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WIDTH = 71
class Sequence(object):
def __init__(self, hdr, seq):
self.header = hdr.strip()
self.sequence = seq.strip()
def __str__(self):
ret = '>' + self.header + '\n'
ret += '\n'.join(self.sequence[x:x + WIDTH]
for x in xrange(0, len(self.sequence), WIDTH))
return ret
class Fasta(object):
def __init__(self):
self.seq_list = []
self.seq_dic = {}
def add_seq(self, seq):
if seq.header in self.seq_dic:
raise Exception("Duplicate fasta header " + seq.header)
self.seq_dic[seq.header] = len(self.seq_list)
self.seq_list.append(seq)
def __len__(self):
return len(self.seq_list)
def __contains__(self, x):
return (type(x) is int and x < len(self.seq_list)
or
type(x) is str and x in self.seq_dic)
def __iter__(self):
return iter(self.seq_list)
def __getitem__(self, x):
if type(x) is int:
return self.seq_list[x]
elif type(x) is str:
return self.seq_list[self.seq_dic[x]]
def read_from(self, filename):
header = None
sequence = None
for line in open(filename).xreadlines():
if line[0] == '>':
if sequence is not None:
self.add_seq(Sequence(header, sequence))
header = line[1:]
sequence = ''
else:
sequence += line.strip()
if sequence:
self.add_seq(Sequence(header, sequence))
def remove(self, x):
if type(x) is int:
s = self.seq_list[x]
del self.seq_dic[s.header]
del self.seq_list[x]
elif type(x) is str:
i = self.seq_dic[x]
del self.seq_dic[x]
del self.seq_list[i]
def save_to(self, filename):
f = open(filename, 'w')
for s in self.seq_list:
print >> f, s
def read_from(filename):
ret = Fasta()
ret.read_from(filename)
return ret