def find(self, reference_dir):
files = [
os.path.join(reference_dir, file)
for file in os.listdir(reference_dir)
if os.path.isfile(os.path.join(reference_dir, file))
and file.endswith("fasta")
]
for file in files:
sys.stdout.write("Processing file " + file + "\n")
for rec in SeqIO.parse_fasta(open(file, "r")):
lines = filter(None, re.split("[\-()]", rec.id))
# print lines
chr = lines[0][3:-1]
left = int(lines[1])
right = int(lines[2])
# print chr, left, right
for variation in self.variations:
if variation.Intersect(chr, left, right):
sys.stdout.write(
"Segment chr_{0}_({1}-{2}) intersected with variation ({3}, {4}, {5}, {6}) \n"
.format(chr, left, right, variation.chr,
variation.start, variation.end,
variation.allele))
def ReadReference(file):
result = dict()
for rec in SeqIO.parse_fasta(open(file, "r")):
result[rec.id] = rec.seq
return result
def ReadReference(file):
result = dict()
for rec in SeqIO.parse_fasta(open(file, "r")):
result[rec.id] = rec.seq
return result
