def parse_fasta(lines):
"""Parses FASTA sequences found in a sequence of lines, and returns
a tuple for each FASTA record: ((name, meta-information), sequence)
No assumptions are made about the line-lengths."""
lines = (line.rstrip() for line in lines)
for record in split_before(lines, lambda v: v.startswith(">")):
name = record[0]
if (not name.startswith(">")) or (len(name) == 1):
raise FASTAError("Unnamed FASTA record")
elif len(record) == 1:
raise FASTAError("FASTA record does not contain sequence: " + name[1:])
# Split out any meta information
name = name[1:].split(None, 1)
while len(name) < 2:
name.append(None)
yield tuple((tuple(name), "".join(record[1:])))
def parse_fasta(lines):
"""Parses FASTA sequences found in a sequence of lines, and returns
a tuple for each FASTA record: ((name, meta-information), sequence)
No assumptions are made about the line-lengths."""
lines = (line.rstrip() for line in lines)
for record in split_before(lines, lambda v: v.startswith(">")):
name = record[0]
if (not name.startswith(">")) or (len(name) == 1):
raise FASTAError("Unnamed FASTA record")
elif len(record) == 1:
raise FASTAError("FASTA record does not contain sequence: " +
name[1:])
# Split out any meta information
name = name[1:].split(None, 1)
while len(name) < 2:
name.append(None)
yield tuple((tuple(name), "".join(record[1:])))
def _do_split(lst, key):
# Convertion to list allows the implementation to be
# lazy, while making comparisons for asserts easier
return list(utils.split_before(lst, key))
def _do_split(lst, key):
# Convertion to list allows the implementation to be
# lazy, while making comparisons for asserts easier
return list(utils.split_before(lst, key))
