| Previous changeset 19:e2942cd87117 (2021-06-09) Next changeset 21:b3b775a4ae1f (2021-07-03) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9fa2234b56facaf70fce12e5c60638d801997594" |
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modified:
scripts/hyphy_summary.py |
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| diff -r e2942cd87117 -r d8092fd69175 scripts/hyphy_summary.py --- a/scripts/hyphy_summary.py Wed Jun 09 17:36:22 2021 +0000 +++ b/scripts/hyphy_summary.py Fri Jun 18 15:29:34 2021 +0000 |
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| @@ -336,6 +336,9 @@ report = self.annotation_json[self.include_in_annotation[i]] report['fade'] = {} for residue, info in self.fade['MLE']['content'].items(): + # Skip anything past the end of this section. + if i >= len(info['0']): + continue if len(residue) == 1: report['fade'][residue] = {'rate': info['0'][i][1], 'BF': info['0'][i][-1]} @@ -373,11 +376,13 @@ def ignore_record(x): pass + for s in self.ref_genes: _align_par(SeqRecord(Seq(s[1]), id=s[0]), [SeqRecord(Seq(ref_seq), id='ref')], self.score_matrix_, False, False, 0.8, ignore_record, output_record) if (self.aligned_str is not None): break + self.ref_map = self.aligned_str.seq.strip('-') c = 0 i = 0 |