def main(): parser = OptionParser(usage=usage) (options, args) = parser.parse_args() if (len(args)!=2): parser.print_help() return 1 results_file = open(args[0], 'r') chromosome = int(args[1]) human_omni_reader = HumanOmniReader() human_omni_reader.read(chromosome) for line in results_file: pair = SNPDeletionPair(line) if not human_omni_reader.snpPresent(pair.snp.position): continue print(line, end = '') results_file.close()
def __init__(self, chromosome, max_major_af = .96): self.max_major_af = max_major_af self.gwas_catalogue_reader = GWASCatalogueReader() self.gwas_catalogue_reader.read(chromosome) self.human_omni_reader = HumanOmniReader() self.human_omni_reader.read(chromosome) self.hg19_reader = HG19Reader() self.hg19_reader.read(chromosome) self.vcf_reader = vcf.Reader(open(self.returnLocation(chromosome)))
class SNPReader: """Reads the deletions from file.""" def __init__(self, chromosome, max_major_af = .96): self.max_major_af = max_major_af self.gwas_catalogue_reader = GWASCatalogueReader() self.gwas_catalogue_reader.read(chromosome) self.human_omni_reader = HumanOmniReader() self.human_omni_reader.read(chromosome) self.hg19_reader = HG19Reader() self.hg19_reader.read(chromosome) self.vcf_reader = vcf.Reader(open(self.returnLocation(chromosome))) def returnLocation(self, chromosome): if chromosome != 1 and chromosome != 22: return '/data2/as/hitSNP-CNV/data/phased-snps-dels/chr' + str(chromosome) + '_snps_and_dels.vcf.gz' elif chromosome == 1: return '/data2/as/hitSNP-CNV/data/phased-snps-dels/chr1_snps_and_dels.vcf' return '/data2/as/hitSNP-CNV/data/phased-snps-dels/chr22_snps_and_dels.vcf' def readHitSNPs(self): """Reads in only the hit SNPs present in the given VCF file.""" self.snps = [] for vcf_record in self.vcf_reader: if not isSNP(vcf_record): # if vcf is not a SNP continue snp = SNP(vcf_record) if snp.major_af > max_major_af: # major allele frequency too high continue if not self.human_omni_reader.snpPresent(snp.position): # not present in the HumanOmni data set continue hit_allele = self.gwas_catalogue_reader.getHitAllele(snp.position) if hit_allele == None: continue snp_type, dist_tss = self.hg19_reader.determineTypeAndDistanceTSS(snp.position) self.snps.append(SNP(vcf_record, snp_type = snp_type, hit_allele = hit_allele, dist_tss = dist_tss)) def readRawList(self, snp_positions): """Reads in all SNPs for which their position is present in the given list. Their distance to TSS, type and (when relevant) hit allele are not determined.""" self.snps = [] for vcf_record in self.vcf_reader: if not isSNP(vcf_record): continue if not vcf_record.POS in snp_positions: continue snp = SNP(vcf_record) if snp.major_af > self.max_major_af: continue self.snps.append(snp) def read(self): """Reads all the SNPs present in the given VCF file. NOTE: this function must be called first before any other function can be called.""" self.snps = [] for vcf_record in self.vcf_reader: if not isSNP(vcf_record): continue snp = SNP(vcf_record) if snp.major_af > self.max_major_af: continue if not self.human_omni_reader.snpPresent(snp.position): continue snp_type, dist_tss = self.hg19_reader.determineTypeAndDistanceTSS(snp.position) hit_allele = self.gwas_catalogue_reader.getHitAllele(snp.position) self.snps.append(SNP(vcf_record, snp_type = snp_type, hit_allele = hit_allele, dist_tss = dist_tss)) def getHitSNPs(self): self.hit_snps = [] for snp in self.snps: if snp.isHitSNP(): self.hit_snps.append(snp) def printAll(self): for snp in snps: snp.print()
