Source code for conkit.io.a3m
# BSD 3-Clause License
#
# Copyright (c) 2016-19, University of Liverpool
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# * Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
#
# * Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# * Neither the name of the copyright holder nor the names of its
# contributors may be used to endorse or promote products derived from
# this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
# FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
# OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
"""
Parser module specific to HH-suite A3M sequence files
Credits
-------
Stefan Seemayer and his A3MIO project [https://github.com/sseemayer/BioPython-A3MIO]
"""
__author__ = "Felix Simkovic"
__credits__ = "Stefan Seemayer"
__date__ = "11 Sep 2016"
__version__ = "0.1"
import numpy as np
import re
from conkit.io._parser import SequenceFileParser
from conkit.core.sequence import Sequence
from conkit.core.sequencefile import SequenceFile
[docs]class A3mParser(SequenceFileParser):
"""Parser class for A3M sequence files
"""
def __init__(self):
super(A3mParser, self).__init__()
[docs] def read(self, f_handle, f_id="a3m", remove_inserts=True):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
remove_inserts : bool, optional
Remove insert states [default: True]
Returns
-------
:obj:`~conkit.core.sequencefile.SequenceFile`
"""
sequence_file = SequenceFile(f_id)
while True:
line = f_handle.readline().rstrip()
if not line:
continue
elif line.startswith("#"):
sequence_file.remark = line[1:]
elif line.startswith(">"):
break
while True:
if not line.startswith(">"):
raise ValueError("Fasta record needs to start with '>'")
id = line[1:]
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)
if remove_inserts:
seq_string = self._remove_inserts(seq_string)
sequence_entry = Sequence(id, seq_string)
try:
sequence_file.add(sequence_entry)
except ValueError:
while True:
new_id = sequence_entry.id + "_{0}".format(np.random.randint(0, 100000))
if new_id in sequence_file:
continue
else:
break
sequence_entry.id = new_id
sequence_file.add(sequence_entry)
if not line:
break
if not remove_inserts:
self._adjust_insert(sequence_file)
return sequence_file
def _adjust_insert(self, hierarchy):
"""Adjust insert states
Credits
-------
This function was adapted from Stefan Seemayer's BioPython-A3MIO
repository - https://github.com/sseemayer/BioPython-A3MIO
"""
# Determine the insert states by splitting the sequences into chunks based
# on the case of the letter.
INSERT_STATE = re.compile(r"([A-Z0-9~-])")
inserts = [INSERT_STATE.split(sequence_entry.seq) for sequence_entry in hierarchy]
# Determine maximum insert length at each position
insert_max_lengths = [max(len(inserts[i][j]) for i in range(len(inserts))) for j in range(len(inserts[0]))]
# Add gaps where gaps are needed
def pad(chunk, length, pad_char="-"):
return chunk + pad_char * (length - len(chunk))
# Manipulate each sequence to match insert states
for sequence_entry, seq in zip(hierarchy, inserts):
sequence_entry.seq = "".join(pad(insert, insert_len) for insert, insert_len in zip(seq, insert_max_lengths))
def _remove_inserts(self, seq):
"""Remove insert states"""
return "".join([char for char in seq if not char.islower()])
[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`
"""
sequence_file = self._reconstruct(hierarchy)
content = ""
for remark in sequence_file.remark:
content += "#{remark}\n".format(remark=remark)
for sequence_entry in sequence_file:
header = ">{id}".format(id=sequence_entry.id)
if len(sequence_entry.remark) > 0:
header = "|".join([header] + sequence_entry.remark)
content += header + "\n"
content += sequence_entry.seq + "\n"
f_handle.write(content)