Mercurial > repos > iuc > hyphy_summary

changeset 2:d7c01f81739b draft

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"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(-) [+]
line wrap: on
line diff
--- 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