1. James Taylor
  2. bx-python

Commits

Bob Harris  committed 8a4101f

recommitting earlier change, involving correction of how intervals are handled on negative strand

  • Participants
  • Parent commits 402cfeb
  • Branches default

Comments (0)

Files changed (1)

File scripts/maf_extract_ranges.py

View file
 
     for maf in bx.align.maf.Reader( sys.stdin ):
         ref_component = maf.components[ refindex ]
+        if ref_component.strand == '-':
+            maf = maf.reverse_complement()
+            ref_component = maf.components[ refindex ]
         # Find overlap with reference component
         intersections = intersecter.find( ref_component.start, ref_component.end )
         # Keep output maf ordered