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altering scaffoldLookup code
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swift-213 committed Sep 29, 2023
1 parent 3dc5355 commit 794e4a2
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3 changes: 2 additions & 1 deletion codingSiteTypes.py
Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,8 @@ def tabixStream(fileName, region = None, chrom = None, start=None, end=None, hea
sequences = sequences_renamed
scaffolds = scaffolds_renamed

if args.scaffoldLookup and args.useAnnotationScaffoldNames:

if args.scaffoldLookup and not args.useAnnotationScaffoldNames:
#if we are going to use the reference scaffold names, change the gene data
with open(args.scaffoldLookup) as lookup:
scafNamesDict = dict([line.split()[::-1] for line in lookup])
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