ADD argNorm version number to tsv outputs

The current argNorm version number is now added to tsv outputs under the 'argNorm_version' column
BigDataBiology · Oct 8, 2024 · 2992163 · 2992163
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commit 2992163
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Showing 29 changed files with 12,909 additions and 12,907 deletions.
diff --git a/argnorm/normalizers.py b/argnorm/normalizers.py
@@ -6,6 +6,7 @@
 from .drug_categorization import confers_resistance_to, drugs_to_drug_classes
 from .lib import get_aro_mapping_table
 from .lib import MAPPING_TABLE_ARO_COL, TARGET_ARO_COL
+from .argnorm_version import __version__
 
 # Column headings for drug categorization output
 CONFERS_RESISTANCE_TO_COL = 'confers_resistance_to'
@@ -41,6 +42,7 @@ def run(self, input_file : str):
         original_annot[RESISTANCE_TO_DRUG_CLASSES_COL] = original_annot[TARGET_ARO_COL].map(
                 lambda a: ','.join(drugs_to_drug_classes(confers_resistance_to(a))),
                 na_action='ignore')
+        original_annot['argNorm_version'] = __version__
 
         return original_annot
 

diff --git a/outputs/hamronized/abricate.argannot.tsv b/outputs/hamronized/abricate.argannot.tsv
diff --git a/outputs/hamronized/abricate.megares.tsv b/outputs/hamronized/abricate.megares.tsv
diff --git a/outputs/hamronized/abricate.ncbi.tsv b/outputs/hamronized/abricate.ncbi.tsv
diff --git a/outputs/hamronized/abricate.resfinder.tsv b/outputs/hamronized/abricate.resfinder.tsv
diff --git a/outputs/hamronized/abricate.resfinderfg.tsv b/outputs/hamronized/abricate.resfinderfg.tsv
diff --git a/outputs/hamronized/amrfinderplus.ncbi.orfs.tsv b/outputs/hamronized/amrfinderplus.ncbi.orfs.tsv
diff --git a/outputs/hamronized/args-oap.sarg.reads.tsv b/outputs/hamronized/args-oap.sarg.reads.tsv
diff --git a/outputs/hamronized/deeparg.deeparg.orfs.tsv b/outputs/hamronized/deeparg.deeparg.orfs.tsv
diff --git a/outputs/hamronized/groot.argannot.tsv b/outputs/hamronized/groot.argannot.tsv
@@ -1,13 +1,13 @@
-input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity	ARO	confers_resistance_to	resistance_to_drug_classes
-groot.argannot.tsv	argannot~~~(Bla)cfiA9~~~AB087234:1-750	argannot~~~(Bla)cfiA9~~~AB087234:1-750	groot	v	argannot~~~(Bla)cfiA9~~~AB087234:1-750	groot	v	gene_presence_detected			79.0																750									ARO:3006921	ARO:0000020	ARO:3000007
-groot.argannot.tsv	argannot~~~(Tet)Tet-40~~~AM419751:14211-15431	argannot~~~(Tet)Tet-40~~~AM419751:14211-15431	groot	v	argannot~~~(Tet)Tet-40~~~AM419751:14211-15431	groot	v	gene_presence_detected			315.0																1221									ARO:3000567	ARO:0000051	ARO:3000050
-groot.argannot.tsv	argannot~~~(MLS)ErmF~~~M14730:241-1041	argannot~~~(MLS)ErmF~~~M14730:241-1041	groot	v	argannot~~~(MLS)ErmF~~~M14730:241-1041	groot	v	gene_presence_detected			321.0																801									ARO:3000498	ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867	ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026
-groot.argannot.tsv	argannot~~~(AGly)Aph7~~~GG774704:686456-687373	argannot~~~(AGly)Aph7~~~GG774704:686456-687373	groot	v	argannot~~~(AGly)Aph7~~~GG774704:686456-687373	groot	v	gene_presence_detected			254.0																918									ARO:3002655	ARO:3000214	ARO:0000016
-groot.argannot.tsv	argannot~~~(Bla)cfxA2~~~AF504910:1-966	argannot~~~(Bla)cfxA2~~~AF504910:1-966	groot	v	argannot~~~(Bla)cfxA2~~~AF504910:1-966	groot	v	gene_presence_detected			338.0																966									ARO:3003002	ARO:0000044	ARO:3000007
-groot.argannot.tsv	argannot~~~(MLS)ErmB~~~M11180:714-1451	argannot~~~(MLS)ErmB~~~M11180:714-1451	groot	v	argannot~~~(MLS)ErmB~~~M11180:714-1451	groot	v	gene_presence_detected			178.0																738									ARO:3000375	ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867	ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026
-groot.argannot.tsv	argannot~~~(Tet)TetQ~~~Z21523:362-2287	argannot~~~(Tet)TetQ~~~Z21523:362-2287	groot	v	argannot~~~(Tet)TetQ~~~Z21523:362-2287	groot	v	gene_presence_detected			539.0																1974									ARO:3000191	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050
-groot.argannot.tsv	argannot~~~(Bla)cfxA5~~~AY769934:28-993	argannot~~~(Bla)cfxA5~~~AY769934:28-993	groot	v	argannot~~~(Bla)cfxA5~~~AY769934:28-993	groot	v	gene_presence_detected			449.0																966									ARO:3003096	ARO:0000044	ARO:3000007
-groot.argannot.tsv	argannot~~~(Bla)OXA-347~~~JN086160:1583-2407	argannot~~~(Bla)OXA-347~~~JN086160:1583-2407	groot	v	argannot~~~(Bla)OXA-347~~~JN086160:1583-2407	groot	v	gene_presence_detected			191.0																825									ARO:3001777	ARO:0000056	ARO:3000007
-groot.argannot.tsv	argannot~~~(Tet)TetW~~~AJ222769:3687-5606	argannot~~~(Tet)TetW~~~AJ222769:3687-5606	groot	v	argannot~~~(Tet)TetW~~~AJ222769:3687-5606	groot	v	gene_presence_detected			203.0																1920									ARO:3000194	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050
-groot.argannot.tsv	argannot~~~(Tet)Tet-32~~~DQ647324:181-2100	argannot~~~(Tet)Tet-32~~~DQ647324:181-2100	groot	v	argannot~~~(Tet)Tet-32~~~DQ647324:181-2100	groot	v	gene_presence_detected			148.0																1920									ARO:3000196	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050
-groot.argannot.tsv	argannot~~~(Bla)cfxA4~~~AY769933:1-966	argannot~~~(Bla)cfxA4~~~AY769933:1-966	groot	v	argannot~~~(Bla)cfxA4~~~AY769933:1-966	groot	v	gene_presence_detected			450.0																966									ARO:3003005	ARO:0000044	ARO:3000007
+input_file_name	gene_symbol	gene_name	reference_database_name	reference_database_version	reference_accession	analysis_software_name	analysis_software_version	genetic_variation_type	antimicrobial_agent	coverage_percentage	coverage_depth	coverage_ratio	drug_class	input_gene_length	input_gene_start	input_gene_stop	input_protein_length	input_protein_start	input_protein_stop	input_sequence_id	nucleotide_mutation	nucleotide_mutation_interpretation	predicted_phenotype	predicted_phenotype_confidence_level	amino_acid_mutation	amino_acid_mutation_interpretation	reference_gene_length	reference_gene_start	reference_gene_stop	reference_protein_length	reference_protein_start	reference_protein_stop	resistance_mechanism	strand_orientation	sequence_identity	ARO	confers_resistance_to	resistance_to_drug_classes	argNorm_version
+groot.argannot.tsv	argannot~~~(Bla)cfiA9~~~AB087234:1-750	argannot~~~(Bla)cfiA9~~~AB087234:1-750	groot	v	argannot~~~(Bla)cfiA9~~~AB087234:1-750	groot	v	gene_presence_detected			79.0																750									ARO:3006921	ARO:0000020	ARO:3000007	0.6.0
+groot.argannot.tsv	argannot~~~(Tet)Tet-40~~~AM419751:14211-15431	argannot~~~(Tet)Tet-40~~~AM419751:14211-15431	groot	v	argannot~~~(Tet)Tet-40~~~AM419751:14211-15431	groot	v	gene_presence_detected			315.0																1221									ARO:3000567	ARO:0000051	ARO:3000050	0.6.0
+groot.argannot.tsv	argannot~~~(MLS)ErmF~~~M14730:241-1041	argannot~~~(MLS)ErmF~~~M14730:241-1041	groot	v	argannot~~~(MLS)ErmF~~~M14730:241-1041	groot	v	gene_presence_detected			321.0																801									ARO:3000498	ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867	ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026	0.6.0
+groot.argannot.tsv	argannot~~~(AGly)Aph7~~~GG774704:686456-687373	argannot~~~(AGly)Aph7~~~GG774704:686456-687373	groot	v	argannot~~~(AGly)Aph7~~~GG774704:686456-687373	groot	v	gene_presence_detected			254.0																918									ARO:3002655	ARO:3000214	ARO:0000016	0.6.0
+groot.argannot.tsv	argannot~~~(Bla)cfxA2~~~AF504910:1-966	argannot~~~(Bla)cfxA2~~~AF504910:1-966	groot	v	argannot~~~(Bla)cfxA2~~~AF504910:1-966	groot	v	gene_presence_detected			338.0																966									ARO:3003002	ARO:0000044	ARO:3000007	0.6.0
+groot.argannot.tsv	argannot~~~(MLS)ErmB~~~M11180:714-1451	argannot~~~(MLS)ErmB~~~M11180:714-1451	groot	v	argannot~~~(MLS)ErmB~~~M11180:714-1451	groot	v	gene_presence_detected			178.0																738									ARO:3000375	ARO:0000006,ARO:0000027,ARO:0000046,ARO:0000057,ARO:0000065,ARO:0000066,ARO:3000145,ARO:3000156,ARO:3000158,ARO:3000176,ARO:3000583,ARO:3000584,ARO:3000669,ARO:3000672,ARO:3000673,ARO:3000674,ARO:3000675,ARO:3000677,ARO:3000678,ARO:3000679,ARO:3000680,ARO:3000681,ARO:3000682,ARO:3000867	ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000000,ARO:0000017,ARO:0000017,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026,ARO:0000026	0.6.0
+groot.argannot.tsv	argannot~~~(Tet)TetQ~~~Z21523:362-2287	argannot~~~(Tet)TetQ~~~Z21523:362-2287	groot	v	argannot~~~(Tet)TetQ~~~Z21523:362-2287	groot	v	gene_presence_detected			539.0																1974									ARO:3000191	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	0.6.0
+groot.argannot.tsv	argannot~~~(Bla)cfxA5~~~AY769934:28-993	argannot~~~(Bla)cfxA5~~~AY769934:28-993	groot	v	argannot~~~(Bla)cfxA5~~~AY769934:28-993	groot	v	gene_presence_detected			449.0																966									ARO:3003096	ARO:0000044	ARO:3000007	0.6.0
+groot.argannot.tsv	argannot~~~(Bla)OXA-347~~~JN086160:1583-2407	argannot~~~(Bla)OXA-347~~~JN086160:1583-2407	groot	v	argannot~~~(Bla)OXA-347~~~JN086160:1583-2407	groot	v	gene_presence_detected			191.0																825									ARO:3001777	ARO:0000056	ARO:3000007	0.6.0
+groot.argannot.tsv	argannot~~~(Tet)TetW~~~AJ222769:3687-5606	argannot~~~(Tet)TetW~~~AJ222769:3687-5606	groot	v	argannot~~~(Tet)TetW~~~AJ222769:3687-5606	groot	v	gene_presence_detected			203.0																1920									ARO:3000194	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	0.6.0
+groot.argannot.tsv	argannot~~~(Tet)Tet-32~~~DQ647324:181-2100	argannot~~~(Tet)Tet-32~~~DQ647324:181-2100	groot	v	argannot~~~(Tet)Tet-32~~~DQ647324:181-2100	groot	v	gene_presence_detected			148.0																1920									ARO:3000196	ARO:0000051,ARO:0000069,ARO:3000152,ARO:3000528,ARO:3000667,ARO:3000668	ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050,ARO:3000050	0.6.0
+groot.argannot.tsv	argannot~~~(Bla)cfxA4~~~AY769933:1-966	argannot~~~(Bla)cfxA4~~~AY769933:1-966	groot	v	argannot~~~(Bla)cfxA4~~~AY769933:1-966	groot	v	gene_presence_detected			450.0																966									ARO:3003005	ARO:0000044	ARO:3000007	0.6.0