Mercurial > repos > greg > draw_amr_matrix
comparison draw_amr_matrix.py @ 12:aa2b737102dc draft
Uploaded
| author | greg |
|---|---|
| date | Mon, 27 Mar 2023 22:14:56 +0000 |
| parents | da1c9c1be421 |
| children | b1a7e04e6371 |
comparison
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| 11:da1c9c1be421 | 12:aa2b737102dc |
|---|---|
| 190 for deletion_idx, deleted_gene in amr_deletions.iterrows(): | 190 for deletion_idx, deleted_gene in amr_deletions.iterrows(): |
| 191 amr_to_draw = amr_to_draw.append(pandas.Series(['\u0394' + deleted_gene[3], deleted_gene[5]], name=amr_to_draw.shape[0], index=amr_to_draw.columns)) | 191 amr_to_draw = amr_to_draw.append(pandas.Series(['\u0394' + deleted_gene[3], deleted_gene[5]], name=amr_to_draw.shape[0], index=amr_to_draw.columns)) |
| 192 ofh.write("\nAfter processing deletions, amr_to_draw: %s\n" % str(amr_to_draw)) | 192 ofh.write("\nAfter processing deletions, amr_to_draw: %s\n" % str(amr_to_draw)) |
| 193 | 193 |
| 194 ofh.write("\namr_to_draw.shape[0]: %s\n" % str(amr_to_draw.shape[0])) | 194 ofh.write("\namr_to_draw.shape[0]: %s\n" % str(amr_to_draw.shape[0])) |
| 195 if amr_to_draw.shape[0] > 0: | 195 if amr_to_draw.shape[0] > 1: |
| 196 ofh.write("\nDrawing AMR matrix...\n") | 196 ofh.write("\nDrawing AMR matrix...\n") |
| 197 present_genes = amr_to_draw['gene'].unique() | 197 present_genes = amr_to_draw['gene'].unique() |
| 198 present_drugs = amr_to_draw['drug'].unique() | 198 present_drugs = amr_to_draw['drug'].unique() |
| 199 amr_matrix = pandas.DataFrame(0, index=present_genes, columns=present_drugs) | 199 amr_matrix = pandas.DataFrame(0, index=present_genes, columns=present_drugs) |
| 200 for hit_idx, hit in amr_to_draw.iterrows(): | 200 for hit_idx, hit in amr_to_draw.iterrows(): |