Source code for conkit.io.a3m
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"""
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 os
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_insert=True):
"""Read a sequence file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique sequence file identifier
remove_insert : bool, optional
Remove insert states [default: True]
Returns
-------
:obj:`SequenceFile <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 line.startswith('#'):
sequence_file.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
# Remove insert states
if remove_insert:
seq_string = self._remove_insert(seq_string)
# Create the sequence record instance
sequence_entry = Sequence(id, seq_string)
# Store the sequence in the file
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
# Match the insert states of the sequence
if not remove_insert:
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))
return
def _remove_insert(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:`SequenceFile <conkit.core.SequenceFile>`, :obj:`Sequence <conkit.core.Sequence>`
"""
# Double check the type of hierarchy and reconstruct if necessary
sequence_file = self._reconstruct(hierarchy)
content = ""
# Write remarks
for remark in sequence_file.remark:
content += '#{remark}'.format(remark=remark) + os.linesep
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 + os.linesep
content += sequence_entry.seq + os.linesep
f_handle.write(content)
