Mercurial > repos > iuc > hyphy_fade
comparison scripts/hyphy_summary.py @ 28:7ae1a772f08e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9fa2234b56facaf70fce12e5c60638d801997594"
| author | iuc |
|---|---|
| date | Fri, 18 Jun 2021 15:25:05 +0000 |
| parents | 60eec78ee26f |
| children | fccaa7ba05fd |
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| 27:d71d20c0ac09 | 28:7ae1a772f08e |
|---|---|
| 334 if len(self.include_in_annotation): | 334 if len(self.include_in_annotation): |
| 335 for i in self.include_in_annotation: | 335 for i in self.include_in_annotation: |
| 336 report = self.annotation_json[self.include_in_annotation[i]] | 336 report = self.annotation_json[self.include_in_annotation[i]] |
| 337 report['fade'] = {} | 337 report['fade'] = {} |
| 338 for residue, info in self.fade['MLE']['content'].items(): | 338 for residue, info in self.fade['MLE']['content'].items(): |
| 339 # Skip anything past the end of this section. | |
| 340 if i >= len(info['0']): | |
| 341 continue | |
| 339 if len(residue) == 1: | 342 if len(residue) == 1: |
| 340 report['fade'][residue] = {'rate': info['0'][i][1], 'BF': info['0'][i][-1]} | 343 report['fade'][residue] = {'rate': info['0'][i][1], 'BF': info['0'][i][-1]} |
| 341 | 344 |
| 342 def bgm_summary(self): | 345 def bgm_summary(self): |
| 343 self.bgm = self._load_json(self.arguments.bgm) | 346 self.bgm = self._load_json(self.arguments.bgm) |
| 371 if len(listified_input) == 1: | 374 if len(listified_input) == 1: |
| 372 self.aligned_str = listified_input[0] | 375 self.aligned_str = listified_input[0] |
| 373 | 376 |
| 374 def ignore_record(x): | 377 def ignore_record(x): |
| 375 pass | 378 pass |
| 379 | |
| 376 for s in self.ref_genes: | 380 for s in self.ref_genes: |
| 377 _align_par(SeqRecord(Seq(s[1]), id=s[0]), [SeqRecord(Seq(ref_seq), id='ref')], | 381 _align_par(SeqRecord(Seq(s[1]), id=s[0]), [SeqRecord(Seq(ref_seq), id='ref')], |
| 378 self.score_matrix_, False, False, 0.8, ignore_record, output_record) | 382 self.score_matrix_, False, False, 0.8, ignore_record, output_record) |
| 379 if (self.aligned_str is not None): | 383 if (self.aligned_str is not None): |
| 380 break | 384 break |
| 385 | |
| 381 self.ref_map = self.aligned_str.seq.strip('-') | 386 self.ref_map = self.aligned_str.seq.strip('-') |
| 382 c = 0 | 387 c = 0 |
| 383 i = 0 | 388 i = 0 |
| 384 map_to_genome = [] | 389 map_to_genome = [] |
| 385 while i < len(self.ref_map): | 390 while i < len(self.ref_map): |