Mercurial > repos > iuc > virhunter
comparison predict.py @ 3:302332b914ef draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 58587e05f604590c70550e13fc51b7425e916ed4
| author | iuc |
|---|---|
| date | Sat, 14 Jan 2023 21:08:33 +0000 |
| parents | ea2cccb9f73e |
| children |
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| 2:ea2cccb9f73e | 3:302332b914ef |
|---|---|
| 151 ds_path=ts, | 151 ds_path=ts, |
| 152 nn_weights_path=weights, | 152 nn_weights_path=weights, |
| 153 length=l_, | 153 length=l_, |
| 154 use_10=use_10 | 154 use_10=use_10 |
| 155 ) | 155 ) |
| 156 print(df) | |
| 157 df = predict_rf( | 156 df = predict_rf( |
| 158 df=df, | 157 df=df, |
| 159 rf_weights_path=weights, | 158 rf_weights_path=weights, |
| 160 length=l_, | 159 length=l_, |
| 161 use_10=use_10 | 160 use_10=use_10 |
| 166 dfs_cont.append(df) | 165 dfs_cont.append(df) |
| 167 # print('prediction finished') | 166 # print('prediction finished') |
| 168 df_500 = dfs_fr[0][(dfs_fr[0]['length'] >= limit) & (dfs_fr[0]['length'] < 1500)] | 167 df_500 = dfs_fr[0][(dfs_fr[0]['length'] >= limit) & (dfs_fr[0]['length'] < 1500)] |
| 169 df_1000 = dfs_fr[1][(dfs_fr[1]['length'] >= 1500)] | 168 df_1000 = dfs_fr[1][(dfs_fr[1]['length'] >= 1500)] |
| 170 df = pd.concat([df_1000, df_500], ignore_index=True) | 169 df = pd.concat([df_1000, df_500], ignore_index=True) |
| 171 pred_fr = Path(out_path, 'predicted_fragments.csv') | 170 pred_fr = Path(out_path, 'predicted_fragments.tsv') |
| 172 df.to_csv(pred_fr) | 171 df.to_csv(pred_fr, sep='\t') |
| 173 | 172 |
| 174 df_500 = dfs_cont[0][(dfs_cont[0]['length'] >= limit) & (dfs_cont[0]['length'] < 1500)] | 173 df_500 = dfs_cont[0][(dfs_cont[0]['length'] >= limit) & (dfs_cont[0]['length'] < 1500)] |
| 175 df_1000 = dfs_cont[1][(dfs_cont[1]['length'] >= 1500)] | 174 df_1000 = dfs_cont[1][(dfs_cont[1]['length'] >= 1500)] |
| 176 df = pd.concat([df_1000, df_500], ignore_index=True) | 175 df = pd.concat([df_1000, df_500], ignore_index=True) |
| 177 pred_contigs = Path(out_path, 'predicted.csv') | 176 pred_contigs = Path(out_path, 'predicted.tsv') |
| 178 df.to_csv(pred_contigs) | 177 df.to_csv(pred_contigs, sep='\t') |
| 179 | 178 |
| 180 if return_viral: | 179 if return_viral: |
| 181 viral_ids = list(df[df["decision"] == "virus"]["id"]) | 180 viral_ids = list(df[df["decision"] == "virus"]["id"]) |
| 182 seqs_ = list(SeqIO.parse(ts, "fasta")) | 181 seqs_ = list(SeqIO.parse(ts, "fasta")) |
| 183 viral_seqs = [s_ for s_ in seqs_ if s_.id in viral_ids] | 182 viral_seqs = [s_ for s_ in seqs_ if s_.id in viral_ids] |