Merge pull request #17 from Novartis/bugfix/issue_15

Fix exon ordering for minus strand transcripts in #15
Novartis · Aug 6, 2021 · 98dc8cd · 98dc8cd
2 parents f0a0f0f + 89aadee
commit 98dc8cd
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/pisces/index.py b/pisces/index.py
@@ -266,10 +266,16 @@ def features_to_string(features, fasta_in, masked=True, strand=True):
                         """ 
                         """
                         sequences = []
+                        feature_strand = "."
                         for feature in features:
+                            feature_strand = feature.strand
                             sequences.append(
                                 feature.sequence(
                                     fasta_in, use_strand=strand))
+                        # if the transcript is on the reverse strand, reverse order of exons 
+                        # before concatenating
+                        if feature_strand == "-":
+                            sequences = sequences[::-1]
                         seq = ''.join(sequences)
                         mask_count = sum(seq.count(a) for a in soft_chars)
                         if masked: