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import os, string
import Bio.Alphabet
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
# This can be made a lot faster by using infile.readlines!
# (Alas, that's a bit complicated to write.)
class FastaReader:
def __init__(self, infile, alphabet = Bio.Alphabet.generic_alphabet):
self.infile = infile
self.alphabet = alphabet
# find the start of data
line = infile.readline()
while line and line[0] != ">":
line = infile.readline()
self._lookahead = line
self._n = 0
def next(self):
self._n = self._n + 1
line = self._lookahead
if not line:
return None
# Like bioperl, I assume the first word is the name/id and the
# rest of the line (after the first whitespace) is a
# description. If there's only one word, it's the id.
x = string.split(line[1:].rstrip(), None, 1)
if len(x) == 1:
id = x[0]
desc = ""
else:
id, desc = x
lines = []
line = self.infile.readline()
while line:
if line[0] == ">":
break
lines.append(line.rstrip())
line = self.infile.readline()
self._lookahead = line
# Unlike bioperl, I assume whitespace is significant.
return SeqRecord(Seq(string.join(lines, ""), self.alphabet),
id = id, name = id, description = desc)
def __getitem__(self, i):
# wrapper to the normal Python "for spam in list:" idiom
assert i == self._n # forward iteration only!
x = self.next()
if x is None:
raise IndexError, i
return x
class FastaWriter:
def __init__(self, outfile):
self.outfile = outfile
def write(self, record):
id = record.id
assert os.linesep not in id
description = record.description
assert os.linesep not in description
self.outfile.write(">%s %s%s" % (id, description,os.linesep))
data = record.seq.tostring()
for i in range(0, len(data), 60):
self.outfile.write(data[i:i+60] + os.linesep)
def write_records(self, records):
# In general, can assume homogenous records... useful?
for record in records:
self.write(record)
def close(self):
return self.outfile.close()
def flush(self):
return self.outfile.flush()
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