052\tcas1_I_II_III_IV_V_VI_10\t4.1e-67\t224.9\t0.993\t0.267\t725\t1005\n+CATH005.0523.00001.002P_06628\tdf_test_prot\t6410\t93\tcas2_I_II_III_IV_V_VI_5\t6.1e-18\t63.5\t0.865\t0.828\t4\t80\n+CATH005.0523.00001.002P_06628\tdf_test_prot\t6410\t93\tcas2_I_II_III_IV_V_VI_13\t5.1e-20\t70.0\t0.958\t0.742\t3\t71\n+CATH005.0523.00001.002P_06628\tdf_test_prot\t6410\t93\tcas2_I_II_III_IV_V_VI_3\t2.0000000000000002e-21\t74.5\t0.949\t0.817\t4\t79\n+CATH005.0523.00001.002P_06666\tdf_test_prot\t6445\t284\tViperin__pVip\t2.2e-91\t304.5\t0.903\t0.986\t5\t284\n+CATH005.0523.00001.002P_06688\tdf_test_prot\t6467\t594\tDISARM__drmB\t2.4e-161\t537.0\t0.974\t0.992\t5\t593\n+CATH005.0523.00001.002P_06689\tdf_test_prot\t6468\t1150\tDISARM__drmA\t0.0\t1225.2\t0.81\t0.994\t2\t1144\n+CATH005.0523.00001.002P_06690\tdf_test_prot\t6469\t155\tPD-T4-9__PD-T4-9_C\t6.4e-06\t24.9\t0.679\t0.594\t59\t150\n+CATH005.0523.00001.002P_06692\tdf_test_prot\t6471\t106\tMqsRAC__mqsR\t2.1e-11\t42.8\t0.773\t0.972\t3\t105\n+CATH005.0523.00001.002P_06695\tdf_test_prot\t6474\t1111\tRM_Type_IIG__Type_IIG_5\t4.4e-221\t736.2\t0.752\t0.976\t27\t1110\n+CATH005.0523.00001.002P_06695\tdf_test_prot\t6474\t1111\tDISARM_1__drmMI\t0.0\t1141.1\t0.809\t0.992\t9\t1110\n' |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/outputs/prot/defense_finder_systems.tsv --- a/test-data/outputs/prot/defense_finder_systems.tsv Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/outputs/prot/defense_finder_systems.tsv Thu Feb 13 15:46:29 2025 +0000 |
| b |
| b'@@ -1,234 +1,68 @@\n sys_id\ttype\tsubtype\tactivity\tsys_beg\tsys_end\tprotein_in_syst\tgenes_count\tname_of_profiles_in_sys\n-df_test_prot_MADS_231\tMADS\tMADS\tDefense\tPSAE004.0722.00032.C001_06398\tPSAE004.0722.00032.C001_06405\tPSAE004.0722.00032.C001_06398,PSAE004.0722.00032.C001_06399,PSAE004.0722.00032.C001_06400,PSAE004.0722.00032.C001_06401,PSAE004.0722.00032.C001_06402,PSAE004.0722.00032.C001_06403,PSAE004.0722.00032.C001_06404,PSAE004.0722.00032.C001_06405\t8\tMADS__mad1,MADS__mad2,MADS__mad3,MADS__mad4,MADS__mad5,MADS__mad6,MADS__mad7,MADS__mad8\n-df_test_prot_Dpd_171\tDpd\tDpd\tDefense\tTHCR001.0722.00001.C001_01127\tTHCR001.0722.00001.C001_01142\tTHCR001.0722.00001.C001_01127,THCR001.0722.00001.C001_01128,THCR001.0722.00001.C001_01129,THCR001.0722.00001.C001_01130,THCR001.0722.00001.C001_01131,THCR001.0722.00001.C001_01132,THCR001.0722.00001.C001_01133,THCR001.0722.00001.C001_01134,THCR001.0722.00001.C001_01135,THCR001.0722.00001.C001_01136,THCR001.0722.00001.C001_01137,THCR001.0722.00001.C001_01138,THCR001.0722.00001.C001_01139,THCR001.0722.00001.C001_01140,THCR001.0722.00001.C001_01142\t15\tDpd__DpdA,Dpd__DpdB,Dpd__DpdC,Dpd__DpdD,Dpd__DpdE,Dpd__DpdF,Dpd__DpdG,Dpd__DpdH,Dpd__DpdI,Dpd__DpdJ,Dpd__DpdK,Dpd__FolE,Dpd__QueC,Dpd__QueD,Dpd__QueE\n-df_test_prot_BREX_II_211\tBREX\tBREX_II\tDefense\tSTPL001.0722.00001.C001_00362\tSTPL001.0722.00001.C001_00375\tSTPL001.0722.00001.C001_00362,STPL001.0722.00001.C001_00363,STPL001.0722.00001.C001_00366,STPL001.0722.00001.C001_00367,STPL001.0722.00001.C001_00374,STPL001.0722.00001.C001_00375\t6\tBREX__brxD,BREX__brxHI,BREX__pglW,BREX__pglX2,BREX__pglY,BREX__pglZ2\n-df_test_prot_Gao_Mza_32\tGao_Mza\tGao_Mza\tDefense\tESCO001.0722.00905.C001_00698\tESCO001.0722.00905.C001_00702\tESCO001.0722.00905.C001_00698,ESCO001.0722.00905.C001_00699,ESCO001.0722.00905.C001_00700,ESCO001.0722.00905.C001_00701,ESCO001.0722.00905.C001_00702\t5\tGao_Mza__MzaA,Gao_Mza__MzaB,Gao_Mza__MzaC,Gao_Mza__MzaD,Gao_Mza__MzaE\n-df_test_prot_DISARM_1_25\tDISARM\tDISARM_1\tDefense\tXACI001.0722.00030.C001_02113\tXACI001.0722.00030.C001_02118\tXACI001.0722.00030.C001_02113,XACI001.0722.00030.C001_02114,XACI001.0722.00030.C001_02115,XACI001.0722.00030.C001_02117,XACI001.0722.00030.C001_02118\t5\tDISARM_1__drmD,DISARM_1__drmMI,DISARM__drmA,DISARM__drmB,DISARM__drmC\n-df_test_prot_SspBCDE_200\tSspBCDE\tSspBCDE\tDefense\tBOHI001.0722.00008.C001_00581\tBOHI001.0722.00008.C001_00587\tBOHI001.0722.00008.C001_00581,BOHI001.0722.00008.C001_00582,BOHI001.0722.00008.C001_00583,BOHI001.0722.00008.C001_00584,BOHI001.0722.00008.C001_00585,BOHI001.0722.00008.C001_00586,BOHI001.0722.00008.C001_00587\t7\tSspBCDE__SspB,SspBCDE__SspC,SspBCDE__SspD,SspBCDE__SspE,SspBCDE__SspF,SspBCDE__SspG,SspBCDE__SspH\n-df_test_prot_Gao_RL_99\tGao_RL\tGao_RL\tDefense\tESCO001.0722.01492.C001_00546\tESCO001.0722.01492.C001_00549\tESCO001.0722.01492.C001_00546,ESCO001.0722.01492.C001_00547,ESCO001.0722.01492.C001_00548,ESCO001.0722.01492.C001_00549\t4\tGao_RL__RL_A,Gao_RL__RL_B,Gao_RL__RL_C,Gao_RL__RL_D\n-df_test_prot_Dnd_ABCDEFGH_169\tDnd\tDnd_ABCDEFGH\tDefense\tVISP026.0722.00001.C001_00835\tVISP026.0722.00001.C001_00844\tVISP026.0722.00001.C001_00835,VISP026.0722.00001.C001_00836,VISP026.0722.00001.C001_00837,VISP026.0722.00001.C001_00840,VISP026.0722.00001.C001_00841,VISP026.0722.00001.C001_00842,VISP026.0722.00001.C001_00843,VISP026.0722.00001.C001_00844\t8\tDnd_ABCDEFGH__DptF,Dnd_ABCDEFGH__DptG,Dnd_ABCDEFGH__DptH,Dnd__DndA,Dnd__DndB,Dnd__DndC,Dnd__DndD,Dnd__DndE\n-df_test_prot_Druantia_I_126\tDruantia\tDruantia_I\tDefense\tESCO001.0722.00005.C001_00834\tESCO001.0722.00005.C001_00838\tESCO001.0722.00005.C001_00834,ESCO001.0722.00005.C001_00835,ESCO001.0722.00005.C001_00836,ESCO001.0722.00005.C001_00837,ESCO001.0722.00005.C001_00838\t5\tDruantia_I__DruA,Druantia_I__DruB,Druantia_I__DruC,Druantia_I__DruD,Druantia__DruE_1\n-df_test_prot_BREX_I_210\tBREX\tBREX_I\tDefense\tDEVU001.0722.00001.C001_01912\tDEVU001.0722.00001.C001_01920\tDEVU001.0722.00001.C001_01912,DEVU001.0722.00001.C001_01913,DEVU001.0722.00001.C001_01915,DEVU001.0722.00'..b'ype_I_MTases_FAM_3,RM__Type_I_S_52\n+df_test_prot_Abi2_1\tAbi2\tAbi2\tDefense\tCATH005.0523.00001.001C_04309\tCATH005.0523.00001.001C_04309\tCATH005.0523.00001.001C_04309\t1\tAbi2__Abi_2\n+df_test_prot_RM_Type_IIG_77\tRM\tRM_Type_IIG\tDefense\tCATH005.0523.00001.001C_04525\tCATH005.0523.00001.001C_04525\tCATH005.0523.00001.001C_04525\t1\tRM_Type_IIG__Type_IIG_FAM_1.einsi_trimmed\n+df_test_prot_RM_Type_I_71\tRM\tRM_Type_I\tDefense\tCATH005.0523.00001.001C_04616\tCATH005.0523.00001.001C_04620\tCATH005.0523.00001.001C_04616,CATH005.0523.00001.001C_04617,CATH005.0523.00001.001C_04620\t3\tRM__Type_I_MTases_FAM_1,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_52\n+df_test_prot_MazEF_22\tMazEF\tMazEF\tDefense\tCATH005.0523.00001.001C_05016\tCATH005.0523.00001.001C_05017\tCATH005.0523.00001.001C_05016,CATH005.0523.00001.001C_05017\t2\tMazEF__MazE,MazEF__MazF\n+df_test_prot_RloC_29\tRloC\tRloC\tDefense\tCATH005.0523.00001.001C_05266\tCATH005.0523.00001.001C_05266\tCATH005.0523.00001.001C_05266\t1\tRloC__RloC\n+df_test_prot_Hma_19\tHma\tHma\tDefense\tCATH005.0523.00001.001C_05427\tCATH005.0523.00001.001C_05431\tCATH005.0523.00001.001C_05427,CATH005.0523.00001.001C_05430,CATH005.0523.00001.001C_05431\t3\tHma__HmaA,Hma__HmaB,Hma__HmaC\n+df_test_prot_PfiAT_27\tPfiAT\tPfiAT\tDefense\tCATH005.0523.00001.001C_05437\tCATH005.0523.00001.001C_05438\tCATH005.0523.00001.001C_05437,CATH005.0523.00001.001C_05438\t2\tPfiAT__PfiA,PfiAT__PfiT\n+df_test_prot_VP1826_38\tVP1826\tVP1826\tDefense\tCATH005.0523.00001.001C_05515\tCATH005.0523.00001.001C_05515\tCATH005.0523.00001.001C_05515\t1\tVP1826__VP1826\n+df_test_prot_PD-T4-3_26\tPD-T4-3\tPD-T4-3\tDefense\tCATH005.0523.00001.001C_05703\tCATH005.0523.00001.001C_05703\tCATH005.0523.00001.001C_05703\t1\tPD-T4-3__PD-T4-3\n+df_test_prot_PsyrTA_28\tPsyrTA\tPsyrTA\tDefense\tCATH005.0523.00001.001C_05801\tCATH005.0523.00001.001C_05802\tCATH005.0523.00001.001C_05801,CATH005.0523.00001.001C_05802\t2\tPsyrTA__PsyrA,PsyrTA__PsyrT\n+df_test_prot_RM_Type_II_72\tRM\tRM_Type_II\tDefense\tCATH005.0523.00001.001C_05854\tCATH005.0523.00001.001C_05855\tCATH005.0523.00001.001C_05854,CATH005.0523.00001.001C_05855\t2\tRM_Type_II__Type_II_MTases_FAM_1,RM_Type_II__Type_II_REase02\n+df_test_prot_AbiE_2\tAbiE\tAbiE\tDefense\tCATH005.0523.00001.003P_06121\tCATH005.0523.00001.003P_06122\tCATH005.0523.00001.003P_06121,CATH005.0523.00001.003P_06122\t2\tAbiEii__AbiEi_4,AbiEii__AbiEii\n+df_test_prot_BREX_II_9\tBREX\tBREX_II\tDefense\tCATH005.0523.00001.003P_06203\tCATH005.0523.00001.003P_06206\tCATH005.0523.00001.003P_06203,CATH005.0523.00001.003P_06204,CATH005.0523.00001.003P_06205,CATH005.0523.00001.003P_06206\t4\tBREX__brxD,BREX__brxHI,BREX__pglY,BREX__pglZ2\n+df_test_prot_Wadjet_I_41\tWadjet\tWadjet_I\tDefense\tCATH005.0523.00001.002P_06400\tCATH005.0523.00001.002P_06403\tCATH005.0523.00001.002P_06400,CATH005.0523.00001.002P_06401,CATH005.0523.00001.002P_06402,CATH005.0523.00001.002P_06403\t4\tWadjet__JetA_I,Wadjet__JetB_I,Wadjet__JetC_I,Wadjet__JetD_I\n+df_test_prot_RM_Type_III_80\tRM\tRM_Type_III\tDefense\tCATH005.0523.00001.002P_06404\tCATH005.0523.00001.002P_06406\tCATH005.0523.00001.002P_06404,CATH005.0523.00001.002P_06406\t2\tRM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed\n+df_test_prot_Gao_RL_14\tGao_RL\tGao_RL\tDefense\tCATH005.0523.00001.002P_06602\tCATH005.0523.00001.002P_06608\tCATH005.0523.00001.002P_06602,CATH005.0523.00001.002P_06606,CATH005.0523.00001.002P_06607,CATH005.0523.00001.002P_06608\t4\tGao_RL__RL_A,Gao_RL__RL_B,Gao_RL__RL_C,Gao_RL__RL_D\n+df_test_prot_CAS_Class1-Subtype-III-D_85\tCas\tCAS_Class1-Subtype-III-D\tDefense\tCATH005.0523.00001.002P_06621\tCATH005.0523.00001.002P_06628\tCATH005.0523.00001.002P_06621,CATH005.0523.00001.002P_06624,CATH005.0523.00001.002P_06625,CATH005.0523.00001.002P_06626,CATH005.0523.00001.002P_06627,CATH005.0523.00001.002P_06628\t6\tcas10_III-D_3,cas1_I_II_III_IV_V_VI_10,cas2_I_II_III_IV_V_VI_3,casR_III-D_6,csm3gr7_III-D_2,csx19_III-D_4\n+df_test_prot_Viperin_39\tViperin\tViperin\tDefense\tCATH005.0523.00001.002P_06666\tCATH005.0523.00001.002P_06666\tCATH005.0523.00001.002P_06666\t1\tViperin__pVip\n' |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a test-data/outputs/prot/defense_finder_systems_with_antidefense.tsv --- a/test-data/outputs/prot/defense_finder_systems_with_antidefense.tsv Mon Jul 22 11:12:44 2024 +0000 +++ b/test-data/outputs/prot/defense_finder_systems_with_antidefense.tsv Thu Feb 13 15:46:29 2025 +0000 |
| b |
| b'@@ -1,238 +1,69 @@\n sys_id\ttype\tsubtype\tactivity\tsys_beg\tsys_end\tprotein_in_syst\tgenes_count\tname_of_profiles_in_sys\n-df_test_prot_MADS_231\tMADS\tMADS\tDefense\tPSAE004.0722.00032.C001_06398\tPSAE004.0722.00032.C001_06405\tPSAE004.0722.00032.C001_06398,PSAE004.0722.00032.C001_06399,PSAE004.0722.00032.C001_06400,PSAE004.0722.00032.C001_06401,PSAE004.0722.00032.C001_06402,PSAE004.0722.00032.C001_06403,PSAE004.0722.00032.C001_06404,PSAE004.0722.00032.C001_06405\t8\tMADS__mad1,MADS__mad2,MADS__mad3,MADS__mad4,MADS__mad5,MADS__mad6,MADS__mad7,MADS__mad8\n-df_test_prot_Dpd_171\tDpd\tDpd\tDefense\tTHCR001.0722.00001.C001_01127\tTHCR001.0722.00001.C001_01142\tTHCR001.0722.00001.C001_01127,THCR001.0722.00001.C001_01128,THCR001.0722.00001.C001_01129,THCR001.0722.00001.C001_01130,THCR001.0722.00001.C001_01131,THCR001.0722.00001.C001_01132,THCR001.0722.00001.C001_01133,THCR001.0722.00001.C001_01134,THCR001.0722.00001.C001_01135,THCR001.0722.00001.C001_01136,THCR001.0722.00001.C001_01137,THCR001.0722.00001.C001_01138,THCR001.0722.00001.C001_01139,THCR001.0722.00001.C001_01140,THCR001.0722.00001.C001_01142\t15\tDpd__DpdA,Dpd__DpdB,Dpd__DpdC,Dpd__DpdD,Dpd__DpdE,Dpd__DpdF,Dpd__DpdG,Dpd__DpdH,Dpd__DpdI,Dpd__DpdJ,Dpd__DpdK,Dpd__FolE,Dpd__QueC,Dpd__QueD,Dpd__QueE\n-df_test_prot_BREX_II_211\tBREX\tBREX_II\tDefense\tSTPL001.0722.00001.C001_00362\tSTPL001.0722.00001.C001_00375\tSTPL001.0722.00001.C001_00362,STPL001.0722.00001.C001_00363,STPL001.0722.00001.C001_00366,STPL001.0722.00001.C001_00367,STPL001.0722.00001.C001_00374,STPL001.0722.00001.C001_00375\t6\tBREX__brxD,BREX__brxHI,BREX__pglW,BREX__pglX2,BREX__pglY,BREX__pglZ2\n-df_test_prot_Gao_Mza_32\tGao_Mza\tGao_Mza\tDefense\tESCO001.0722.00905.C001_00698\tESCO001.0722.00905.C001_00702\tESCO001.0722.00905.C001_00698,ESCO001.0722.00905.C001_00699,ESCO001.0722.00905.C001_00700,ESCO001.0722.00905.C001_00701,ESCO001.0722.00905.C001_00702\t5\tGao_Mza__MzaA,Gao_Mza__MzaB,Gao_Mza__MzaC,Gao_Mza__MzaD,Gao_Mza__MzaE\n-df_test_prot_DISARM_1_25\tDISARM\tDISARM_1\tDefense\tXACI001.0722.00030.C001_02113\tXACI001.0722.00030.C001_02118\tXACI001.0722.00030.C001_02113,XACI001.0722.00030.C001_02114,XACI001.0722.00030.C001_02115,XACI001.0722.00030.C001_02117,XACI001.0722.00030.C001_02118\t5\tDISARM_1__drmD,DISARM_1__drmMI,DISARM__drmA,DISARM__drmB,DISARM__drmC\n-df_test_prot_SspBCDE_200\tSspBCDE\tSspBCDE\tDefense\tBOHI001.0722.00008.C001_00581\tBOHI001.0722.00008.C001_00587\tBOHI001.0722.00008.C001_00581,BOHI001.0722.00008.C001_00582,BOHI001.0722.00008.C001_00583,BOHI001.0722.00008.C001_00584,BOHI001.0722.00008.C001_00585,BOHI001.0722.00008.C001_00586,BOHI001.0722.00008.C001_00587\t7\tSspBCDE__SspB,SspBCDE__SspC,SspBCDE__SspD,SspBCDE__SspE,SspBCDE__SspF,SspBCDE__SspG,SspBCDE__SspH\n-df_test_prot_Gao_RL_99\tGao_RL\tGao_RL\tDefense\tESCO001.0722.01492.C001_00546\tESCO001.0722.01492.C001_00549\tESCO001.0722.01492.C001_00546,ESCO001.0722.01492.C001_00547,ESCO001.0722.01492.C001_00548,ESCO001.0722.01492.C001_00549\t4\tGao_RL__RL_A,Gao_RL__RL_B,Gao_RL__RL_C,Gao_RL__RL_D\n-df_test_prot_Dnd_ABCDEFGH_169\tDnd\tDnd_ABCDEFGH\tDefense\tVISP026.0722.00001.C001_00835\tVISP026.0722.00001.C001_00844\tVISP026.0722.00001.C001_00835,VISP026.0722.00001.C001_00836,VISP026.0722.00001.C001_00837,VISP026.0722.00001.C001_00840,VISP026.0722.00001.C001_00841,VISP026.0722.00001.C001_00842,VISP026.0722.00001.C001_00843,VISP026.0722.00001.C001_00844\t8\tDnd_ABCDEFGH__DptF,Dnd_ABCDEFGH__DptG,Dnd_ABCDEFGH__DptH,Dnd__DndA,Dnd__DndB,Dnd__DndC,Dnd__DndD,Dnd__DndE\n-df_test_prot_Druantia_I_126\tDruantia\tDruantia_I\tDefense\tESCO001.0722.00005.C001_00834\tESCO001.0722.00005.C001_00838\tESCO001.0722.00005.C001_00834,ESCO001.0722.00005.C001_00835,ESCO001.0722.00005.C001_00836,ESCO001.0722.00005.C001_00837,ESCO001.0722.00005.C001_00838\t5\tDruantia_I__DruA,Druantia_I__DruB,Druantia_I__DruC,Druantia_I__DruD,Druantia__DruE_1\n-df_test_prot_BREX_I_210\tBREX\tBREX_I\tDefense\tDEVU001.0722.00001.C001_01912\tDEVU001.0722.00001.C001_01920\tDEVU001.0722.00001.C001_01912,DEVU001.0722.00001.C001_01913,DEVU001.0722.00001.C001_01915,DEVU001.0722.00'..b'ype_I_MTases_FAM_3,RM__Type_I_S_52\n+df_test_prot_Abi2_1\tAbi2\tAbi2\tDefense\tCATH005.0523.00001.001C_04309\tCATH005.0523.00001.001C_04309\tCATH005.0523.00001.001C_04309\t1\tAbi2__Abi_2\n+df_test_prot_RM_Type_IIG_77\tRM\tRM_Type_IIG\tDefense\tCATH005.0523.00001.001C_04525\tCATH005.0523.00001.001C_04525\tCATH005.0523.00001.001C_04525\t1\tRM_Type_IIG__Type_IIG_FAM_1.einsi_trimmed\n+df_test_prot_RM_Type_I_71\tRM\tRM_Type_I\tDefense\tCATH005.0523.00001.001C_04616\tCATH005.0523.00001.001C_04620\tCATH005.0523.00001.001C_04616,CATH005.0523.00001.001C_04617,CATH005.0523.00001.001C_04620\t3\tRM__Type_I_MTases_FAM_1,RM__Type_I_REases_FAM_2.einsi_trimmed,RM__Type_I_S_52\n+df_test_prot_MazEF_22\tMazEF\tMazEF\tDefense\tCATH005.0523.00001.001C_05016\tCATH005.0523.00001.001C_05017\tCATH005.0523.00001.001C_05016,CATH005.0523.00001.001C_05017\t2\tMazEF__MazE,MazEF__MazF\n+df_test_prot_RloC_29\tRloC\tRloC\tDefense\tCATH005.0523.00001.001C_05266\tCATH005.0523.00001.001C_05266\tCATH005.0523.00001.001C_05266\t1\tRloC__RloC\n+df_test_prot_Hma_19\tHma\tHma\tDefense\tCATH005.0523.00001.001C_05427\tCATH005.0523.00001.001C_05431\tCATH005.0523.00001.001C_05427,CATH005.0523.00001.001C_05430,CATH005.0523.00001.001C_05431\t3\tHma__HmaA,Hma__HmaB,Hma__HmaC\n+df_test_prot_PfiAT_27\tPfiAT\tPfiAT\tDefense\tCATH005.0523.00001.001C_05437\tCATH005.0523.00001.001C_05438\tCATH005.0523.00001.001C_05437,CATH005.0523.00001.001C_05438\t2\tPfiAT__PfiA,PfiAT__PfiT\n+df_test_prot_VP1826_38\tVP1826\tVP1826\tDefense\tCATH005.0523.00001.001C_05515\tCATH005.0523.00001.001C_05515\tCATH005.0523.00001.001C_05515\t1\tVP1826__VP1826\n+df_test_prot_PD-T4-3_26\tPD-T4-3\tPD-T4-3\tDefense\tCATH005.0523.00001.001C_05703\tCATH005.0523.00001.001C_05703\tCATH005.0523.00001.001C_05703\t1\tPD-T4-3__PD-T4-3\n+df_test_prot_PsyrTA_28\tPsyrTA\tPsyrTA\tDefense\tCATH005.0523.00001.001C_05801\tCATH005.0523.00001.001C_05802\tCATH005.0523.00001.001C_05801,CATH005.0523.00001.001C_05802\t2\tPsyrTA__PsyrA,PsyrTA__PsyrT\n+df_test_prot_RM_Type_II_72\tRM\tRM_Type_II\tDefense\tCATH005.0523.00001.001C_05854\tCATH005.0523.00001.001C_05855\tCATH005.0523.00001.001C_05854,CATH005.0523.00001.001C_05855\t2\tRM_Type_II__Type_II_MTases_FAM_1,RM_Type_II__Type_II_REase02\n+df_test_prot_AbiE_2\tAbiE\tAbiE\tDefense\tCATH005.0523.00001.003P_06121\tCATH005.0523.00001.003P_06122\tCATH005.0523.00001.003P_06121,CATH005.0523.00001.003P_06122\t2\tAbiEii__AbiEi_4,AbiEii__AbiEii\n+df_test_prot_BREX_II_9\tBREX\tBREX_II\tDefense\tCATH005.0523.00001.003P_06203\tCATH005.0523.00001.003P_06206\tCATH005.0523.00001.003P_06203,CATH005.0523.00001.003P_06204,CATH005.0523.00001.003P_06205,CATH005.0523.00001.003P_06206\t4\tBREX__brxD,BREX__brxHI,BREX__pglY,BREX__pglZ2\n+df_test_prot_Wadjet_I_41\tWadjet\tWadjet_I\tDefense\tCATH005.0523.00001.002P_06400\tCATH005.0523.00001.002P_06403\tCATH005.0523.00001.002P_06400,CATH005.0523.00001.002P_06401,CATH005.0523.00001.002P_06402,CATH005.0523.00001.002P_06403\t4\tWadjet__JetA_I,Wadjet__JetB_I,Wadjet__JetC_I,Wadjet__JetD_I\n+df_test_prot_RM_Type_III_80\tRM\tRM_Type_III\tDefense\tCATH005.0523.00001.002P_06404\tCATH005.0523.00001.002P_06406\tCATH005.0523.00001.002P_06404,CATH005.0523.00001.002P_06406\t2\tRM_Type_III__Type_III_MTases_FAM_0,RM_Type_III__Type_III_REases_FAM_0.einsi_trimmed\n+df_test_prot_Gao_RL_14\tGao_RL\tGao_RL\tDefense\tCATH005.0523.00001.002P_06602\tCATH005.0523.00001.002P_06608\tCATH005.0523.00001.002P_06602,CATH005.0523.00001.002P_06606,CATH005.0523.00001.002P_06607,CATH005.0523.00001.002P_06608\t4\tGao_RL__RL_A,Gao_RL__RL_B,Gao_RL__RL_C,Gao_RL__RL_D\n+df_test_prot_CAS_Class1-Subtype-III-D_85\tCas\tCAS_Class1-Subtype-III-D\tDefense\tCATH005.0523.00001.002P_06621\tCATH005.0523.00001.002P_06628\tCATH005.0523.00001.002P_06621,CATH005.0523.00001.002P_06624,CATH005.0523.00001.002P_06625,CATH005.0523.00001.002P_06626,CATH005.0523.00001.002P_06627,CATH005.0523.00001.002P_06628\t6\tcas10_III-D_3,cas1_I_II_III_IV_V_VI_10,cas2_I_II_III_IV_V_VI_3,casR_III-D_6,csm3gr7_III-D_2,csx19_III-D_4\n+df_test_prot_Viperin_39\tViperin\tViperin\tDefense\tCATH005.0523.00001.002P_06666\tCATH005.0523.00001.002P_06666\tCATH005.0523.00001.002P_06666\t1\tViperin__pVip\n' |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a tool-data/defense-finder.2.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/defense-finder.2.loc.sample Thu Feb 13 15:46:29 2025 +0000 |
| b |
| @@ -0,0 +1,7 @@ +# this is a tab separated file describing the location of defense finder models +# +# the columns are: +# value, dbkey, name, version, description, path +# +# for example +# defense-finder-models_2.0.2 defense-finder-models version 2.0.2 2.0.0 MacSyFinder models allowing for a systematic search of anti-phage systems ${__HERE__}/defense-finder/defense-finder-models_2.0.2 \ No newline at end of file |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a tool-data/defense-finder.loc.sample --- a/tool-data/defense-finder.loc.sample Mon Jul 22 11:12:44 2024 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -# this is a tab separated file describing the location of defense finder models -# -# the columns are: -# value, dbkey, name, version, description, path -# -# for example -# defense-finder-models_1.2.2 defense-finder-models Defense Finder models (version 1.2.2) 1.2.2 MacSyFinder models allowing for a systematic search of anti-phage systems tool-data/defense-finder/defense-finder-models_1.2.2 |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Mon Jul 22 11:12:44 2024 +0000 +++ b/tool_data_table_conf.xml.sample Thu Feb 13 15:46:29 2025 +0000 |
| b |
| @@ -1,6 +1,6 @@ <tables> <table name="defense-finder" comment_char="#" allow_duplicate_entries="False"> - <columns>value, dbkey, name, version, description, path</columns> - <file path="tool-data/defense-finder.loc.sample" /> + <columns>value, dbkey, name, version, soft compatibility version, description, path</columns> + <file path="tool-data/defense-finder.2.loc.sample" /> </table> </tables> \ No newline at end of file |
| b |
| diff -r 4ff81ce331f9 -r f5b9109b889a tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Mon Jul 22 11:12:44 2024 +0000 +++ b/tool_data_table_conf.xml.test Thu Feb 13 15:46:29 2025 +0000 |
| b |
| @@ -2,7 +2,7 @@ changed in revision 4550:535d276c92bc--> <tables> <table name="defense-finder" comment_char="#" allow_duplicate_entries="False"> - <columns>value, dbkey, name, version, description, path</columns> - <file path="${__HERE__}/test-data/defense-finder.loc" /> + <columns>value, dbkey, name, version, soft compatibility version, description, path</columns> + <file path="${__HERE__}/test-data/defense-finder.2.loc" /> </table> </tables> \ No newline at end of file |