def main(args):
fo = open(args['file'])
for line in fo:
if line.startswith("ID\t"): continue
m = MisaSSR(line)
if m.type != "c" and m.type != "c*": print m.to_s()
else:
startpos = m.startpos
separatepatterns = re.findall("\([ATGC]+\)\d+[*]{0,1}", m.pattern)
for separatepattern in separatepatterns:
motif = separatepattern[1:separatepattern.index(")")]
if separatepattern.endswith("*"):
repeats = int(separatepattern[separatepattern.index(")") +
1:-1])
else:
repeats = int(separatepattern[separatepattern.index(")") +
1:])
length = len(motif) * repeats
endpos = startpos + length - 1
print string.join([
m.geneid,
str(m.ssrnr), "p" + str(len(motif)), separatepattern,
str(length),
str(startpos),
str(endpos)
], "\t")
startpos = endpos + 1
def get_ssrs(file):
hash = {}
fo = open(file)
for line in fo:
if line.startswith("ID\t"): continue
m = MisaSSR(line)
hash[m.geneid + "|" + str(m.startpos)] = m
fo.close()
return hash
def get_ssrs(file):
hash = defaultdict(list)
fo = open(file)
for line in fo:
if line.startswith("ID\t"): continue
m = MisaSSR(line)
hash[m.geneid].append(m)
fo.close()
return hash
def get_ssrs(file):
hash = defaultdict(list)
fo = open(file)
for line in fo:
if line.startswith("ID\t"): continue
m = MisaSSR(line)
hash[m.geneid].append(m)
fo.close()
print >> sys.stderr, "read %s microsatellites" % len(hash)
return hash