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# Copyright (c) 2016, The Regents of the University of California.
from __future__ import absolute_import
from . import DBConstants
from .screedRecord import Record
from .utils import to_str
FieldTypes = (('name', DBConstants._INDEXED_TEXT_KEY),
('description', DBConstants._STANDARD_TEXT),
('sequence', DBConstants._SLICEABLE_TEXT))
def fasta_iter(handle, parse_description=False, line=None):
"""
Iterator over the given FASTA file handle, returning records. handle
is a handle to a file opened for reading
"""
if line is None:
line = handle.readline()
while line:
data = {}
line = to_str(line.strip())
if not line.startswith('>'):
msg = f"Bad FASTA format: no '>' at beginning of line: {line}"
raise IOError(msg)
if parse_description: # Try to grab the name and optional description
try:
data['name'], data['description'] = line[1:].split(' ', 1)
except ValueError: # No optional description
data['name'] = line[1:]
data['description'] = ''
else:
data['name'] = line[1:]
data['description'] = ''
data['name'] = data['name'].strip()
data['description'] = data['description'].strip()
# Collect sequence lines into a list
sequenceList = []
line = to_str(handle.readline())
while line and not line.startswith('>'):
sequenceList.append(line.strip())
line = to_str(handle.readline())
data['sequence'] = ''.join(sequenceList)
yield Record(**data)
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