Source code for conkit.io.StockholmIO
"""
Parser module specific to Stockholm 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
import re
V_RECORD = re.compile(r'^#(\s+STOCKHOLM.*)$')
GF_RECORD = re.compile(r'^#=GF\s+\S+\s+(.*)$')
GR_RECORD = re.compile(r'^#=GR\s+(\S+)\s+(\S+)\s+(.*)$')
GS_RECORD = re.compile(r'^#=GS\s+(\S+)\s+(\S+)\s+(.*)$')
SEQ_RECORD = re.compile(r'^(\S+)\s+([A-Z0-9~-]+)$')
END_RECORD = re.compile(r'^//$')
[docs]class StockholmIO(_SequenceFileParser):
"""Parser class for Stockholm sequence files
"""
def __init__(self):
super(StockholmIO, self).__init__()
[docs] def read(self, f_handle, f_id='stockholm'):
"""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
sequence_file = SequenceFile(f_id)
# Read any possible comments and store in file remarks
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif V_RECORD.match(line):
version = V_RECORD.match(line).group(1)
# sequence_file.add_remark(version)
elif GF_RECORD.match(line) or GS_RECORD.match(line):
break
# Read the sequence record(s)
while True:
if GF_RECORD.match(line):
ident = GF_RECORD.match(line).group(1)[:-3]
sequence_entry = Sequence(ident, "")
sequence_file.add(sequence_entry)
elif GS_RECORD.match(line):
ident, _, desc = GS_RECORD.match(line).groups()
sequence_entry = Sequence(ident, "")
sequence_entry.remark = desc
sequence_file.add(sequence_entry)
elif GR_RECORD.match(line):
pass
elif SEQ_RECORD.match(line):
ident, seq = SEQ_RECORD.match(line).groups()
sequence_file[ident].seq = sequence_file[ident].seq + seq
line = f_handle.readline().rstrip()
# // char in alignment reached
if END_RECORD.match(line):
break
return sequence_file
[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` or :obj:`conkit.core.Sequence`
"""
# Double check the type of sequence_file and reconstruct if necessary
sequence_file = self._reconstruct(hierarchy)
f_handle.write("# STOCKHOLM 1.0" + os.linesep)
f_handle.write("#=GF ID {ident}{ls}{ls}".format(ident=sequence_file.top_sequence.id,
ls=os.linesep))
chunks = []
for i, sequence_entry in enumerate(sequence_file):
if i != 0:
f_handle.write(
'#=GS {ident:33} DE {remark}{ls}'.format(
ident=sequence_entry.id,
remark=" ".join(sequence_entry.remark),
ls=os.linesep,
)
)
# Cut the sequence into chunks [ <= 200 seq chars per line]
chunk = []
sequence_string = sequence_entry.seq
sequence_string = sequence_string.upper() # UPPER CASE !!!
for j in range(0, sequence_entry.seq_len, 200):
chunk.append(sequence_string[j:j + 200])
chunks.append(tuple([sequence_entry.id, chunk]))
# Write the sequence out in chunks
for j in range(len(chunks[0][1])):
f_handle.write(os.linesep)
for i in range(len(chunks)):
f_handle.write(
"{ident:41} {seq_chunk}{ls}".format(
ident=chunks[i][0],
seq_chunk=chunks[i][1][j],
ls=os.linesep,
)
)
f_handle.write("//" + os.linesep)
return