Source code for conkit.io.fasta
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"""
Parser module specific to FASTA sequence files
"""
__author__ = "Felix Simkovic"
__date__ = "09 Sep 2016"
__version__ = "0.1"
from conkit.io._parser import SequenceFileParser
from conkit.core.sequence import Sequence
from conkit.core.sequencefile import SequenceFile
[docs]class FastaParser(SequenceFileParser):
"""Parser class for FASTA sequence files
"""
def __init__(self):
super(FastaParser, 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.SequenceFile`
Raises
------
:exc:`ValueError`
FASTA record needs to start with >
"""
hierarchy = SequenceFile(f_id)
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif line.startswith('#'):
hierarchy.remark = line[1:]
elif line.startswith('>'):
break
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
sequence_entry = Sequence(id, _seq_string)
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.SequenceFile`, :obj:`~conkit.core.sequence.Sequence`
"""
hierarchy = self._reconstruct(hierarchy)
content = ''
for remark in hierarchy.remark:
content += '#{}\n'.format(remark)
for sequence_entry in hierarchy:
header = '>{}'.format(sequence_entry.id)
if len(sequence_entry.remark) > 0:
header = '|'.join([header] + sequence_entry.remark)
content += header + '\n'
sequence_string = sequence_entry.seq.upper() # UPPER CASE !!!
for i in range(0, sequence_entry.seq_len, 60):
content += sequence_string[i:i + 60] + '\n'
f_handle.write(content)