Source code for conkit.io.FastaIO
"""
Parser module specific to FASTA sequence files
"""
__author__ = "Felix Simkovic"
__date__ = "09 Sep 2016"
__version__ = 0.1
from conkit.core import Sequence
from conkit.core import SequenceFile
from conkit.io._ParserIO import _SequenceFileParser
import os
[docs]class FastaIO(_SequenceFileParser):
"""Parser class for FASTA sequence files
"""
def __init__(self):
super(FastaIO, self).__init__()
[docs] def read(self, f_handle, f_id='fasta'):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
Returns
-------
:obj:`conkit.core.SequenceFile`
"""
# Create a new sequence file instance
hierarchy = SequenceFile(f_id)
# Read any possible comments and store in file remarks
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif line.startswith('#'):
hierarchy.remark = line[1:]
elif line.startswith('>'):
break
# Read the sequence record(s) and store them
while True:
if not line.startswith('>'):
raise ValueError("Fasta record needs to start with '>'")
id = line[1:] # Header without '>'
chunks = []
line = f_handle.readline().rstrip()
while True:
if not line:
break
elif line.startswith('>'):
break
chunks.append(line)
line = f_handle.readline().rstrip()
_seq_string = "".join(chunks) # Sequence from chunks
# Create the sequence record instance
sequence_entry = Sequence(id, _seq_string)
# Store the sequence in the file
hierarchy.add(sequence_entry)
if not line:
break
return hierarchy
[docs] def write(self, f_handle, hierarchy):
"""Write a sequence file instance to to file
Parameters
----------
f_handle
Open file handle [write permissions]
hierarchy : :obj:`conkit.core.SequenceFile`, :obj:`conkit.core.Sequence`
"""
# Double check the type of hierarchy and reconstruct if necessary
hierarchy = self._reconstruct(hierarchy)
# Write remarks
for remark in hierarchy.remark:
f_handle.write('#{remark}'.format(remark=remark) + os.linesep)
for sequence_entry in hierarchy:
header = '>{id}'.format(id=sequence_entry.id)
if len(sequence_entry.remark) > 0:
header = '|'.join([header] + sequence_entry.remark)
f_handle.write(header + os.linesep)
# Cut the sequence into chunks [FASTA <= 60 chars per line]
sequence_string = sequence_entry.seq.upper() # UPPER CASE !!!
for i in range(0, sequence_entry.seq_len, 60):
f_handle.write(sequence_string[i:i+60] + os.linesep)
return