Mercurial > repos > iuc > hyphy_summary
changeset 2:d7c01f81739b draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 9fa2234b56facaf70fce12e5c60638d801997594"
| author | iuc |
|---|---|
| date | Fri, 18 Jun 2021 15:37:03 +0000 |
| parents | 37887c2733a3 |
| children | bd90215b7d15 |
| files | hyphy_summary.xml scripts/hyphy_summary.py |
| diffstat | 2 files changed, 6 insertions(+), 1 deletions(-) [+] |
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--- a/hyphy_summary.xml Wed Jun 09 17:29:30 2021 +0000 +++ b/hyphy_summary.xml Fri Jun 18 15:37:03 2021 +0000 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="hyphy_summary" version="1.0.0" name="HyPhy-Summary" profile="21.01"> +<tool id="hyphy_summary" version="1.1.0" name="HyPhy-Summary" profile="21.01"> <description>generate summary report of HyPhy analyses</description> <requirements> <requirement type="package" version="0.19.7">python-bioext</requirement>
--- a/scripts/hyphy_summary.py Wed Jun 09 17:29:30 2021 +0000 +++ b/scripts/hyphy_summary.py Fri Jun 18 15:37:03 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