def discoverFromVCFWithoutFilter(self, inputFname=None, outputFname=None, **keywords):
"""
2012.9.11
read minDepth from self.minDepth
2012.9.5
add minDepth=0 to VCFFile
#2012.8.20 locus_id2row_index from VCFFile is using (chr, pos) as key, not chr_pos
need a conversion in between
2012.5.8
"""
vcfFile = VCFFile(inputFname=inputFname, minDepth=self.minDepth)
vcfFile.parseFile()
read_group2col_index = vcfFile.sample_id2index
locus_id2row_index = vcfFile.locus_id2row_index
#2012.8.20 locus_id2row_index from VCFFile is using (chr, pos) as key, not chr_pos
new_locus_id2row_index = {}
for locus_id, row_index in locus_id2row_index.iteritems():
new_locus_id = '%s_%s'%(locus_id[0], locus_id[1])
new_locus_id2row_index[new_locus_id] = row_index
locus_id2row_index = new_locus_id2row_index
data_matrix = vcfFile.genotype_call_matrix
self.outputCallMatrix(data_matrix, refFastaFname=None, outputFname=outputFname, refNameSet=None, \
read_group2col_index=read_group2col_index, \
locus_id2row_index=locus_id2row_index, outputDelimiter=self.outputDelimiter)
def run(self):
"""
"""
if self.debug:
import pdb
pdb.set_trace()
vcfFile1 = VCFFile(inputFname=self.inputFname)
vcfFile1.parseFile()
vcfFile2 = VCFFile(inputFname=self.jnputFname)
vcfFile2.parseFile()
writer = csv.writer(open(self.outputFname, 'w'), delimiter='\t')
header = ['#chromosome', 'position', 'mismatchRate']
no_of_sites_of_input1 = len(vcfFile1.locus_id_ls)
no_of_sites_of_input2 = len(vcfFile2.locus_id_ls)
overlapping_sites_set = set(vcfFile1.locus_id_ls)&set(vcfFile2.locus_id_ls)
no_of_overlapping_sites = len(overlapping_sites_set)
no_of_total_sites = no_of_sites_of_input1+no_of_sites_of_input2-no_of_overlapping_sites
no_of_samples = len(vcfFile1.sample_id2index)
no_of_samples_in_vcf2 = len(vcfFile2.sample_id2index)
overlapping_sample_id_set = set(vcfFile1.sample_id2index.keys()) & set(vcfFile2.sample_id2index.keys())
overlapping_sample_id_list = list(overlapping_sample_id_set)
overlapping_sample_id_list.sort()
if no_of_samples!=no_of_samples_in_vcf2:
sys.stderr.write("Warning: sample size in %s is %s, in %s is %s. not matching.\n"%\
(self.inputFname, no_of_samples, self.jnputFname, no_of_samples_in_vcf2))
no_of_samples_to_compare = len(overlapping_sample_id_set)
writer.writerow(header)
locus_id2mismatchData = {}
for locus_id in overlapping_sites_set:
row_index1 = vcfFile1.locus_id2row_index[locus_id]
row_index2 = vcfFile2.locus_id2row_index[locus_id]
no_of_mismatches = 0
no_of_non_NA_pairs = 0.0
for j in xrange(len(overlapping_sample_id_list)):
sample_id = overlapping_sample_id_list[j]
col_index1 = vcfFile1.sample_id2index.get(sample_id)
col_index2 = vcfFile2.sample_id2index.get(sample_id)
call1 = vcfFile1.genotype_call_matrix[row_index1][col_index1]
call2 = vcfFile2.genotype_call_matrix[row_index2][col_index2]
if call1!='NA' and call2!='NA':
no_of_non_NA_pairs += 1
if call1!=call2:
no_of_mismatches += 1
else:
#do nothing
pass
if no_of_non_NA_pairs>0:
mismatchRate = no_of_mismatches/float(no_of_non_NA_pairs)
else:
mismatchRate = -1
locus_id2mismatchData[locus_id] = [mismatchRate, no_of_mismatches, no_of_non_NA_pairs]
counter = 0
locus_id_ls = locus_id2mismatchData.keys()
locus_id_ls.sort()
for locus_id in locus_id_ls:
mismatchData = locus_id2mismatchData.get(locus_id)
mismatchRate = mismatchData[0]
if mismatchRate<=self.maxMismatchRate:
counter += 1
chr, pos = locus_id[:2]
writer.writerow([chr, pos, mismatchRate])
sys.stderr.write("%s loci passed the maxMismatchRate out of %s overlapped loci.\n"%(counter, len(overlapping_sites_set)))
