From c3479848fef6d0871fbcae9a7468b60610fecc32 Mon Sep 17 00:00:00 2001 From: Vedanth Date: Wed, 5 Mar 2025 19:42:47 +0530 Subject: [PATCH 1/2] ENH mention which statistic is being quoted within print statements in benchmark.py --- benchmark.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/benchmark.py b/benchmark.py index 670677b..f28f99b 100644 --- a/benchmark.py +++ b/benchmark.py @@ -15,7 +15,7 @@ def count_num_args(): return output -print(count_num_args()) +print(f'Tot num of ARGs: {count_num_args()}\n') def get_num_manual_curation(): output = {} @@ -26,7 +26,7 @@ def get_num_manual_curation(): return output -print(get_num_manual_curation()) +print(f'Num manual curation: {get_num_manual_curation()}\n') def get_num_unmapped_args(): output = {} @@ -35,11 +35,11 @@ def get_num_unmapped_args(): mapping_table = get_aro_mapping_table(db) count = mapping_table['ARO'].isnull().sum() - output.update({db: count}) + output.update({db: int(count)}) return output -print(get_num_manual_curation()) +print(f'Num unmapped ARGs: {get_num_unmapped_args()}\n') def get_num_unique_args(): output = {} @@ -52,4 +52,4 @@ def get_num_unique_args(): return output -print(get_num_unique_args()) \ No newline at end of file +print(f'Num unique AROs: {get_num_unique_args()}\n') \ No newline at end of file From 7ea52ebd66592cfcdb2f59aa12ca6928471de290 Mon Sep 17 00:00:00 2001 From: Vedanth Date: Wed, 5 Mar 2025 19:42:55 +0530 Subject: [PATCH 2/2] Update readme with drug category information for new databases for latest argNorm (v0.7.0) --- readme.md | 97 +++++++++++++++++++++++++++---------------------------- 1 file changed, 48 insertions(+), 49 deletions(-) diff --git a/readme.md b/readme.md index e270a95..9020315 100644 --- a/readme.md +++ b/readme.md @@ -3,10 +3,10 @@ ## ARO | | Counts | |:-------------------|---------:| -| Total descendants | 602 | -| Direct descendants | 61 | -| Intermediate nodes | 33 | -| Leaves | 508 | +| Total descendants | 658 | +| Direct descendants | 62 | +| Intermediate nodes | 41 | +| Leaves | 555 | ## Other databases ### ARG-ANNOT @@ -83,7 +83,7 @@ Number of unique antibiotic classes: 32 | fluoroquinolones | 319 | | tetracyclines | 301 | | glycopeptides | 300 | -| mls | 297 | +| mls | 290 | | drug_and_biocide_resistance | 189 | | phenicol | 150 | | trimethoprim | 147 | @@ -103,10 +103,10 @@ Number of unique antibiotic classes: 32 | drug_and_biocide_and_metal_resistance | 6 | | mupirocin | 5 | | multi-metal_resistance | 5 | -| oxazolidinone | 4 | +| oxazolidinone | 3 | | phenolic_compound_resistance | 4 | | mercury_resistance | 4 | -| pleuromutilin | 4 | +| pleuromutilin | 3 | | thiopeptides | 2 | | tellurium_resistance | 2 | | spiropyrimidinetriones | 1 | @@ -121,68 +121,67 @@ Number of unique antibiotic classes: 37 ### NCBI | Original ID | count | |:---------------------------------------------------------------|--------:| -| beta-lactam | 4579 | -| | 1026 | -| aminoglycoside | 695 | -| tetracycline | 241 | -| glycopeptide | 236 | -| quinolone | 139 | -| phenicol | 131 | -| trimethoprim | 127 | -| colistin | 116 | -| stx2 | 113 | +| beta-lactam | 5020 | +| aminoglycoside | 698 | +| tetracycline | 242 | +| glycopeptide | 237 | +| quinolone | 145 | +| phenicol | 132 | +| trimethoprim | 131 | +| colistin | 118 | +| stx2 | 229 | | macrolide | 81 | | lincosamide/macrolide/streptogramin | 80 | -| efflux | 71 | -| fosfomycin | 64 | +| efflux | 76 | +| fosfomycin | 65 | | arsenic | 52 | | mercury | 48 | -| phenicol/quinolone | 43 | +| phenicol/quinolone | 44 | | intimin | 43 | | sulfonamide | 41 | | quaternary_ammonium | 40 | -| lincosamide | 37 | +| lincosamide | 39 | +| stx1 | 33 | | copper | 26 | | rifamycin | 21 | -| stx1 | 20 | | streptogramin | 19 | | lincosamide/macrolide | 17 | | streptothricin | 14 | | macrolide/streptogramin | 13 | | nickel | 12 | -| nitroimidazole | 10 | -| aminoglycoside/quinolone | 10 | | lincosamide/streptogramin | 10 | +| aminoglycoside/quinolone | 10 | | bleomycin | 10 | +| nitroimidazole | 10 | | phenicol/lincosamide/oxazolidinone/pleuromutilin/streptogramin | 9 | +| lincosamide/pleuromutilin/streptogramin | 9 | | tellurium | 9 | | copper/silver | 8 | | cadmium | 7 | -| lincosamide/pleuromutilin/streptogramin | 7 | | fusidic_acid | 7 | | phenicol/oxazolidinone | 4 | | pleuromutilin | 4 | | mupirocin | 3 | | bacitracin | 3 | -| copper/nickel | 2 | | thiostrepton | 2 | -| chromate | 2 | +| copper/nickel | 2 | | cadmium/cobalt/nickel | 2 | -| ionophore | 2 | | silver | 2 | +| ionophore | 2 | +| fluoroquinolone | 2 | | tuberactinomycin | 2 | -| macrolide/phenicol | 1 | -| cadmium/lead/zinc | 1 | -| tetracenomycin | 1 | -| fluoroquinolone | 1 | +| chromate | 2 | +| aminoglycoside/phenicol | 1 | | lincosamide/pleuromutilin | 1 | | avilamycin | 1 | -| gold | 1 | | copper/gold | 1 | -| aminoglycoside/phenicol | 1 | +| gold | 1 | | fluoride | 1 | +| macrolide/phenicol | 1 | +| cadmium/lead/zinc | 1 | +| tetracenomycin | 1 | -Number of unique antibiotic classes: 60 +Number of unique antibiotic classes: 59 ### SARG | Type | count | @@ -208,15 +207,15 @@ Number of unique antibiotic classes: 60 | fusidic_acid | 10 | | tetracenomycin_C | 8 | | streptothricin | 7 | -| pleuromutilin_tiamulin | 5 | | defensin | 5 | +| pleuromutilin_tiamulin | 5 | | tunicamycin | 4 | | puromycin | 3 | | mupirocin | 3 | | antibacterial_fatty_acid | 2 | +| edeine | 1 | | bicyclomycin | 1 | | factumycin | 1 | -| edeine | 1 | Number of unique antibiotic classes: 30 @@ -235,26 +234,26 @@ Number of unique antibiotic classes: 30 | Amphenicol | 41 | | Macrolide | 39 | | Oxazolidinone, Amphenicol | 20 | -| Nitroimidazole | 14 | | Streptogramin A | 14 | +| Nitroimidazole | 14 | | Lincosamide, Streptogramin A, Pleuromutilin | 13 | | Lincosamide | 12 | | Rifamycin | 10 | -| Oxazolidinone, Amphenicol, Lincosamide, Streptogramin A, Pleuromutilin | 7 | | Macrolide, Streptogramin B | 7 | +| Oxazolidinone, Amphenicol, Lincosamide, Streptogramin A, Pleuromutilin | 7 | +| Pseudomonic acid | 3 | | Aminoglycoside, Quinolone | 3 | | Steroid antibacterial | 3 | -| Pseudomonic acid | 3 | | Lincosamide, Streptogramin A | 3 | | Amphenicol, Oxazolidinone, Tetracycline | 2 | -| Streptogramin B | 2 | | Amphenicol, Quinolone, Folate pathway antagonist | 2 | | Ionophores | 2 | -| Pleuromutilin | 1 | +| Streptogramin B | 2 | +| Macrolide, Lincosamide | 1 | | Macrolide, Tetracycline | 1 | -| Streptogramin A, Streptogramin B | 1 | | Macrolide, Lincosamide, Streptogramin A, Streptogramin B, Tetracycline | 1 | -| Macrolide, Lincosamide | 1 | +| Streptogramin A, Streptogramin B | 1 | +| Pleuromutilin | 1 | Number of unique antibiotic classes: 32 @@ -283,25 +282,25 @@ Number of unique antibiotic classes: 32 | FEP | 33 | | CST | 21 | | SPT | 12 | -| OXY | 11 | | MIN | 11 | -| bLac | 9 | +| OXY | 11 | | CDR | 9 | +| bLac | 9 | | SIS | 9 | | ERY | 8 | | CEF | 6 | -| AZM | 5 | | SMZ | 5 | +| AZM | 5 | +| SDX | 4 | | TET/AMP | 4 | | STX | 4 | -| SDX | 4 | | MEM | 3 | | STG | 2 | | AMK | 2 | | TYL | 1 | +| TZB | 1 | | CIP | 1 | | APR | 1 | | STR | 1 | -| TZB | 1 | Number of unique antibiotic classes: 42 \ No newline at end of file