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Update figures for argnorm v0.7.0 #5

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Update figures for argnorm v0.7.0 #5

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c347984
ENH mention which statistic is being quoted within print statements i…
Vedanth-Ramji Mar 5, 2025
7ea52eb
Update readme with drug category information for new databases for la…
Vedanth-Ramji Mar 5, 2025
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10 changes: 5 additions & 5 deletions benchmark.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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 = {}
Expand All @@ -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 = {}
Expand All @@ -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 = {}
Expand All @@ -52,4 +52,4 @@ def get_num_unique_args():

return output

print(get_num_unique_args())
print(f'Num unique AROs: {get_num_unique_args()}\n')
97 changes: 48 additions & 49 deletions readme.md
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Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -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 |
Expand All @@ -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 |
Expand All @@ -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 |
Expand All @@ -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

Expand All @@ -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

Expand Down Expand Up @@ -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