# HG changeset patch # User iuc # Date 1624030223 0 # Node ID b8a7f604708e09c56a62574daeb8dd473b982205 # Parent 8c388fd08c09a04369ebef061c049b0968bb35af "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9fa2234b56facaf70fce12e5c60638d801997594" diff -r 8c388fd08c09 -r b8a7f604708e scripts/hyphy_summary.py --- a/scripts/hyphy_summary.py Wed Jun 09 17:34:05 2021 +0000 +++ b/scripts/hyphy_summary.py Fri Jun 18 15:30:23 2021 +0000 @@ -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