def write_output(reader, outf, logger=None):
logger = logger or NullLogger()
bad_count = 0
for r in reader:
label = r['Probe Set ID']
if r['dbSNP RS ID'].startswith('rs'):
rs_label = r['dbSNP RS ID']
else:
rs_label = 'None'
mask = r['Flank']
problem = check_mask(mask)
if problem:
mask = 'None'
logger.warn("%r: %s, setting mask to 'None'" % (label, problem))
bad_count += 1
outf.write("%s\t%s\t%s\t%s\t%s\n" %
(label, rs_label, mask, r['Allele A'], r['Allele B']))
return bad_count
def write_output(reader, outf, logger=None):
logger = logger or NullLogger()
bad_count = 0
for r in reader:
label = r['IlmnID']
if r['Name'].startswith('rs'):
rs_label = r['Name']
else:
rs_label = 'None'
mask = r['TopGenomicSeq']
# alleles are the same as those extracted from the mask if strand
# is TOP; if strand is BOT they are their complement (NOT reversed)
allele_a, allele_b = r['SNP'].strip("[]").split("/")
problem = check_mask(mask)
if problem:
mask = 'None'
logger.warn("%r: %s, setting mask to 'None'" % (label, problem))
bad_count += 1
outf.write("%s\t%s\t%s\t%s\t%s\n" %
(label, rs_label, mask, allele_a, allele_b))
return bad_count
def write_output(reader, outf, logger=None):
logger = logger or NullLogger()
bad_count = 0
for r in reader:
label = r['IlmnID']
if r['Name'].startswith('rs'):
rs_label = r['Name']
else:
rs_label = 'None'
mask = r['TopGenomicSeq']
# alleles are the same as those extracted from the mask if strand
# is TOP; if strand is BOT they are their complement (NOT reversed)
allele_a, allele_b = r['SNP'].strip("[]").split("/")
problem = check_mask(mask)
if problem:
mask = 'None'
logger.warn("%r: %s, setting mask to 'None'" % (label, problem))
bad_count += 1
outf.write("%s\t%s\t%s\t%s\t%s\n" %
(label, rs_label, mask, allele_a, allele_b))
return bad_count
