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Fixed bug so that the strand, alternate, and reference columns are now moved correctly 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3342 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd 2010-05-10 17:59:39 +00:00
parent f36726554f
commit f120a00433
1 changed files with 4 additions and 4 deletions
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8
python/genomicAnnotatorScripts/ConvertTableToAnnotatorRod.py
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@ -264,7 +264,7 @@ OUTPUT_FORMAT_DELIMITER = "\t"
for line in open(input_filename):
line = line.strip()
if counter % 1000000 == 0:
if counter % 1000000 == 0 and counter > 0:
print("Processed %d records" % counter )
counter+=1
@ -384,13 +384,13 @@ for line in open(input_filename):
if haplotype_strand_column:
line_fields.insert(3, haplotype_strand_value)
line_fields.insert(0, haplotype_strand_value)
if haplotype_alternate_column:
line_fields.insert(2, haplotype_alternate_value)
line_fields.insert(0, haplotype_alternate_value)
if haplotype_reference_column:
line_fields.insert(1, haplotype_reference_value)
line_fields.insert(0, haplotype_reference_value)
line_fields.insert(0, chrpos_value)