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