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# Copyright (c) 2006, The Regents of the University of California, through
# Lawrence Berkeley National Laboratory (subject to receipt of any required
# approvals from the U.S. Dept. of Energy). All rights reserved.
# This software is distributed under the new BSD Open Source License.
# <http://www.opensource.org/licenses/bsd-license.html>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
#
# (1) Redistributions of source code must retain the above copyright notice,
# this list of conditions and the following disclaimer.
#
# (2) 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.
#
# (3) Neither the name of the University of California, Lawrence Berkeley
# National Laboratory, U.S. Dept. of Energy 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 OWNER 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.
"""Sequence IO for NBRF/PIR format.
The format is similar to fasta. The header line consistins of '>', a two-
letter sequence type (P1, F1, DL, DC, RL, RC, or XX), a semicolon, and a
sequence ID. The next line is a textual description of the sequence,
followed by one or more lines containing the sequence data. The end of
the sequence is marked by a "*" (asterisk) character.
type_code -- A map between NBRF two letter type codes and Alphabets.
see: http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html
--- Example NBRF File ---
>P1;CRAB_ANAPL
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
SDVPERSIPI TREEKPAIAG AQRK*
>P1;CRAB_BOVIN
ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR
PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK
QASGPERTIP ITREEKPAVT AAPKK*
"""
from typing import Iterator, Optional, TextIO
from ..seq import (
Alphabet,
Seq,
SeqList,
dna_alphabet,
generic_alphabet,
protein_alphabet,
rna_alphabet,
)
names = (
"nbrf",
"pir",
)
extensions = ("nbrf", "pir", "ali")
type_code = {
"P1": protein_alphabet, # Protein (complete)
"F1": protein_alphabet, # Protein (fragment)
"DL": dna_alphabet, # DNA (linear)
"DC": dna_alphabet, # DNA (circular)
"RC": rna_alphabet, # RNA (linear)
"RL": rna_alphabet, # RNA (circular)
"N3": rna_alphabet, # tRNA
"N1": rna_alphabet, # other functional RNA
"XX": generic_alphabet,
}
def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList:
"""Read and parse a NBRF sequence file.
Args:
fin -- A stream or file to read
alphabet -- The expected alphabet of the data. If not supplied, then
an appropriate alphabet will be inferred from the data.
Returns:
SeqList -- A list of sequences
Raises:
ValueError -- If the file is unparsable
"""
seqs = [s for s in iterseq(fin, alphabet)]
return SeqList(seqs)
def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]:
"""Generate sequences from an NBRF file.
arguments:
fin -- A stream or file to read
alphabet --
yields :
Seq
raises :
ValueError -- On a parse error.
"""
body, header, sequence = range(3) # Internal states
state = body
seq_id = None
seq_desc = None
seq_alpha = None
seqs = []
for lineno, line in enumerate(fin):
if state == body:
if line == "" or line.isspace():
continue
if line[0] == ">":
seq_type, seq_id = line[1:].split(";")
if alphabet:
seq_alpha = alphabet
else:
seq_alpha = type_code[seq_type]
state = header
continue
raise ValueError("Parse error on line: %d" % lineno)
elif state == header:
seq_desc = line.strip()
state = sequence
continue
elif state == sequence:
data = "".join(line.split()) # Strip out white space
if data[-1] == "*":
# End of sequence data
seqs.append(data[:-1])
seq = Seq(
"".join(seqs),
name=seq_id.strip(), # type: ignore
description=seq_desc,
alphabet=seq_alpha,
)
yield seq
state = body
seq_id = None
seq_desc = None
seqs = []
continue
else:
seqs.append(data)
continue
else:
# If we ever get here something has gone terrible wrong
assert False # pragma: no cover
# end for
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