def outputSNPDataInNewCoordinate(self, querySNPDataFname=None, querySNPID2NewReferenceCoordinateLs=None,\
newSNPDataOutputFname=None, newSNPDataOutputFormat=1):
"""
2013.07.03 added argument newSNPDataOutputFormat
2012.10.14
split out of findSNPPositionOnNewRef()
"""
sys.stderr.write("Converting querySNPDataFname %s into individual X SNP format, format=%s ... "%\
(querySNPDataFname, newSNPDataOutputFormat))
"""
Sample Geno SNP
1999010 CC cs_primer1082_247
1999068 CC cs_primer1082_247
2000022 CT cs_primer1082_247
2000064 CT cs_primer1082_247
2000117 CC cs_primer1082_247
"""
inf = utils.openGzipFile(querySNPDataFname)
reader = csv.reader(inf, delimiter=figureOutDelimiter(inf))
col_name2index = getColName2IndexFromHeader(reader.next())
sampleIndex = col_name2index.get("Sample")
genotypeIndex = col_name2index.get("Geno")
SNPIDIndex = col_name2index.get("SNP")
row_id2index = {}
row_id_ls = []
col_id_ls = []
col_id2index = {}
row_col_index2genotype = {}
for row in reader:
sampleID = row[sampleIndex]
genotype = row[genotypeIndex]
querySNPID = row[SNPIDIndex]
if querySNPID in querySNPID2NewReferenceCoordinateLs:
newRefCoordinateLs = querySNPID2NewReferenceCoordinateLs.get(querySNPID)
if len(newRefCoordinateLs)==1:
newRefCoordinate = newRefCoordinateLs[0]
if newSNPDataOutputFormat==2:
col_id = '%s_%s'%(newRefCoordinate.newChr, newRefCoordinate.newRefStart)
else:
col_id = '%s_%s_%s'%(newRefCoordinate.newChr, newRefCoordinate.newRefStart, newRefCoordinate.newRefStop)
queryStrand = newRefCoordinate.queryStrand
if col_id not in col_id2index:
col_id2index[col_id] = len(col_id2index)
col_id_ls.append(col_id)
if sampleID not in row_id2index:
row_id2index[sampleID] = len(row_id2index)
row_id_ls.append(sampleID)
if queryStrand == "-":
genotype = SNP.reverseComplement(genotype)
row_index = row_id2index[sampleID]
col_index = col_id2index[col_id]
row_col_index2genotype[(row_index, col_index)] = genotype
else:
continue
data_matrix = numpy.zeros([len(row_id_ls), len(col_id2index)], dtype=numpy.int8)
for row_col_index, genotype in row_col_index2genotype.iteritems():
row_index, col_index = row_col_index[:2]
data_matrix[row_index, col_index] = SNP.nt2number[genotype]
sys.stderr.write("\n")
snpData = SNP.SNPData(row_id_ls=row_id_ls, col_id_ls=col_id_ls, data_matrix=data_matrix)
snpData.tofile(newSNPDataOutputFname)
