Use pandas in the post treatment #59
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jeanrjc
reviewed
Apr 9, 2024
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Still need to change the tests files (and to check if everything is the same) |
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Add pandas requirements |
… into posttreat_pandas
… into posttreat_pandas
… into posttreat_pandas
jeanrjc
approved these changes
Apr 24, 2024
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| def export_defense_finder_systems(defense_finder_genes, outdir, filename): | ||
| systems = build_defense_finder_systems(defense_finder_genes) | ||
| systems_list = systems_to_list(systems) | ||
| write_defense_finder_systems(systems_list, outdir, filename) | ||
| systems.to_csv(outdir+'/'+filename+'_defense_finder_systems.tsv',sep='\t',index=False) |
| return [ 'sys_id', 'type', 'subtype', 'sys_beg', 'sys_end', 'protein_in_syst', 'genes_count', 'name_of_profiles_in_sys' ] | ||
| sys_beg=defense_finder_genes.sort_values('hit_pos').drop_duplicates('sys_id').rename({'hit_id' : 'sys_beg'},axis=1)[['sys_id','sys_beg']] | ||
| sys_end=defense_finder_genes.sort_values('hit_pos' , ascending=False).drop_duplicates('sys_id').rename({'hit_id' : 'sys_end'},axis=1)[['sys_id','sys_end']] | ||
| protein_in_syst=defense_finder_genes.groupby('sys_id').hit_id.apply(lambda x: ",".join(x.sort_values())).reset_index().rename({'hit_id':'protein_in_syst'},axis=1) |
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simplify to get sys_beg and sys_end from protein in syst
defense_finder_posttreat/df_genes.py
Outdated
| from defense_finder_posttreat import best_solution | ||
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| def export_defense_finder_genes(defense_finder_genes, outdir, filename): | ||
| defense_finder_genes_list = defense_finder_genes_to_list(defense_finder_genes) | ||
| write_defense_finder_genes(defense_finder_genes_list, outdir, filename) | ||
| defense_finder_genes.to_csv(outdir+'/'+filename+'_defense_finder_genes.tsv',sep='\t',index=False) |
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This PR has been inactive for 60 days and is now marked as stale. It will be closed in 7 days without further activity. We might have missed your issue, if you still have it, don't hesitate to comment again. |
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This could be merged @FlorianTesson ? |
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Close in favor to PR #64 |
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