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"""
Parser module specific to Pcons predictions
This module can be used to parse all versions
of the Pcons programs, i.e. PconsC, PconsC2,
and PconsC3.
"""
__author__ = "Felix Simkovic"
__date__ = "26 Oct 2016"
__version__ = "0.1"
import os
import re
from conkit.io._parser import ContactFileParser
from conkit.core.contact import Contact
from conkit.core.contactmap import ContactMap
from conkit.core.contactfile import ContactFile
from conkit.core.sequence import Sequence
RE_COMMENT = re.compile(r"^#+\s*$")
RE_JUNK = re.compile(r"^(PconsC3|Total|Sequence number|Sequence length).*\s*$")
RE_GENERATED = re.compile(r'^Generated.*$')
RE_SEQUENCE_NAME = re.compile(r"^Sequence name:\s+(.*)\s*$")
RE_SEQUENCE = re.compile(r"^Sequence:\s*$")
RE_PRED_CONTACTS = re.compile(r"^Predicted\s+contacts:\s*$")
RE_CONTACT_HEADER = re.compile(r"^Res1\s+Res2\s+Score\s*$")
RE_CONTACT = re.compile(r"^\s*(\d+)\s+(\d+)\s+(-?\d*\.\d+|\d+)\s*$")
[docs]class PconsParser(ContactFileParser):
"""Class to parse a Pcons output
This module can be used to parse all versions of the
Pcons programs, i.e. PconsC, PconsC2, and PconsC3.
"""
def __init__(self):
super(PconsParser, self).__init__()
[docs] def read(self, f_handle, f_id="pcons"):
"""Read a contact file
Parameters
----------
f_handle
Open file handle [read permissions]
f_id : str, optional
Unique contact file identifier
Returns
-------
:obj:`ContactFile <conkit.core.ContactFile>`
"""
contact_file = ContactFile(f_id)
contact_map = ContactMap("1")
contact_file.add(contact_map)
lines = iter([l.rstrip() for l in f_handle if l.rstrip()])
done = object()
line = next(lines, done)
seq = ''
seq_id = 'seq_1'
while line is not done:
if not line:
pass
elif RE_GENERATED.match(line):
contact_file.remark = line
elif RE_SEQUENCE_NAME.match(line):
seq_id = RE_SEQUENCE_NAME.match(line).group(1)
elif RE_SEQUENCE.match(line):
line = next(lines, done)
while line is not done:
if not line:
break
elif RE_CONTACT_HEADER.match(line):
break
elif RE_PRED_CONTACTS.match(line):
break
elif RE_CONTACT.match(line):
break
else:
seq += line
line = next(lines, done)
if RE_CONTACT.match(line):
res1_seq, res2_seq, raw_score = line.split()
contact = Contact(
int(res1_seq), int(res2_seq),
float(raw_score)
)
contact_map.add(contact)
line = next(lines, done)
if seq:
contact_map.sequence = Sequence(seq_id, seq)
contact_file.method = 'Contact map predicted using Pcons'
return contact_file
[docs] def write(self, f_handle, hierarchy, write_header_footer=True):
"""Write a contact file instance to to file
Default format is ``PconsC3`` style, including comments
and sequence information (if provided).
Parameters
----------
f_handle
Open file handle [write permissions]
hierarchy : :obj:`ContactFile <conkit.core.ContactFile>`, :obj:`ContactMap <conkit.core.ContactMap>`
or :obj:`Contact <conkit.core.Contact>`
write_header_footer : bool
Write a PconsC3-typical header
Raises
------
RuntimeError
More than one contact map in the hierarchy
"""
# Double check the type of hierarchy and reconstruct if necessary
contact_file = self._reconstruct(hierarchy)
if len(contact_file) > 1:
raise RuntimeError('More than one contact map provided')
comment_line = "##############################################################################"
content = ""
for contact_map in contact_file:
if write_header_footer:
content += comment_line + os.linesep
content += "PconsC3 result file" + os.linesep
content += "Generated using ConKit" + os.linesep
content += comment_line + os.linesep
if contact_map.sequence is not None:
content += "Sequence number: 1" + os.linesep
content += "Sequence name: {0}".format(
contact_map.sequence.id) + os.linesep
content += "Sequence length: {0} aa.".format(
contact_map.sequence.seq_len) + os.linesep
content += "Sequence:" + os.linesep
content += contact_map.sequence.seq + os.linesep * 3
content += "Predicted contacts:" + os.linesep
content += "Res1 Res2 Score" + os.linesep
for contact in contact_map:
res1_seq = contact.res1_seq
res2_seq = contact.res2_seq
raw_score = contact.raw_score
l = "{res1_seq:>4} {res2_seq:>4} {raw_score:>.6f}".format(res1_seq=res1_seq, res2_seq=res2_seq,
raw_score=raw_score)
content += l + os.linesep
if write_header_footer:
content += os.linesep + comment_line + os.linesep
f_handle.write(content)
