| Previous changeset 5:596fa7bf596f (2024-03-07) Next changeset 7:f5b9109b889a (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 4f977cd93fcfda53ee4d6544c0ac6ec1f6cc5aa8 |
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modified:
defense_finder.xml macros.xml test-data/defense-finder.loc 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_hmmer.tsv test-data/outputs/prot/defense_finder_systems.tsv |
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added:
test-data/outputs/prot/defense_finder_genes_with_antidefense.tsv test-data/outputs/prot/defense_finder_hmmer_with_antidefense.tsv test-data/outputs/prot/defense_finder_systems_with_antidefense.tsv |
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| diff -r 596fa7bf596f -r 4ff81ce331f9 defense_finder.xml --- a/defense_finder.xml Thu Mar 07 16:45:46 2024 +0000 +++ b/defense_finder.xml Mon Jul 22 11:12:44 2024 +0000 |
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| @@ -1,7 +1,7 @@ <tool id="defense_finder" name="DefenseFinder" version="@TOOL_VERSION@+@WRAPPER_VERSION@" python_template_version="3.5" profile="21.05"> <description>systematically detect known anti-phage systems</description> <macros> - <token name="@WRAPPER_VERSION@">galaxy1</token> + <token name="@WRAPPER_VERSION@">galaxy0</token> <import>macros.xml</import> </macros> <expand macro="edam_ontology"/> @@ -18,7 +18,10 @@ -o out ${preserve_raw} ${no_cut_ga} - ]]></command> + ${antidefensefinder} + ${antidefensefinder_only} + + ]]> </command> <inputs> <param type="data" name="genome" format="fasta" label="Sequence dataset" help="has to be under the format of protein fasta, where all proteins are in the order of their position in the genome"/> <param type="select" name="db_type" label="The type of dataset to deal with" help="The type of dataset to deal with. 'unordered' corresponds to a non-assembled genome or set of unassembled genes, 'ordered_replicon' to an assembled genome, 'gembase' to a set of replicons where sequence identifiers follow this convention: '>RepliconName_SequenceID'"> @@ -35,24 +38,36 @@ </param> <param argument="--coverage" type="float" value="0.4" min="0" max="1" label="Coverage" help="Minimal percentage of coverage for each profiles"/> <param argument="--preserve-raw" type="boolean" truevalue="--preserve-raw" falsevalue="" label="Preserve raw MacsyFinder outputs" help="Preserve raw MacsyFinder outputs alongside Defense Finder results inside the output directory"/> + <param argument="--antidefensefinder" type="boolean" truevalue="--antidefensefinder" falsevalue="" label="AntiDefenseFinder" help="Also run AntiDefenseFinder models to find antidefense systems"/> + <param argument="--antidefensefinder-only" type="boolean" truevalue="--antidefensefinder-only" falsevalue="" label="AntiDefenseFinder Only" help="Run only AntiDefenseFinder for antidefense system and not DefenseFinder"/> + </inputs> <outputs> <data format="tabular" name="genes" from_work_dir="out/*_defense_finder_genes.tsv" label="${tool.name} on ${on_string}: genes"/> <data format="tabular" name="hmmer" from_work_dir="out/*_defense_finder_hmmer.tsv" label="${tool.name} on ${on_string}: hmmer"/> <data format="tabular" name="systems" from_work_dir="out/*_defense_finder_systems.tsv" label="${tool.name} on ${on_string}: systems"/> - <data format="fasta" name="proteins" from_work_dir="out/*.prt" label="${tool.name} on ${on_string}: proteins" /> + <data format="fasta" name="proteins" from_work_dir="out/*.prt" label="${tool.name} on ${on_string}: proteins" /> </outputs> <tests> <test> <param name="genome" value="inputs/df_test_prot.faa"/> - <param name="models" value="defense-finder-models_1.2.4"/> + <param name="models" value="defense-finder-models_1.3.0"/> <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="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"/> + <output name="systems" compare="contains" file="outputs/prot/defense_finder_systems_with_antidefense.tsv"/> + </test> + + <test> <param name="genome" value="inputs/df_test_nt.fna"/> - <param name="models" value="defense-finder-models_1.2.4"/> + <param name="models" value="defense-finder-models_1.3.0"/> <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"/> |
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| diff -r 596fa7bf596f -r 4ff81ce331f9 macros.xml --- a/macros.xml Thu Mar 07 16:45:46 2024 +0000 +++ b/macros.xml Mon Jul 22 11:12:44 2024 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">1.2.2</token> + <token name="@TOOL_VERSION@">1.3.0</token> <xml name="edam_ontology"> <edam_topics> <edam_topic>topic_0085</edam_topic> |
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| diff -r 596fa7bf596f -r 4ff81ce331f9 test-data/defense-finder.loc --- a/test-data/defense-finder.loc Thu Mar 07 16:45:46 2024 +0000 +++ b/test-data/defense-finder.loc Mon Jul 22 11:12:44 2024 +0000 |
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| @@ -1,4 +1,5 @@ # <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 \ No newline at end of file +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 596fa7bf596f -r 4ff81ce331f9 test-data/outputs/nt/defense_finder_genes.tsv --- a/test-data/outputs/nt/defense_finder_genes.tsv Thu Mar 07 16:45:46 2024 +0000 +++ b/test-data/outputs/nt/defense_finder_genes.tsv Mon Jul 22 11:12:44 2024 +0000 |
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| b'@@ -1,50 +1,50 @@\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\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2084\tDnd__DndB\t2084\tdefense-finder-models/DefenseFinder_4/Dnd/Dnd_ABCDE\tKOAN001.0722.00001.C001_Dnd_ABCDE_16\t1\t1\t0.800\t4.000\t2\tDnd__DndB\tmandatory\t450\t8.6e-10\t35.900\t0.428\t0.540\t17\t259\t\t\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2086\tDnd__DndE\t2086\tdefense-finder-models/DefenseFinder_4/Dnd/Dnd_ABCDE\tKOAN001.0722.00001.C001_Dnd_ABCDE_16\t1\t1\t0.800\t4.000\t2\tDnd__DndE\tmandatory\t518\t4.5e-14\t50.800\t0.784\t0.292\t5\t155\t\t\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2087\tDnd__DndD\t2087\tdefense-finder-models/DefenseFinder_4/Dnd/Dnd_ABCDE\tKOAN001.0722.00001.C001_Dnd_ABCDE_16\t1\t1\t0.800\t4.000\t2\tDnd__DndD\tmandatory\t705\t4e-152\t506.300\t0.872\t0.983\t1\t693\t\t\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2089\tDnd__DndE\t2089\tdefense-finder-models/DefenseFinder_4/Dnd/Dnd_ABCDE\tKOAN001.0722.00001.C001_Dnd_ABCDE_16\t1\t1\t0.800\t4.000\t2\tDnd__DndE\tmandatory\t133\t8.8e-19\t66.200\t0.577\t0.805\t2\t108\t\t\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2090\tDnd__DndD\t2090\tdefense-finder-models/DefenseFinder_4/Dnd/Dnd_ABCDE\tKOAN001.0722.00001.C001_Dnd_ABCDE_16\t1\t1\t0.800\t4.000\t2\tDnd__DndD\tmandatory\t689\t5.6e-129\t429.800\t0.863\t0.971\t1\t669\t\t\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2091\tDnd__DndC\t2091\tdefense-finder-models/DefenseFinder_4/Dnd/Dnd_ABCDE\tKOAN001.0722.00001.C001_Dnd_ABCDE_16\t1\t1\t0.800\t4.000\t2\tDnd__DndC\tmandatory\t452\t1.9e-178\t593.200\t0.715\t0.989\t3\t449\t\t\r\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\t1.000\t2.000\t1\tRM_Type_II__Type_II_REases\tmandatory\t401\t5.2e-44\t149.400\t0.996\t0.933\t10\t383\t\t\r\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\t1.000\t2.000\t1\tRM_Type_II__Type_II_MTases\tmandatory\t836\t7.6e-54\t181.400\t0.986\t0.463\t2\t388\t\t\r\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\t1.000\t2.500\t1\tRM__Type_I_S\taccessory\t407\t7e-60\t201.400\t0.464\t0.985\t3\t403\t\t\r\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\t1.000\t2.500\t1\tRM__Type_I_MTases\tmandatory\t543\t2.7e-114\t380.900\t0.990\t0.983\t8\t541\t\t\r\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\t1.000\t2.500\t1\tRM__Type_I_REases\tmandatory\t1023\t9.7e-91\t303.600\t0.965\t0.943\t1\t965\t\t\r\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\t1.000\t1.000\t1\tRM_Type_IIG__Type_IIG\tmandatory\t676\t3.2e-233\t775.000\t0.705\t0.991\t1\t670\t\t\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2943\tRM_Type_II__Type_II_MTases\t2943\tdefense-finder-models/RM/RM/RM_Type_II\tKOAN001.0722.00001.C001_RM_Type_II_24\t1\t1\t1.000\t2.000\t1\tRM_Type_II__Type_II_MTases\tmandatory\t424\t6.9e-97\t323.000\t0.981\t0.785\t73\t405\t\t\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2944\tRM_Type_II__Type_II_REases\t2944\tdefense-finder-models/RM/RM/RM_Type_II\tKOAN001.0722.00001.C001_RM_Type_II_24\t1\t1\t1.000\t2.000\t1\tRM_Type_II__Type_II_REases\tmandatory\t237\t5.1e-11\t41.300\t0.771\t0.835\t7\t204\t\t\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4033\tRM__Type_I_REases\t4033\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_22\t1\t1\t1.000\t2.500\t1\tRM__Type_I_REases\tmandatory\t1087\t1.8e-184\t613.800\t0.972\t0.954\t13\t1049\t\t\r\n-KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4036\tRM__Type_I_S\t4036\tdefense-finder-models/RM'..b'06\t25.6\t0.49\t0.119\t37\t60\t\t\tAbiE\tAbiE\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2844\tSanaTA__SanaA\t2844\tdefense-finder-models/DefenseFinder_5/SanaTA/SanaTA\tKOAN001.0722.00001.C001_SanaTA_19\t1\t1\t1.0\t2.0\t1\tSanaTA__SanaA\tmandatory\t201\t1e-13\t49.9\t0.955\t0.627\t4\t129\t\t\tSanaTA\tSanaTA\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2943\tRM_Type_II__Type_II_MTases\t2943\tdefense-finder-models/RM/RM/RM_Type_II\tKOAN001.0722.00001.C001_RM_Type_II_24\t1\t1\t1.0\t2.0\t1\tRM_Type_II__Type_II_MTases\tmandatory\t424\t6.9e-97\t323.0\t0.981\t0.785\t73\t405\t\t\tRM\tRM_Type_II\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_2944\tRM_Type_II__Type_II_REases\t2944\tdefense-finder-models/RM/RM/RM_Type_II\tKOAN001.0722.00001.C001_RM_Type_II_24\t1\t1\t1.0\t2.0\t1\tRM_Type_II__Type_II_REases\tmandatory\t237\t5.1e-11\t41.3\t0.771\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_1/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_5/Retron/Retron_VI\tKOAN001.0722.00001.C001_Retron_VI_18\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\t3147\tdefense-finder-models/DefenseFinder_5/Retron/Retron_VI\tKOAN001.0722.00001.C001_Retron_VI_18\t1\t1\t1.0\t2.0\t1\tRetron__RT_Tot\tmandatory\t285\t3.8000000000000004e-80\t267.6\t0.811\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_1/AbiH/AbiH\tKOAN001.0722.00001.C001_AbiH_3\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_2/NLR/NLR_like_bNACHT01\tKOAN001.0722.00001.C001_NLR_like_bNACHT01_10\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\t4033\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_22\t1\t1\t1.0\t2.5\t1\tRM__Type_I_REases\tmandatory\t1087\t1.8e-184\t613.8\t0.972\t0.954\t13\t1049\t\t\tRM\tRM_Type_I\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4034\tCBASS__2TM_5\t4034\tdefense-finder-models/DefenseFinder_5/Pycsar/Pycsar\tKOAN001.0722.00001.C001_Pycsar_17\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_5/Pycsar/Pycsar\tKOAN001.0722.00001.C001_Pycsar_17\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\t4036\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_22\t1\t1\t1.0\t2.5\t1\tRM__Type_I_S\taccessory\t413\t6e-80\t267.0\t0.584\t0.969\t12\t411\t\t\tRM\tRM_Type_I\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4038\tRM__Type_I_MTases\t4038\tdefense-finder-models/RM/RM/RM_Type_I\tKOAN001.0722.00001.C001_RM_Type_I_22\t1\t1\t1.0\t2.5\t1\tRM__Type_I_MTases\tmandatory\t501\t7.4e-176\t584.0\t0.996\t0.998\t1\t500\t\t\tRM\tRM_Type_I\tDefense\n+KOAN001.0722.00001.C001\tKOAN001.0722.00001.C001_4280\tViperin__pVip\t4280\tdefense-finder-models/DefenseFinder_1/Viperin/Viperin\tKOAN001.0722.00001.C001_Viperin_8\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_1/RloC/RloC\tKOAN001.0722.00001.C001_RloC_7\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' 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| diff -r 596fa7bf596f -r 4ff81ce331f9 test-data/outputs/nt/defense_finder_hmmer.tsv --- a/test-data/outputs/nt/defense_finder_hmmer.tsv Thu Mar 07 16:45:46 2024 +0000 +++ b/test-data/outputs/nt/defense_finder_hmmer.tsv Mon Jul 22 11:12:44 2024 +0000 |
| b |
| b'@@ -1,285 +1,209 @@\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\r\n-KOAN001.0722.00001.C001_1059\tKOAN001.0722.00001.C001\t1059\t234\tDpd__FolE\t5.400e-45\t151.300\t0.917\t0.714\t53\t219\r\n-KOAN001.0722.00001.C001_1071\tKOAN001.0722.00001.C001\t1071\t633\tShango__SngC\t4.200e-12\t43.500\t0.510\t0.528\t13\t346\r\n-KOAN001.0722.00001.C001_1071\tKOAN001.0722.00001.C001\t1071\t633\tPsyrTA__PsyrT\t1.100e-95\t319.300\t0.530\t0.559\t5\t358\r\n-KOAN001.0722.00001.C001_1086\tKOAN001.0722.00001.C001\t1086\t676\tRM_Type_II__Type_II_MTases\t3.500e-12\t43.900\t0.691\t0.348\t357\t591\r\n-KOAN001.0722.00001.C001_1086\tKOAN001.0722.00001.C001\t1086\t676\tRM_Type_IIG__Type_IIG\t3.200e-233\t775.000\t0.705\t0.991\t1\t670\r\n-KOAN001.0722.00001.C001_1137\tKOAN001.0722.00001.C001\t1137\t1610\tShango__SngC\t2.200e-11\t41.200\t0.512\t0.221\t268\t623\r\n-KOAN001.0722.00001.C001_1137\tKOAN001.0722.00001.C001\t1137\t1610\tGabija__GajB_2\t6.000e-60\t201.500\t0.742\t0.285\t1019\t1477\r\n-KOAN001.0722.00001.C001_1137\tKOAN001.0722.00001.C001\t1137\t1610\tPsyrTA__PsyrT\t5.400e-74\t247.600\t0.525\t0.231\t270\t641\r\n-KOAN001.0722.00001.C001_1160\tKOAN001.0722.00001.C001\t1160\t213\tAbiL__AbiLii\t5.700e-06\t23.700\t0.475\t0.671\t50\t192\r\n-KOAN001.0722.00001.C001_1161\tKOAN001.0722.00001.C001\t1161\t432\tAbiL__AbiLi2\t3.500e-41\t139.900\t0.980\t0.981\t1\t424\r\n-KOAN001.0722.00001.C001_1161\tKOAN001.0722.00001.C001\t1161\t432\tAbiL__AbiLi\t3.000e-13\t47.700\t0.621\t0.637\t1\t275\r\n-KOAN001.0722.00001.C001_1161\tKOAN001.0722.00001.C001\t1161\t432\tParis_I__AAA_15\t7.100e-15\t53.600\t0.997\t0.847\t1\t366\r\n-KOAN001.0722.00001.C001_1161\tKOAN001.0722.00001.C001\t1161\t432\tParis_II__AAA_21\t1.200e-30\t105.500\t1.000\t0.750\t45\t368\r\n-KOAN001.0722.00001.C001_1161\tKOAN001.0722.00001.C001\t1161\t432\tRetron_I_B__ATPase_TOPRIM_COG3593\t1.200e-20\t72.300\t0.562\t0.817\t45\t397\r\n-KOAN001.0722.00001.C001_1167\tKOAN001.0722.00001.C001\t1167\t223\tRetron_I_A__HNH_TIGR02646\t8.100e-11\t40.100\t0.786\t0.785\t29\t203\r\n-KOAN001.0722.00001.C001_1167\tKOAN001.0722.00001.C001\t1167\t223\tSeptu__PtuB\t1.500e-21\t75.700\t0.902\t0.942\t1\t210\r\n-KOAN001.0722.00001.C001_1167\tKOAN001.0722.00001.C001\t1167\t223\tRetron_I_A__HNH_TIGR02646\t8.100e-11\t40.100\t0.786\t0.785\t29\t203\r\n-KOAN001.0722.00001.C001_1167\tKOAN001.0722.00001.C001\t1167\t223\tSeptu__PtuB\t1.500e-21\t75.700\t0.902\t0.942\t1\t210\r\n-KOAN001.0722.00001.C001_1168\tKOAN001.0722.00001.C001\t1168\t412\tParis_II__AriA_AAA21\t2.400e-25\t87.700\t0.937\t0.854\t2\t353\r\n-KOAN001.0722.00001.C001_1168\tKOAN001.0722.00001.C001\t1168\t412\tParis_I__AAA_15\t1.400e-12\t46.000\t0.576\t0.580\t71\t309\r\n-KOAN001.0722.00001.C001_1168\tKOAN001.0722.00001.C001\t1168\t412\tParis_II__AAA_21\t2.900e-16\t58.200\t0.993\t0.677\t32\t310\r\n-KOAN001.0722.00001.C001_1168\tKOAN001.0722.00001.C001\t1168\t412\tSeptu__PtuA\t8.000e-57\t192.000\t0.972\t0.976\t4\t405\r\n-KOAN001.0722.00001.C001_1168\tKOAN001.0722.00001.C001\t1168\t412\tSeptu__PtuA\t8.000e-57\t192.000\t0.972\t0.976\t4\t405\r\n-KOAN001.0722.00001.C001_1168\tKOAN001.0722.00001.C001\t1168\t412\tRetron_I_A__ATPase_TypeIA\t1.800e-37\t127.700\t0.506\t0.638\t146\t408\r\n-KOAN001.0722.00001.C001_1202\tKOAN001.0722.00001.C001\t1202\t701\tShango__SngC\t2.100e-14\t51.200\t0.492\t0.455\t16\t334\r\n-KOAN001.0722.00001.C001_1202\tKOAN001.0722.00001.C001\t1202\t701\tPsyrTA__PsyrT\t1.900e-100\t335.100\t0.512\t0.486\t6\t346\r\n-KOAN001.0722.00001.C001_131\tKOAN001.0722.00001.C001\t131\t552\tRetron_I_A__ATPase_TypeIA\t1.300e-06\t25.800\t0.500\t0.505\t2\t280\r\n-KOAN001.0722.00001.C001_1324\tKOAN001.0722.00001.C001\t1324\t852\tDodola__DolB\t1.600e-20\t71.600\t0.416\t0.198\t526\t694\r\n-KOAN001.0722.00001.C001_1369\tKOAN001.0722.00001.C001\t1369\t827\tDodola__DolB\t6.400e-12\t43.300\t0.707\t0.328\t329\t599\r\n-KOAN001.0722.00001.C001_1421\tKOAN001.0722.00001.C001\t1421\t524\tcas3HD_I_1\t1.400e-08\t32.900\t0.591\t0.181\t333\t427\r\n-KOAN001.0722.00001.C001_1455\tKOAN001.0722.00001.C001\t1455\t383\tDnd__DndA\t9.200e-92\t306.000\t0.984\t0.977\t4\t377\r\n-KOAN001.0722.00001.C001_147\tKOAN001.0722.00001.C001\t147\t455\tDEDDh_I_II_III_IV_V_VI_1\t2.000e-42\t143.100\t0.994\t0.341\t4\t158\r\n-KOAN001.0722.00001.C001_1659\tKOAN001.0722.00001.C001\t1659\t227\tDpd__FolE\t1.600e-43\t146.600\t0.994\t0.7'..b'7.7\t0.499\t0.543\t39\t239\n+KOAN001.0722.00001.C001_3572\tKOAN001.0722.00001.C001\t3572\t370\tRosmerTA__RmrA_2677172838\t2.3e-08\t31.3\t0.547\t0.573\t32\t243\n+KOAN001.0722.00001.C001_3574\tKOAN001.0722.00001.C001\t3574\t532\tZorya__ZorB\t6.4e-06\t23.7\t0.521\t0.227\t408\t528\n+KOAN001.0722.00001.C001_3594\tKOAN001.0722.00001.C001\t3594\t1461\tDEDDh_I_II_III_IV_V_VI_1\t4.600000000000001e-28\t96.5\t0.994\t0.124\t3\t183\n+KOAN001.0722.00001.C001_3691\tKOAN001.0722.00001.C001\t3691\t698\tRetron_IX__HEPN\t7.1e-07\t27.5\t0.632\t0.11\t581\t657\n+KOAN001.0722.00001.C001_3809\tKOAN001.0722.00001.C001\t3809\t456\tDEDDh_I_II_III_IV_V_VI_1\t2.0999999999999999e-41\t139.8\t0.988\t0.331\t4\t154\n+KOAN001.0722.00001.C001_3811\tKOAN001.0722.00001.C001\t3811\t449\tShango__SngC\t3.1e-19\t67.1\t0.517\t0.777\t9\t357\n+KOAN001.0722.00001.C001_3811\tKOAN001.0722.00001.C001\t3811\t449\tPsyrTA__PsyrT\t9.7e-21\t71.6\t0.492\t0.764\t34\t376\n+KOAN001.0722.00001.C001_3833\tKOAN001.0722.00001.C001\t3833\t254\tDpd__QueE\t6.600000000000001e-26\t89.3\t0.955\t0.909\t14\t244\n+KOAN001.0722.00001.C001_3843\tKOAN001.0722.00001.C001\t3843\t325\tDISARM_2__drmMII\t1.7999999999999997e-51\t173.4\t0.542\t0.6\t1\t195\n+KOAN001.0722.00001.C001_3843\tKOAN001.0722.00001.C001\t3843\t325\tDruantia_II__DruM\t7e-67\t224.3\t0.853\t0.948\t3\t310\n+KOAN001.0722.00001.C001_3843\tKOAN001.0722.00001.C001\t3843\t325\tRM_Type_II__Type_II_MTases\t3.4e-108\t359.7\t0.858\t0.945\t1\t307\n+KOAN001.0722.00001.C001_3951\tKOAN001.0722.00001.C001\t3951\t1230\tThoeris__ThsB_Global\t1.6e-06\t26.2\t0.565\t0.092\t1044\t1156\n+KOAN001.0722.00001.C001_3973\tKOAN001.0722.00001.C001\t3973\t648\tGao_Iet__IetA\t5e-32\t109.4\t0.566\t0.352\t204\t431\n+KOAN001.0722.00001.C001_4004\tKOAN001.0722.00001.C001\t4004\t1361\tMokosh_type_I__MkoA_C\t2.7e-77\t258.7\t0.447\t0.377\t654\t1166\n+KOAN001.0722.00001.C001_4006\tKOAN001.0722.00001.C001\t4006\t474\tDISARM__drmC\t5e-11\t40.7\t0.532\t0.304\t44\t187\n+KOAN001.0722.00001.C001_4017\tKOAN001.0722.00001.C001\t4017\t885\tRM_Type_II__Type_II_MTases\t5.6e-09\t33.2\t0.418\t0.16\t636\t777\n+KOAN001.0722.00001.C001_4033\tKOAN001.0722.00001.C001\t4033\t1087\tRM__Type_I_REases\t1.8e-184\t613.8\t0.972\t0.954\t13\t1049\n+KOAN001.0722.00001.C001_4034\tKOAN001.0722.00001.C001\t4034\t173\tCBASS__2TM_5\t1.4e-27\t94.4\t0.931\t0.954\t4\t168\n+KOAN001.0722.00001.C001_4035\tKOAN001.0722.00001.C001\t4035\t334\tPycsar__AG_cyclase\t4.4e-31\t106.3\t0.586\t0.545\t11\t192\n+KOAN001.0722.00001.C001_4036\tKOAN001.0722.00001.C001\t4036\t413\tRM__Type_I_S\t6e-80\t267.0\t0.584\t0.969\t12\t411\n+KOAN001.0722.00001.C001_4038\tKOAN001.0722.00001.C001\t4038\t501\tRM_Type_II__Type_II_MTases\t2.9e-41\t139.9\t0.724\t0.507\t157\t410\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_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_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_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 596fa7bf596f -r 4ff81ce331f9 test-data/outputs/nt/defense_finder_systems.tsv --- a/test-data/outputs/nt/defense_finder_systems.tsv Thu Mar 07 16:45:46 2024 +0000 +++ b/test-data/outputs/nt/defense_finder_systems.tsv Mon Jul 22 11:12:44 2024 +0000 |
| b |
| b'@@ -1,26 +1,28 @@\n-sys_id\ttype\tsubtype\tsys_beg\tsys_end\tprotein_in_syst\tgenes_count\tname_of_profiles_in_sys\r\n-KOAN001.0722.00001.C001_Dnd_ABCDE_16\tDnd\tDnd_ABCDE\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__DndE,Dnd__DndD,Dnd__DndE,Dnd__DndD,Dnd__DndC\r\n-KOAN001.0722.00001.C001_RM_Type_II_23\tRM\tRM_Type_II\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_REases,RM_Type_II__Type_II_MTases\r\n-KOAN001.0722.00001.C001_RM_Type_I_21\tRM\tRM_Type_I\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_S,RM__Type_I_MTases,RM__Type_I_REases\r\n-KOAN001.0722.00001.C001_RM_Type_IIG_25\tRM\tRM_Type_IIG\tKOAN001.0722.00001.C001_1086\tKOAN001.0722.00001.C001_1086\tKOAN001.0722.00001.C001_1086\t1\tRM_Type_IIG__Type_IIG\r\n-KOAN001.0722.00001.C001_RM_Type_II_24\tRM\tRM_Type_II\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,RM_Type_II__Type_II_REases\r\n-KOAN001.0722.00001.C001_RM_Type_I_22\tRM\tRM_Type_I\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_REases,RM__Type_I_S,RM__Type_I_MTases\r\n-KOAN001.0722.00001.C001_AbiZ_5\tAbiZ\tAbiZ\tKOAN001.0722.00001.C001_680\tKOAN001.0722.00001.C001_680\tKOAN001.0722.00001.C001_680\t1\tAbiZ__AbiZ\r\n-KOAN001.0722.00001.C001_AbiL_4\tAbiL\tAbiL\tKOAN001.0722.00001.C001_1160\tKOAN001.0722.00001.C001_1161\tKOAN001.0722.00001.C001_1160,KOAN001.0722.00001.C001_1161\t2\tAbiL__AbiLii,AbiL__AbiLi2\r\n-KOAN001.0722.00001.C001_Gabija_6\tGabija\tGabija\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\r\n-KOAN001.0722.00001.C001_AbiE_2\tAbiE\tAbiE\tKOAN001.0722.00001.C001_2843\tKOAN001.0722.00001.C001_2844\tKOAN001.0722.00001.C001_2843,KOAN001.0722.00001.C001_2844\t2\tAbiEii__AbiEii,AbiEii__AbiEi_4\r\n-KOAN001.0722.00001.C001_AbiD_1\tAbiD\tAbiD\tKOAN001.0722.00001.C001_3068\tKOAN001.0722.00001.C001_3068\tKOAN001.0722.00001.C001_3068\t1\tAbiD__AbiD\r\n-KOAN001.0722.00001.C001_AbiH_3\tAbiH\tAbiH\tKOAN001.0722.00001.C001_3309\tKOAN001.0722.00001.C001_3309\tKOAN001.0722.00001.C001_3309\t1\tAbiH__AbiH\r\n-KOAN001.0722.00001.C001_Viperin_8\tViperin\tViperin\tKOAN001.0722.00001.C001_4280\tKOAN001.0722.00001.C001_4280\tKOAN001.0722.00001.C001_4280\t1\tViperin__pVip\r\n-KOAN001.0722.00001.C001_RloC_7\tRloC\tRloC\tKOAN001.0722.00001.C001_4361\tKOAN001.0722.00001.C001_4361\tKOAN001.0722.00001.C001_4361\t1\tRloC__RloC\r\n-KOAN001.0722.00001.C001_SpbK_15\tSpbK\tSpbK\tKOAN001.0722.00001.C001_2040\tKOAN001.0722.00001.C001_2040\tKOAN001.0722.00001.C001_2040\t1\tSpbK__SpbK\r\n-KOAN001.0722.00001.C001_CAS_Class2-Subtype-II-C_26\tCasFinder\tCAS_Class2-Subtype-II-C\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\tcas2_I_II_III_IV_V_VI_6,cas1_I_II_III_IV_V_VI_5,cas9_II-A_II-B_II-C_1\r\n-KOAN001.0722.00001.C001_Septu_11\tSeptu\tSeptu\tKOAN001.0722.00001.C001_254\tKOAN001.0722.00001.C001_255\tKOAN001.0722.00001.C001_254,KOAN001.0722.00001.C001_255\t2\tSeptu__PtuB,Septu__PtuA\r\n-KOAN001.0722.00001.C001_Septu_12\tSeptu\tSeptu\tKOAN001.0722.00001.C001_1167\tKOAN001.0722.00001.C001_1168\tKOAN001.0722.00001.C001_1167,KOAN001.0722.00001.C001_1168\t2\tSeptu__PtuB,Septu__PtuA\r\n-KOAN001.0722.00001.C001_Wadjet_I_14\tWadjet\tWadjet_I\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__JetD_I,Wadjet__JetC_I,Wadjet__JetB_I,Wadjet__JetA_I\r\n-KOAN001.0722.00001.C001_NLR_lik'..b'ja__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_24\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,RM_Type_II__Type_II_REases\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' |
| b |
| diff -r 596fa7bf596f -r 4ff81ce331f9 test-data/outputs/prot/defense_finder_genes.tsv --- a/test-data/outputs/prot/defense_finder_genes.tsv Thu Mar 07 16:45:46 2024 +0000 +++ b/test-data/outputs/prot/defense_finder_genes.tsv Mon Jul 22 11:12:44 2024 +0000 |
| b |
| b'@@ -1,562 +1,562 @@\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\r\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\t1.000\t13.000\t1\tDpd__QueE\taccessory\t222\t4.3e-122\t403.000\t1.000\t0.995\t2\t222\t\t\r\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\t1.000\t13.000\t1\tDpd__DpdE\tmandatory\t1002\t0.0\t1044.800\t0.925\t0.978\t1\t980\t\t\r\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\t1.000\t13.000\t1\tDpd__DpdF\tmandatory\t851\t4.6e-299\t991.800\t0.995\t0.994\t5\t850\t\t\r\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\t1.000\t13.000\t1\tDpd__DpdG\tmandatory\t310\t2e-87\t290.700\t0.997\t0.997\t1\t309\t\t\r\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\t1.000\t13.000\t1\tDpd__DpdH\tmandatory\t1031\t0.0\t1143.700\t0.999\t0.997\t1\t1028\t\t\r\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\t1.000\t13.000\t1\tDpd__DpdI\tmandatory\t249\t6e-43\t144.700\t0.984\t0.988\t4\t249\t\t\r\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\t1.000\t13.000\t1\tDpd__DpdJ\tmandatory\t1495\t0.0\t1757.100\t0.997\t0.998\t3\t1494\t\t\r\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\t1.000\t13.000\t1\tDpd__DpdK\tmandatory\t178\t2.6e-62\t207.000\t0.889\t0.983\t1\t175\t\t\r\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\t1.000\t13.000\t1\tDpd__DpdD\tmandatory\t720\t2.6e-282\t935.600\t0.994\t0.999\t1\t719\t\t\r\n-df_test_prot\tTHCR001.0722.00001.C001_01136\tDpd__QueC\t27\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.000\t13.000\t1\tDpd__QueC\taccessory\t219\t7e-122\t402.000\t0.986\t0.991\t2\t218\t\t\r\n-df_test_prot\tTHCR001.0722.00001.C001_01137\tDpd__DpdB\t28\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.000\t13.000\t1\tDpd__DpdB\tmandatory\t399\t3.1e-62\t207.500\t0.880\t0.932\t17\t388\t\t\r\n-df_test_prot\tTHCR001.0722.00001.C001_01138\tDpd__DpdA\t29\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.000\t13.000\t1\tDpd__DpdA\tmandatory\t468\t1.9e-104\t346.900\t0.971\t0.959\t5\t453\t\t\r\n-df_test_prot\tTHCR001.0722.00001.C001_01139\tDpd__DpdC\t30\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.000\t13.000\t1\tDpd__DpdC\tmandatory\t287\t1.1e-85\t284.700\t0.906\t0.972\t6\t284\t\t\r\n-df_test_prot\tTHCR001.0722.00001.C001_01140\tDpd__QueD\t31\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.000\t13.000\t1\tDpd__QueD\taccessory\t120\t9.2e-59\t194.300\t1.000\t1.000\t1\t120\t\t\r\n-df_test_prot\tTHCR001.0722.00001.C001_01142\tDpd__FolE\t32\tdefense-finder-models/DefenseFinder_4/Dpd/Dpd\tdf_test_prot_Dpd_171\t1\t1\t1.000\t13.000\t1\tDpd__FolE\taccessory\t186\t2.5e-103\t340.600\t0.989\t0.962\t5\t183\t\t\r\n-df_test_prot\tBOHI001.0722.00008.C001_00581\tSspBCDE__SspF\t85\tdefense-finder-models/DefenseFinder_4/SspBCDE/SspBCDE\tdf_test_prot_SspBCDE_200\t1\t1\t1.000\t5.000\t1\tSspBCDE__SspF\taccessory\t640\t1e-205\t681.800\t0.992\t0.963\t22\t637\t\t\r\n-df_test_prot\tBOHI001.0722.00008.C001_00582\tSspBCDE__SspG\t86\tdefense-finder-models/DefenseFinder_4/SspBCDE/SspBCDE\tdf_test_prot_SspBCDE_200\t1\t1\t1.000\t5.000\t1\tSspBCDE__SspG\taccessory\t515\t1.2e-192\t638.500\t0.994\t0.986\t1\t508\t\t\r\n-df_test_prot\tBOHI001.0722.00008.C001_00583\tSspBCDE__SspH\t87\tdefense-finder-models/DefenseFinder_4/SspBCDE/SspBCDE\tdf_test_prot_SspBCDE_200\t1\t1\t1.000\t5.000\t1\tSspBCDE__SspH\taccessory\t1805\t0.0\t2093.700\t0.999\t0.998\t1\t1801\t\t\r\n-df_test_prot\t'..b'54.2\t1.0\t1.0\t1\t179\t\t\tLamassu-Fam\tLamassu-Fam\tDefense\n+df_test_prot\tSHHA001.0722.00001.C001_00541\tLamassu-Fam__LmuA_effector_Protease\t2630\tdefense-finder-models/DefenseFinder_1/Lamassu-Fam/Lamassu-Fam\tdf_test_prot_Lamassu-Fam_44\t1\t1\t0.333\t2.5\t1\tLamassu-Fam__LmuA_effector_Protease\taccessory\t442\t3.7999999999999995e-136\t451.9\t0.995\t0.991\t5\t442\t\t\tLamassu-Fam\tLamassu-Fam\tDefense\n+df_test_prot\tSHHA001.0722.00001.C001_00542\tLamassu-Fam__LmuA_effector_Hydrolase\t2631\tdefense-finder-models/DefenseFinder_1/Lamassu-Fam/Lamassu-Fam\tdf_test_prot_Lamassu-Fam_44\t1\t1\t0.333\t2.5\t1\tLamassu-Fam__LmuA_effector_Hydrolase\taccessory\t351\t7.4e-131\t433.4\t0.997\t0.994\t1\t349\t\t\tLamassu-Fam\tLamassu-Fam\tDefense\n+df_test_prot\tSHHA001.0722.00001.C001_00544\tLamassu-Fam__LmuA_effector_Lipase\t2632\tdefense-finder-models/DefenseFinder_1/Lamassu-Fam/Lamassu-Fam\tdf_test_prot_Lamassu-Fam_44\t1\t1\t0.333\t2.5\t1\tLamassu-Fam__LmuA_effector_Lipase\taccessory\t398\t3.3e-19\t67.0\t0.437\t0.364\t8\t152\t\t\tLamassu-Fam\tLamassu-Fam\tDefense\n+df_test_prot\tPSSA001.0722.00001.C001_01671\tpAgo__GbbAgaS\t2642\tdefense-finder-models/DefenseFinder_5/pAgo/pAgo\tdf_test_prot_pAgo_254\t1\t1\t0.273\t2.0\t1\tpAgo__GbbAgaS\taccessory\t445\t1.5e-13\t47.6\t0.431\t0.409\t183\t364\t\t\tpAgo\tpAgo\tDefense\n+df_test_prot\tPSSA001.0722.00001.C001_01672\tpAgo__pAgo_SPARTA\t2643\tdefense-finder-models/DefenseFinder_5/pAgo/pAgo\tdf_test_prot_pAgo_254\t1\t1\t0.273\t2.0\t1\tpAgo__pAgo_SPARTA\tmandatory\t502\t3.9000000000000004e-210\t695.9\t0.992\t0.996\t3\t502\t\t\tpAgo\tpAgo\tDefense\n+df_test_prot\tPSSA001.0722.00001.C001_01673\tpAgo__TIRAPAZ\t2644\tdefense-finder-models/DefenseFinder_5/pAgo/pAgo\tdf_test_prot_pAgo_254\t1\t1\t0.273\t2.0\t1\tpAgo__TIRAPAZ\taccessory\t452\t7.900000000000001e-165\t546.1\t0.981\t0.989\t1\t447\t\t\tpAgo\tpAgo\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00104\tcas1_I-E_1\t2654\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcas1_I-E_1\taccessory\t277\t1.2e-94\t313.7\t1.0\t0.913\t17\t269\t\tdf_test_prot_CAS_Class1-Subtype-I-E_269,df_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00105\tcas6e_I_II_III_IV_V_VI_3\t2655\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcas6e_I_II_III_IV_V_VI_3\taccessory\t168\t3.7e-09\t34.4\t0.446\t0.53\t78\t166\t\tdf_test_prot_CAS_Class1-Subtype-I-E_269,df_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00106\tcsf3gr5_IV-A_2\t2656\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf3gr5_IV-A_1\tmandatory\t226\t1.6e-94\t312.9\t1.0\t0.938\t3\t214\t\tdf_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00107\tcsf2gr7_IV-A_1\t2657\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf2gr7_IV-A_1\tmandatory\t376\t1.3e-140\t465.6\t0.997\t0.843\t17\t333\t\tdf_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00108\tcsf5gr6_IV-A_1\t2658\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf5gr6_IV-A_1\tmandatory\t178\t6.8e-10\t36.2\t0.694\t0.944\t3\t170\t\tdf_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00109\tcsf1gr8_IV-A_2\t2659\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf1gr8_IV-A_3\tmandatory\t270\t2.5e-100\t331.6\t1.0\t0.744\t39\t239\t\tdf_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00110\tcsf4_IV-A1_2\t2660\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf4_IV-A_1\taccessory\t813\t3.7000000000000004e-125\t416.2\t0.956\t0.962\t27\t808\t\tdf_test_prot_CAS_Class1-Type-IV_271\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n' |
| b |
| diff -r 596fa7bf596f -r 4ff81ce331f9 test-data/outputs/prot/defense_finder_genes_with_antidefense.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/prot/defense_finder_genes_with_antidefense.tsv Mon Jul 22 11:12:44 2024 +0000 |
| b |
| b'@@ -0,0 +1,564 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su-Fam\tdf_test_prot_Lamassu-Fam_44\t1\t1\t0.333\t2.5\t1\tLamassu-Fam__LmuA_effector_Hydrolase\taccessory\t351\t7.4e-131\t433.4\t0.997\t0.994\t1\t349\t\t\tLamassu-Fam\tLamassu-Fam\tDefense\n+df_test_prot\tSHHA001.0722.00001.C001_00544\tLamassu-Fam__LmuA_effector_Lipase\t2632\tdefense-finder-models/DefenseFinder_1/Lamassu-Fam/Lamassu-Fam\tdf_test_prot_Lamassu-Fam_44\t1\t1\t0.333\t2.5\t1\tLamassu-Fam__LmuA_effector_Lipase\taccessory\t398\t3.3e-19\t67.0\t0.437\t0.364\t8\t152\t\t\tLamassu-Fam\tLamassu-Fam\tDefense\n+df_test_prot\tPSSA001.0722.00001.C001_01671\tpAgo__GbbAgaS\t2642\tdefense-finder-models/DefenseFinder_5/pAgo/pAgo\tdf_test_prot_pAgo_254\t1\t1\t0.273\t2.0\t1\tpAgo__GbbAgaS\taccessory\t445\t1.5e-13\t47.6\t0.431\t0.409\t183\t364\t\t\tpAgo\tpAgo\tDefense\n+df_test_prot\tPSSA001.0722.00001.C001_01672\tpAgo__pAgo_SPARTA\t2643\tdefense-finder-models/DefenseFinder_5/pAgo/pAgo\tdf_test_prot_pAgo_254\t1\t1\t0.273\t2.0\t1\tpAgo__pAgo_SPARTA\tmandatory\t502\t3.9000000000000004e-210\t695.9\t0.992\t0.996\t3\t502\t\t\tpAgo\tpAgo\tDefense\n+df_test_prot\tPSSA001.0722.00001.C001_01673\tpAgo__TIRAPAZ\t2644\tdefense-finder-models/DefenseFinder_5/pAgo/pAgo\tdf_test_prot_pAgo_254\t1\t1\t0.273\t2.0\t1\tpAgo__TIRAPAZ\taccessory\t452\t7.900000000000001e-165\t546.1\t0.981\t0.989\t1\t447\t\t\tpAgo\tpAgo\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00104\tcas1_I-E_1\t2654\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcas1_I-E_1\taccessory\t277\t1.2e-94\t313.7\t1.0\t0.913\t17\t269\t\tdf_test_prot_CAS_Class1-Subtype-I-E_269,df_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00105\tcas6e_I_II_III_IV_V_VI_3\t2655\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcas6e_I_II_III_IV_V_VI_3\taccessory\t168\t3.7e-09\t34.4\t0.446\t0.53\t78\t166\t\tdf_test_prot_CAS_Class1-Subtype-I-E_269,df_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00106\tcsf3gr5_IV-A_2\t2656\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf3gr5_IV-A_1\tmandatory\t226\t1.6e-94\t312.9\t1.0\t0.938\t3\t214\t\tdf_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00107\tcsf2gr7_IV-A_1\t2657\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf2gr7_IV-A_1\tmandatory\t376\t1.3e-140\t465.6\t0.997\t0.843\t17\t333\t\tdf_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00108\tcsf5gr6_IV-A_1\t2658\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf5gr6_IV-A_1\tmandatory\t178\t6.8e-10\t36.2\t0.694\t0.944\t3\t170\t\tdf_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00109\tcsf1gr8_IV-A_2\t2659\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf1gr8_IV-A_3\tmandatory\t270\t2.5e-100\t331.6\t1.0\t0.744\t39\t239\t\tdf_test_prot_CAS_Class1-Type-IV_271,df_test_prot_CAS_Cluster_272\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n+df_test_prot\tRHFE001.0722.00001.P002_00110\tcsf4_IV-A1_2\t2660\tCasFinder/CAS_Class1-Subtype-IV-A\tdf_test_prot_CAS_Class1-Subtype-IV-A_270\t1\t1\t1.4\t7.0\t1\tcsf4_IV-A_1\taccessory\t813\t3.7000000000000004e-125\t416.2\t0.956\t0.962\t27\t808\t\tdf_test_prot_CAS_Class1-Type-IV_271\tCas\tCAS_Class1-Subtype-IV-A\tDefense\n' |
| b |
| diff -r 596fa7bf596f -r 4ff81ce331f9 test-data/outputs/prot/defense_finder_hmmer.tsv --- a/test-data/outputs/prot/defense_finder_hmmer.tsv Thu Mar 07 16:45:46 2024 +0000 +++ b/test-data/outputs/prot/defense_finder_hmmer.tsv Mon Jul 22 11:12:44 2024 +0000 |
| b |
| b'@@ -1,1247 +1,912 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|
| b |
| diff -r 596fa7bf596f -r 4ff81ce331f9 test-data/outputs/prot/defense_finder_hmmer_with_antidefense.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/prot/defense_finder_hmmer_with_antidefense.tsv Mon Jul 22 11:12:44 2024 +0000 |
| b |
| b'@@ -0,0 +1,914 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|
| b |
| diff -r 596fa7bf596f -r 4ff81ce331f9 test-data/outputs/prot/defense_finder_systems.tsv --- a/test-data/outputs/prot/defense_finder_systems.tsv Thu Mar 07 16:45:46 2024 +0000 +++ b/test-data/outputs/prot/defense_finder_systems.tsv Mon Jul 22 11:12:44 2024 +0000 |
| b |
| b'@@ -1,234 +1,234 @@\n-sys_id\ttype\tsubtype\tsys_beg\tsys_end\tprotein_in_syst\tgenes_count\tname_of_profiles_in_sys\r\n-df_test_prot_Dpd_171\tDpd\tDpd\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__QueE,Dpd__DpdE,Dpd__DpdF,Dpd__DpdG,Dpd__DpdH,Dpd__DpdI,Dpd__DpdJ,Dpd__DpdK,Dpd__DpdD,Dpd__QueC,Dpd__DpdB,Dpd__DpdA,Dpd__DpdC,Dpd__QueD,Dpd__FolE\r\n-df_test_prot_SspBCDE_200\tSspBCDE\tSspBCDE\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__SspF,SspBCDE__SspG,SspBCDE__SspH,SspBCDE__SspE,SspBCDE__SspD,SspBCDE__SspC,SspBCDE__SspB\r\n-df_test_prot_Dnd_ABCDEFGH_169\tDnd\tDnd_ABCDEFGH\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__DndE,Dnd__DndD,Dnd__DndC,Dnd__DndB,Dnd__DndA\r\n-df_test_prot_Zorya_TypeI_201\tZorya\tZorya_TypeI\tPSAE004.0722.00062.C001_04977\tPSAE004.0722.00062.C001_04980\tPSAE004.0722.00062.C001_04977,PSAE004.0722.00062.C001_04978,PSAE004.0722.00062.C001_04979,PSAE004.0722.00062.C001_04980\t4\tZorya_TypeI__ZorD,Zorya_TypeI__ZorC,Zorya__ZorB,Zorya__ZorA\r\n-df_test_prot_Dnd_ABCDE_168\tDnd\tDnd_ABCDE\tTHCU001.0722.00001.C001_00170\tTHCU001.0722.00001.C001_00174\tTHCU001.0722.00001.C001_00170,THCU001.0722.00001.C001_00171,THCU001.0722.00001.C001_00172,THCU001.0722.00001.C001_00173,THCU001.0722.00001.C001_00174\t5\tDnd__DndA,Dnd__DndB,Dnd__DndC,Dnd__DndD,Dnd__DndE\r\n-df_test_prot_Mokosh_Type_I_A_188\tMokosh\tMokosh_Type_I_A\tVIAL003.0722.00025.C001_02349\tVIAL003.0722.00025.C001_02350\tVIAL003.0722.00025.C001_02349,VIAL003.0722.00025.C001_02350\t2\tMokosh_type_I__MkoB_A,Mokosh_type_I__MkoA_A\r\n-df_test_prot_Mokosh_Type_I_E_192\tMokosh\tMokosh_Type_I_E\tNOSP054.0722.00001.C001_01954\tNOSP054.0722.00001.C001_01957\tNOSP054.0722.00001.C001_01954,NOSP054.0722.00001.C001_01957\t2\tMokosh_type_I__MkoA_E,Mokosh_type_I__MkoB_E\r\n-df_test_prot_Shango_199\tShango\tShango\tPSSP124.0722.00001.C001_03189\tPSSP124.0722.00001.C001_03191\tPSSP124.0722.00001.C001_03189,PSSP124.0722.00001.C001_03190,PSSP124.0722.00001.C001_03191\t3\tShango__SngA,Shango__SngB,Shango__SngC\r\n-df_test_prot_Mokosh_Type_I_B_189\tMokosh\tMokosh_Type_I_B\tALFR002.0722.00001.P002_00046\tALFR002.0722.00001.P002_00047\tALFR002.0722.00001.P002_00046,ALFR002.0722.00001.P002_00047\t2\tMokosh_type_I__MkoB_B,Mokosh_type_I__MkoA_B\r\n-df_test_prot_Mokosh_Type_I_C_190\tMokosh\tMokosh_Type_I_C\tPSAE004.0722.00242.C001_03385\tPSAE004.0722.00242.C001_03386\tPSAE004.0722.00242.C001_03385,PSAE004.0722.00242.C001_03386\t2\tMokosh_type_I__MkoA_C,Mokosh_type_I__MkoB_C\r\n-df_test_prot_Mokosh_TypeII_181\tMokosh\tMokosh_TypeII\tSAEN001.0722.00009.C001_04168\tSAEN001.0722.00009.C001_04168\tSAEN001.0722.00009.C001_04168\t1\tMokosh_TypeII__MkoC\r\n-df_test_prot_Detocs_REase_155\tDetocs\tDetocs_REase\tFLIN002.0722.00001.C001_01174\tFLIN002.0722.00001.C001_01176\tFLIN002.0722.00001.C001_01174,FLIN002.0722.00001.C001_01175,FLIN002.0722.00001.C001_01176\t3\tDetocs__dtcA,Detocs__dtcB,Detocs__dtcC_REase\r\n-df_test_prot_Hachiman_175\tHachiman\tHachiman\tENSP011.0722.00001.C001_03190\tENSP011.0722.00001.C001_03191\tENSP011.0722.00001.C001_03190,ENSP011.0722.00001.C001_03191\t2\tHachiman__HamA_1,Ha'..b'03\tENMU001.0722.00001.P004_00003\t1\tAbiH__AbiH\n+df_test_prot_AbiN_11\tAbiN\tAbiN\tDefense\tSTPS003.0722.00004.C001_02116\tSTPS003.0722.00004.C001_02116\tSTPS003.0722.00004.C001_02116\t1\tAbiN__AbiN\n+df_test_prot_Charlie_gp32_124\tCharlie_gp32\tCharlie_gp32\tDefense\tMYST001.0722.00001.C001_03552\tMYST001.0722.00001.C001_03552\tMYST001.0722.00001.C001_03552\t1\tCharlie_gp32__gp32\n+df_test_prot_Mok_Hok_Sok_180\tMok_Hok_Sok\tMok_Hok_Sok\tDefense\tCIAM001.0722.00007.P003_00063\tCIAM001.0722.00007.P003_00064\tCIAM001.0722.00007.P003_00063,CIAM001.0722.00007.P003_00064\t2\tMok_Hok_Sok__Hok,Mok_Hok_Sok__Mok\n+df_test_prot_Abi2_1\tAbi2\tAbi2\tDefense\tMESP082.0722.00001.C001_04745\tMESP082.0722.00001.C001_04745\tMESP082.0722.00001.C001_04745\t1\tAbi2__Abi_2\n+df_test_prot_Eleos_230\tEleos\tEleos\tDefense\tESCO001.0722.01243.C001_00310\tESCO001.0722.01243.C001_00312\tESCO001.0722.01243.C001_00310,ESCO001.0722.01243.C001_00311,ESCO001.0722.01243.C001_00312\t3\tEleos__LeoA2,Eleos__LeoB,Eleos__LeoC\n+df_test_prot_Retron_III_237\tRetron\tRetron_III\tDefense\tSHHA001.0722.00001.C001_00530\tSHHA001.0722.00001.C001_00534\tSHHA001.0722.00001.C001_00530,SHHA001.0722.00001.C001_00532,SHHA001.0722.00001.C001_00533,SHHA001.0722.00001.C001_00534\t4\tRetron_III__PRTase,Retron_III__PRTase_WH,Retron__RT_Tot,Retron__RT_Tot\n+df_test_prot_CARD_NLR_like_24\tCARD_NLR\tCARD_NLR_like\tDefense\tPSSP190.0722.00001.C001_03844\tPSSP190.0722.00001.C001_03848\tPSSP190.0722.00001.C001_03844,PSSP190.0722.00001.C001_03845,PSSP190.0722.00001.C001_03846,PSSP190.0722.00001.C001_03847,PSSP190.0722.00001.C001_03848\t5\tCARD_NLR__CARD_Protease_supposed,CARD_NLR__Endonuclease_new,CARD_NLR__NLR_new,CARD_NLR__Subtilase_small_new,CARD_NLR__Trypsin_new\n+df_test_prot_Lamassu-Amidase_40\tLamassu-Fam\tLamassu-Amidase\tDefense\tBOFL001.0722.00001.C001_04681\tBOFL001.0722.00001.C001_04682\tBOFL001.0722.00001.C001_04681,BOFL001.0722.00001.C001_04682\t2\tLamassu-Fam__LmuA_effector_Amidase,Lamassu-Fam__LmuB_SMC_Amidase\n+df_test_prot_BREX_208\tBREX\tBREX\tDefense\tMESU001.0722.00002.C001_00682\tMESU001.0722.00002.C001_00696\tMESU001.0722.00002.C001_00682,MESU001.0722.00002.C001_00683,MESU001.0722.00002.C001_00689,MESU001.0722.00002.C001_00690,MESU001.0722.00002.C001_00691,MESU001.0722.00002.C001_00692,MESU001.0722.00002.C001_00695,MESU001.0722.00002.C001_00696\t8\tBREX__brxA_DUF1819,BREX__brxB_DUF1788,BREX__brxC,BREX__brxD,BREX__brxHI,BREX__brxL,BREX__pglX1,BREX__pglZA\n+df_test_prot_BREX_III_212\tBREX\tBREX_III\tDefense\tRUBR001.0722.00001.C001_01109\tRUBR001.0722.00001.C001_01114\tRUBR001.0722.00001.C001_01109,RUBR001.0722.00001.C001_01110,RUBR001.0722.00001.C001_01111,RUBR001.0722.00001.C001_01113,RUBR001.0722.00001.C001_01114\t5\tBREX__brxC,BREX__brxF,BREX__brxHII,BREX__pglXI,BREX__pglZ3\n+df_test_prot_DRT7_83\tDRT\tDRT7\tDefense\tVIVU001.0722.00013.C001_00184\tVIVU001.0722.00013.C001_00184\tVIVU001.0722.00013.C001_00184\t1\tDRT7__DRT7\n+df_test_prot_Lamassu-Fam_44\tLamassu-Fam\tLamassu-Fam\tDefense\tSHHA001.0722.00001.C001_00539\tSHHA001.0722.00001.C001_00544\tSHHA001.0722.00001.C001_00539,SHHA001.0722.00001.C001_00540,SHHA001.0722.00001.C001_00541,SHHA001.0722.00001.C001_00542,SHHA001.0722.00001.C001_00544\t5\tLamassu-Fam__LmuA_effector_Hydrolase,Lamassu-Fam__LmuA_effector_Lipase,Lamassu-Fam__LmuA_effector_Protease,Lamassu-Fam__LmuB_SMC_Hydrolase_protease,Lamassu-Fam__LmuC_acc_hydrolase_protease\n+df_test_prot_pAgo_254\tpAgo\tpAgo\tDefense\tPSSA001.0722.00001.C001_01671\tPSSA001.0722.00001.C001_01673\tPSSA001.0722.00001.C001_01671,PSSA001.0722.00001.C001_01672,PSSA001.0722.00001.C001_01673\t3\tpAgo__GbbAgaS,pAgo__TIRAPAZ,pAgo__pAgo_SPARTA\n+df_test_prot_CAS_Class1-Subtype-IV-A_270\tCas\tCAS_Class1-Subtype-IV-A\tDefense\tRHFE001.0722.00001.P002_00104\tRHFE001.0722.00001.P002_00110\tRHFE001.0722.00001.P002_00104,RHFE001.0722.00001.P002_00105,RHFE001.0722.00001.P002_00106,RHFE001.0722.00001.P002_00107,RHFE001.0722.00001.P002_00108,RHFE001.0722.00001.P002_00109,RHFE001.0722.00001.P002_00110\t7\tcas1_I-E_1,cas6e_I_II_III_IV_V_VI_3,csf1gr8_IV-A_2,csf2gr7_IV-A_1,csf3gr5_IV-A_2,csf4_IV-A1_2,csf5gr6_IV-A_1\n' |
| b |
| diff -r 596fa7bf596f -r 4ff81ce331f9 test-data/outputs/prot/defense_finder_systems_with_antidefense.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs/prot/defense_finder_systems_with_antidefense.tsv Mon Jul 22 11:12:44 2024 +0000 |
| b |
| b'@@ -0,0 +1,238 @@\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,DEVU001.0722.000'..b'03\tENMU001.0722.00001.P004_00003\t1\tAbiH__AbiH\n+df_test_prot_AbiN_11\tAbiN\tAbiN\tDefense\tSTPS003.0722.00004.C001_02116\tSTPS003.0722.00004.C001_02116\tSTPS003.0722.00004.C001_02116\t1\tAbiN__AbiN\n+df_test_prot_Charlie_gp32_124\tCharlie_gp32\tCharlie_gp32\tDefense\tMYST001.0722.00001.C001_03552\tMYST001.0722.00001.C001_03552\tMYST001.0722.00001.C001_03552\t1\tCharlie_gp32__gp32\n+df_test_prot_Mok_Hok_Sok_180\tMok_Hok_Sok\tMok_Hok_Sok\tDefense\tCIAM001.0722.00007.P003_00063\tCIAM001.0722.00007.P003_00064\tCIAM001.0722.00007.P003_00063,CIAM001.0722.00007.P003_00064\t2\tMok_Hok_Sok__Hok,Mok_Hok_Sok__Mok\n+df_test_prot_Abi2_1\tAbi2\tAbi2\tDefense\tMESP082.0722.00001.C001_04745\tMESP082.0722.00001.C001_04745\tMESP082.0722.00001.C001_04745\t1\tAbi2__Abi_2\n+df_test_prot_Eleos_230\tEleos\tEleos\tDefense\tESCO001.0722.01243.C001_00310\tESCO001.0722.01243.C001_00312\tESCO001.0722.01243.C001_00310,ESCO001.0722.01243.C001_00311,ESCO001.0722.01243.C001_00312\t3\tEleos__LeoA2,Eleos__LeoB,Eleos__LeoC\n+df_test_prot_Retron_III_237\tRetron\tRetron_III\tDefense\tSHHA001.0722.00001.C001_00530\tSHHA001.0722.00001.C001_00534\tSHHA001.0722.00001.C001_00530,SHHA001.0722.00001.C001_00532,SHHA001.0722.00001.C001_00533,SHHA001.0722.00001.C001_00534\t4\tRetron_III__PRTase,Retron_III__PRTase_WH,Retron__RT_Tot,Retron__RT_Tot\n+df_test_prot_CARD_NLR_like_24\tCARD_NLR\tCARD_NLR_like\tDefense\tPSSP190.0722.00001.C001_03844\tPSSP190.0722.00001.C001_03848\tPSSP190.0722.00001.C001_03844,PSSP190.0722.00001.C001_03845,PSSP190.0722.00001.C001_03846,PSSP190.0722.00001.C001_03847,PSSP190.0722.00001.C001_03848\t5\tCARD_NLR__CARD_Protease_supposed,CARD_NLR__Endonuclease_new,CARD_NLR__NLR_new,CARD_NLR__Subtilase_small_new,CARD_NLR__Trypsin_new\n+df_test_prot_Lamassu-Amidase_40\tLamassu-Fam\tLamassu-Amidase\tDefense\tBOFL001.0722.00001.C001_04681\tBOFL001.0722.00001.C001_04682\tBOFL001.0722.00001.C001_04681,BOFL001.0722.00001.C001_04682\t2\tLamassu-Fam__LmuA_effector_Amidase,Lamassu-Fam__LmuB_SMC_Amidase\n+df_test_prot_BREX_208\tBREX\tBREX\tDefense\tMESU001.0722.00002.C001_00682\tMESU001.0722.00002.C001_00696\tMESU001.0722.00002.C001_00682,MESU001.0722.00002.C001_00683,MESU001.0722.00002.C001_00689,MESU001.0722.00002.C001_00690,MESU001.0722.00002.C001_00691,MESU001.0722.00002.C001_00692,MESU001.0722.00002.C001_00695,MESU001.0722.00002.C001_00696\t8\tBREX__brxA_DUF1819,BREX__brxB_DUF1788,BREX__brxC,BREX__brxD,BREX__brxHI,BREX__brxL,BREX__pglX1,BREX__pglZA\n+df_test_prot_BREX_III_212\tBREX\tBREX_III\tDefense\tRUBR001.0722.00001.C001_01109\tRUBR001.0722.00001.C001_01114\tRUBR001.0722.00001.C001_01109,RUBR001.0722.00001.C001_01110,RUBR001.0722.00001.C001_01111,RUBR001.0722.00001.C001_01113,RUBR001.0722.00001.C001_01114\t5\tBREX__brxC,BREX__brxF,BREX__brxHII,BREX__pglXI,BREX__pglZ3\n+df_test_prot_DRT7_83\tDRT\tDRT7\tDefense\tVIVU001.0722.00013.C001_00184\tVIVU001.0722.00013.C001_00184\tVIVU001.0722.00013.C001_00184\t1\tDRT7__DRT7\n+df_test_prot_Lamassu-Fam_44\tLamassu-Fam\tLamassu-Fam\tDefense\tSHHA001.0722.00001.C001_00539\tSHHA001.0722.00001.C001_00544\tSHHA001.0722.00001.C001_00539,SHHA001.0722.00001.C001_00540,SHHA001.0722.00001.C001_00541,SHHA001.0722.00001.C001_00542,SHHA001.0722.00001.C001_00544\t5\tLamassu-Fam__LmuA_effector_Hydrolase,Lamassu-Fam__LmuA_effector_Lipase,Lamassu-Fam__LmuA_effector_Protease,Lamassu-Fam__LmuB_SMC_Hydrolase_protease,Lamassu-Fam__LmuC_acc_hydrolase_protease\n+df_test_prot_pAgo_254\tpAgo\tpAgo\tDefense\tPSSA001.0722.00001.C001_01671\tPSSA001.0722.00001.C001_01673\tPSSA001.0722.00001.C001_01671,PSSA001.0722.00001.C001_01672,PSSA001.0722.00001.C001_01673\t3\tpAgo__GbbAgaS,pAgo__TIRAPAZ,pAgo__pAgo_SPARTA\n+df_test_prot_CAS_Class1-Subtype-IV-A_270\tCas\tCAS_Class1-Subtype-IV-A\tDefense\tRHFE001.0722.00001.P002_00104\tRHFE001.0722.00001.P002_00110\tRHFE001.0722.00001.P002_00104,RHFE001.0722.00001.P002_00105,RHFE001.0722.00001.P002_00106,RHFE001.0722.00001.P002_00107,RHFE001.0722.00001.P002_00108,RHFE001.0722.00001.P002_00109,RHFE001.0722.00001.P002_00110\t7\tcas1_I-E_1,cas6e_I_II_III_IV_V_VI_3,csf1gr8_IV-A_2,csf2gr7_IV-A_1,csf3gr5_IV-A_2,csf4_IV-A1_2,csf5gr6_IV-A_1\n' 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