/usr/lib/python3/dist-packages/screed/fasta.py is in python3-screed 0.9-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 | from __future__ import absolute_import
from . import DBConstants
from .screedRecord import Record, _Writer
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 = Record()
line = to_str(line.strip())
if not line.startswith('>'):
raise IOError("Bad FASTA format: no '>' at beginning of line")
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 data
class FASTA_Writer(_Writer):
def write(self, record):
s = ">%s %s\n%s\n" % (record.name, record.description,
record.sequence,)
self.fp.write(s)
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