def testall(): os.chdir("../xml files") for f in glob.glob("*.xml"): try: print "trying file %s..." % f parsexml.returnSNPs(f) except ParseError as e: print "File %s has invalid xml syntax: %s" % (f, str(e)) print "\n"
def testall(): os.chdir("../xml files") for f in glob.glob("*.xml"): try: print "trying file %s..." % f parsexml.returnSNPs(f) except ParseError as e: print "File %s has invalid xml syntax: %s" % (f, str(e)) print '\n'
def get_subset(genome): ''' Returns subset of genome containing SNPs relevant xml files. ''' genome_dict = {} snps_list = [] #iterate through files to get all snps for f in get_xml_filelist(): try: #get all the SNPs in a file snps = returnSNPs(f) except ParseError: pass finally: if len(snps) >= 1: snps_list.extend(snps) #iterate through genome to find all relevant snps gensnpy = loadgensnpy(genome) for s in gensnpy: if s.name in snps_list: genome_dict[s.name]=s.genotype #print genome_dict return genome_dict