From 026d42fb81655cd966a054deef14e2c87a2577e5 Mon Sep 17 00:00:00 2001 From: Amine Ghozlane Date: Tue, 19 Nov 2024 19:20:07 +0100 Subject: [PATCH] Activate resfinder and resfinderfg annotation --- meteor/merging.py | 4 +++ meteor/profiler.py | 20 ++++++++++++--- .../sample1_resfinder_as_genes_sum.tsv.xz | Bin 0 -> 192 bytes .../sample1_resfinder_as_msp_sum.tsv.xz | Bin 0 -> 172 bytes .../sample1_resfinderfg_as_genes_sum.tsv.xz | Bin 0 -> 192 bytes .../sample1_resfinderfg_as_msp_sum.tsv.xz | Bin 0 -> 172 bytes .../sample2_resfinder_as_genes_sum.tsv.xz | Bin 0 -> 188 bytes .../sample2_resfinder_as_msp_sum.tsv.xz | Bin 0 -> 172 bytes .../sample2_resfinderfg_as_genes_sum.tsv.xz | Bin 0 -> 188 bytes .../sample2_resfinderfg_as_msp_sum.tsv.xz | Bin 0 -> 172 bytes .../sample3_resfinder_as_genes_sum.tsv.xz | Bin 0 -> 184 bytes .../sample3_resfinder_as_msp_sum.tsv.xz | Bin 0 -> 172 bytes .../sample3_resfinderfg_as_genes_sum.tsv.xz | Bin 0 -> 184 bytes .../sample3_resfinderfg_as_msp_sum.tsv | 24 ++++++++++++++++++ .../sample3_resfinderfg_as_msp_sum.tsv.xz | Bin 0 -> 172 bytes .../catalogue/catalogue_reference.json | 8 ++++++ .../database/catalogue_resfinder.tsv | 4 +++ .../database/catalogue_resfinderfg.tsv | 4 +++ 18 files changed, 61 insertions(+), 3 deletions(-) create mode 100644 meteor/tests/test_merging/profiles/sample1/sample1_resfinder_as_genes_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample1/sample1_resfinder_as_msp_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample1/sample1_resfinderfg_as_genes_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample1/sample1_resfinderfg_as_msp_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample2/sample2_resfinder_as_genes_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample2/sample2_resfinder_as_msp_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample2/sample2_resfinderfg_as_genes_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample2/sample2_resfinderfg_as_msp_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample3/sample3_resfinder_as_genes_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample3/sample3_resfinder_as_msp_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample3/sample3_resfinderfg_as_genes_sum.tsv.xz create mode 100644 meteor/tests/test_merging/profiles/sample3/sample3_resfinderfg_as_msp_sum.tsv create mode 100644 meteor/tests/test_merging/profiles/sample3/sample3_resfinderfg_as_msp_sum.tsv.xz create mode 100644 meteor/tests/test_profiler/catalogue/database/catalogue_resfinder.tsv create mode 100644 meteor/tests/test_profiler/catalogue/database/catalogue_resfinderfg.tsv diff --git a/meteor/merging.py b/meteor/merging.py index d5b1b05..49dad93 100644 --- a/meteor/merging.py +++ b/meteor/merging.py @@ -319,7 +319,11 @@ def execute(self) -> None: "modules_completeness": ["msp_name", "mod_id"], "modules": ["mod_id"], "mustard_as_genes_sum": ["annotation"], + "resfinder_as_genes_sum": ["annotation"], + "resfinderfg_as_genes_sum": ["annotation"], "mustard_as_msp_sum": ["annotation"], + "resfinder_as_msp_sum": ["annotation"], + "resfinderfg_as_msp_sum": ["annotation"], "dbcan_as_genes_sum": ["annotation"], "dbcan_as_msp_sum": ["annotation"], "kegg_as_genes_sum": ["annotation"], diff --git a/meteor/profiler.py b/meteor/profiler.py index 01a89f5..0d8d0bb 100644 --- a/meteor/profiler.py +++ b/meteor/profiler.py @@ -155,7 +155,15 @@ def __post_init__(self): # Get functional db filenames if self.database_type == "complete": self.db_filenames = {} - for db in ["kegg", "mustard", "dbcan", "eggnog", "tigrfam"]: + for db in [ + "kegg", + "mustard", + "dbcan", + "eggnog", + "tigrfam", + "resfinder", + "resfinderfg", + ]: self.db_filenames[db] = ( self.meteor.ref_dir / self.ref_config["reference_file"]["database_dir"] @@ -646,8 +654,14 @@ def execute(self) -> None: ) # Part 3: FUNCTIONAL PROFILING if self.database_type == "complete": - single_fun_db = ["mustard", "kegg", "dbcan"] - single_fun_by_msp_db = ["mustard", "kegg", "dbcan"] + single_fun_db = ["mustard", "kegg", "dbcan", "resfinder", "resfinderfg"] + single_fun_by_msp_db = [ + "mustard", + "kegg", + "dbcan", + "resfinder", + "resfinderfg", + ] for db, db_filename in self.db_filenames.items(): # By sum of genes if db in single_fun_db: diff --git a/meteor/tests/test_merging/profiles/sample1/sample1_resfinder_as_genes_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample1/sample1_resfinder_as_genes_sum.tsv.xz new file mode 100644 index 0000000000000000000000000000000000000000..63a66de9f6531868a1b8fd63f25642bd8099f88d GIT binary patch literal 192 zcmV;x06+izH+ooF000E$*0e?f03iVu0001VFXf})0GvnftloEY$6yVnn$bxU zvO3ulylvx6=+o{R*e&FPgJ>4S*S*riGJ)fe6d^%!$SfsTtUW+n&7*~DkfQ3 literal 0 HcmV?d00001 diff --git a/meteor/tests/test_merging/profiles/sample1/sample1_resfinder_as_msp_sum.tsv.xz 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b/meteor/tests/test_merging/profiles/sample1/sample1_resfinderfg_as_msp_sum.tsv.xz new file mode 100644 index 0000000000000000000000000000000000000000..218f164e31c8c94fcfbf1cbf5e17c8d6d4af19bd GIT binary patch literal 172 zcmV;d08{_{H+ooF000E$*0e?f03iVu0001VFXf})0H*+JT>vnftloEY$6yVnn$bxU zvO3ulxb<3SHC%3HMX5s04@o98X0CSZOG(L9i_`GYhOA{pO{ww a0fzyo0RRBdf}M1+#Ao{g000001X)_k$41Ej literal 0 HcmV?d00001 diff --git a/meteor/tests/test_merging/profiles/sample2/sample2_resfinder_as_genes_sum.tsv.xz b/meteor/tests/test_merging/profiles/sample2/sample2_resfinder_as_genes_sum.tsv.xz new file mode 100644 index 0000000000000000000000000000000000000000..2155eeec9b053061353cce5182561fba8e1a99d0 GIT binary patch literal 188 zcmV;t07L)%H+ooF000E$*0e?f03iVu0001VFXf})0G$APT>vnftloEY$6yVnn$bxU zvO3ulylvx6=+o{XetD(y*4d$8*G5z8#}i^ROnx>(9KYc?>V1lLs(<9L@=O2uQyzb8 z^vcmR5VTNh3Csv~uDZ32>D{?*>(;*usKJ{`Z{%1dfXY#YzfUS=5iPIB7uE5?gvM9Y qnAiva00008#6XbcF$uW<0ha-u0RR9tCkvvn#Ao{g000001X)@$yHvjb literal 0 HcmV?d00001 diff 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fde2aeb..5c97c91 100644 --- a/meteor/tests/test_profiler/catalogue/catalogue_reference.json +++ b/meteor/tests/test_profiler/catalogue/catalogue_reference.json @@ -30,6 +30,14 @@ "tigrfam": { "filename": "catalogue_tigrfam.tsv", "version": "15.0" + }, + "resfinder": { + "filename": "catalogue_resfinder.tsv", + "version": "2.4.0" + }, + "resfinderfg": { + "filename": "catalogue_resfinderfg.tsv", + "version": "2.0" } } } \ No newline at end of file diff --git a/meteor/tests/test_profiler/catalogue/database/catalogue_resfinder.tsv b/meteor/tests/test_profiler/catalogue/database/catalogue_resfinder.tsv new file mode 100644 index 0000000..6a8c003 --- /dev/null +++ b/meteor/tests/test_profiler/catalogue/database/catalogue_resfinder.tsv @@ -0,0 +1,4 @@ +gene_id gene_name annotation +3 gene_3 ARD1 +4 gene_4 ARD2 +8 gene_8 ARD2 diff --git a/meteor/tests/test_profiler/catalogue/database/catalogue_resfinderfg.tsv b/meteor/tests/test_profiler/catalogue/database/catalogue_resfinderfg.tsv new file mode 100644 index 0000000..6a8c003 --- /dev/null +++ b/meteor/tests/test_profiler/catalogue/database/catalogue_resfinderfg.tsv @@ -0,0 +1,4 @@ +gene_id gene_name annotation +3 gene_3 ARD1 +4 gene_4 ARD2 +8 gene_8 ARD2