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
