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# Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
"""Read a multiple sequence alignment in STOCKHOLM format.
This file format is used by PFAM and HMMER. At present, all annotation
information is ignored.
See:
- http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html
- HMMER manual
"""
import re
from typing import Iterator, Optional, TextIO
from ..seq import Alphabet, Seq, SeqList
from ..utils import Token
example = """
# STOCKHOLM 1.0
#=GF ID CBS
#=GF AC PF00571
#=GF DE CBS domain
#=GF AU Bateman A
#=GF CC CBS domains are small intracellular modules mostly found
#=GF CC in 2 or four copies within a protein.
#=GF SQ 67
#=GS O31698/18-71 AC O31698
#=GS O83071/192-246 AC O83071
#=GS O83071/259-312 AC O83071
#=GS O31698/88-139 AC O31698
#=GS O31698/88-139 OS Bacillus subtilis
O83071/192-246 MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS
#=GR O83071/192-246 SA 999887756453524252..55152525....36463774777
O83071/259-312 MQHVSAPVFVFECTRLAY..VQHKLRAH....SRAVAIVLDEY
#=GR O83071/259-312 SS CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEE
O31698/18-71 MIEADKVAHVQVGNNLEH..ALLVLTKT....GYTAIPVLDPS
#=GR O31698/18-71 SS CCCHHHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEHHH
O31698/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE
#=GR O31698/88-139 SS CCCCCCCHHHHHHHHHHH..HEEEEEEE....EEEEEEEEEEH
#=GC SS_cons CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEH
O31699/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE
#=GR O31699/88-139 AS ________________*__________________________
#=GR_O31699/88-139_IN ____________1______________2__________0____
//
"""
names = (
"stockholm",
"pfam",
)
extensions = ("sth", "stockholm", "align")
header_line = re.compile(r"#\s+STOCKHOLM\s+1.\d\s+$")
def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]:
"""Iterate over the sequences in the file."""
# Default implementation
return iter(read(fin, alphabet))
def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList:
alphabet = Alphabet(alphabet)
seq_ids = []
seqs: list = []
block_count = 0
for token in _scan(fin):
if token.typeof == "begin_block":
block_count = 0
elif token.typeof == "seq_id":
if len(seqs) <= block_count:
seq_ids.append(token.data)
seqs.append([])
elif token.typeof == "seq":
data = token.data
assert data is not None
if not alphabet.alphabetic(data):
raise ValueError(
"Character on line: %d not in alphabet: %s : %s"
% (token.lineno, alphabet, data)
)
seqs[block_count].append(data)
block_count += 1
seqs = [Seq("".join(s), alphabet, name=i) for s, i in zip(seqs, seq_ids)]
return SeqList(seqs)
def _scan(fin: TextIO) -> Iterator[Token]:
header, body, block = range(3)
yield Token("begin")
state = header
for L, line in enumerate(fin):
if state == header:
if line.isspace():
continue
m = header_line.match(line)
state = body
if m is not None:
# print("header: ", m.group())
yield Token("header", m.group())
continue
else:
raise ValueError("Parse error on line: %d" % L)
if state == body:
if line.isspace():
continue # pragma: no cover
yield Token("begin_block")
state = block
# fall through to block
if state == block:
if line.isspace():
yield Token("end_block")
state = body
continue
if line.strip() == "//":
yield Token("end_block")
return
if line[0] == "#": # Comment or annotation line
continue
name_seq = line.split(None, 1) # Split into two parts at first whitespace
if len(name_seq) != 2:
raise ValueError("Parse error on line: %d" % L) # pragma: no cover
yield Token("seq_id", name_seq[0].strip())
yield Token("seq", name_seq[1].strip())
continue
# END state blocks. If I ever get here something has gone terrible wrong
raise RuntimeError() # pragma: no cover
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