mirror of
https://github.com/biopython/biopython.git
synced 2025-10-20 13:43:47 +08:00
293 lines
9.8 KiB
Python
293 lines
9.8 KiB
Python
# Copyright 2008-2015 by Peter Cock. All rights reserved.
|
|
#
|
|
# This file is part of the Biopython distribution and governed by your
|
|
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
|
|
# Please see the LICENSE file that should have been included as part of this
|
|
# package.
|
|
"""Bio.SeqIO support for the "pir" (aka PIR or NBRF) file format.
|
|
|
|
This module is for reading and writing PIR or NBRF format files as
|
|
SeqRecord objects.
|
|
|
|
You are expected to use this module via the Bio.SeqIO functions, or if
|
|
the file contains a sequence alignment, optionally via Bio.AlignIO instead.
|
|
|
|
This format was introduced for the Protein Information Resource (PIR), a
|
|
project of the National Biomedical Research Foundation (NBRF). The PIR
|
|
database itself is now part of UniProt.
|
|
|
|
The file format is described online at:
|
|
http://www.ebi.ac.uk/help/pir_frame.html
|
|
http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html (currently down)
|
|
|
|
An example file in this format would be::
|
|
|
|
>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*
|
|
|
|
Or, an example of a multiple sequence alignment::
|
|
|
|
>P1;S27231
|
|
rhodopsin - northern leopard frog
|
|
MNGTEGPNFY IPMSNKTGVV RSPFDYPQYY LAEPWKYSVL AAYMFLLILL GLPINFMTLY
|
|
VTIQHKKLRT PLNYILLNLG VCNHFMVLCG FTITMYTSLH GYFVFGQTGC YFEGFFATLG
|
|
GEIALWSLVV LAIERYIVVC KPMSNFRFGE NHAMMGVAFT WIMALACAVP PLFGWSRYIP
|
|
EGMQCSCGVD YYTLKPEVNN ESFVIYMFVV HFLIPLIIIS FCYGRLVCTV KEAAAQQQES
|
|
ATTQKAEKEV TRMVIIMVIF FLICWVPYAY VAFYIFTHQG SEFGPIFMTV PAFFAKSSAI
|
|
YNPVIYIMLN KQFRNCMITT LCCGKNPFGD DDASSAATSK TEATSVSTSQ VSPA*
|
|
|
|
>P1;I51200
|
|
rhodopsin - African clawed frog
|
|
MNGTEGPNFY VPMSNKTGVV RSPFDYPQYY LAEPWQYSAL AAYMFLLILL GLPINFMTLF
|
|
VTIQHKKLRT PLNYILLNLV FANHFMVLCG FTVTMYTSMH GYFIFGPTGC YIEGFFATLG
|
|
GEVALWSLVV LAVERYIVVC KPMANFRFGE NHAIMGVAFT WIMALSCAAP PLFGWSRYIP
|
|
EGMQCSCGVD YYTLKPEVNN ESFVIYMFIV HFTIPLIVIF FCYGRLLCTV KEAAAQQQES
|
|
LTTQKAEKEV TRMVVIMVVF FLICWVPYAY VAFYIFTHQG SNFGPVFMTV PAFFAKSSAI
|
|
YNPVIYIVLN KQFRNCLITT LCCGKNPFGD EDGSSAATSK TEASSVSSSQ VSPA*
|
|
|
|
>P1;JN0120
|
|
rhodopsin - Japanese lamprey
|
|
MNGTEGDNFY VPFSNKTGLA RSPYEYPQYY LAEPWKYSAL AAYMFFLILV GFPVNFLTLF
|
|
VTVQHKKLRT PLNYILLNLA MANLFMVLFG FTVTMYTSMN GYFVFGPTMC SIEGFFATLG
|
|
GEVALWSLVV LAIERYIVIC KPMGNFRFGN THAIMGVAFT WIMALACAAP PLVGWSRYIP
|
|
EGMQCSCGPD YYTLNPNFNN ESYVVYMFVV HFLVPFVIIF FCYGRLLCTV KEAAAAQQES
|
|
ASTQKAEKEV TRMVVLMVIG FLVCWVPYAS VAFYIFTHQG SDFGATFMTL PAFFAKSSAL
|
|
YNPVIYILMN KQFRNCMITT LCCGKNPLGD DE-SGASTSKT EVSSVSTSPV SPA*
|
|
|
|
|
|
As with the FASTA format, each record starts with a line beginning with ">"
|
|
character. There is then a two letter sequence type (P1, F1, DL, DC, RL,
|
|
RC, or XX), a semi colon, and the identification code. The second like is
|
|
free text description. The remaining lines contain the sequence itself,
|
|
terminating in an asterisk. Space separated blocks of ten letters as shown
|
|
above are typical.
|
|
|
|
Sequence codes and their meanings:
|
|
- P1 - Protein (complete)
|
|
- F1 - Protein (fragment)
|
|
- D1 - DNA (e.g. EMBOSS seqret output)
|
|
- DL - DNA (linear)
|
|
- DC - DNA (circular)
|
|
- RL - RNA (linear)
|
|
- RC - RNA (circular)
|
|
- N3 - tRNA
|
|
- N1 - Other functional RNA
|
|
- XX - Unknown
|
|
|
|
"""
|
|
|
|
from Bio.Seq import Seq
|
|
from Bio.SeqRecord import SeqRecord
|
|
|
|
from .Interfaces import _get_seq_string
|
|
from .Interfaces import SequenceIterator
|
|
from .Interfaces import SequenceWriter
|
|
|
|
_pir_mol_type = {
|
|
"P1": "protein",
|
|
"F1": "protein",
|
|
"D1": "DNA",
|
|
"DL": "DNA",
|
|
"DC": "DNA",
|
|
"RL": "RNA",
|
|
"RC": "RNA",
|
|
"N3": "RNA",
|
|
"XX": None,
|
|
}
|
|
|
|
|
|
class PirIterator(SequenceIterator):
|
|
"""Parser for PIR files."""
|
|
|
|
modes = "t"
|
|
|
|
def __init__(self, source):
|
|
"""Iterate over a PIR file and yield SeqRecord objects.
|
|
|
|
source - file-like object or a path to a file.
|
|
|
|
Examples
|
|
--------
|
|
>>> with open("NBRF/DMB_prot.pir") as handle:
|
|
... for record in PirIterator(handle):
|
|
... print("%s length %i" % (record.id, len(record)))
|
|
HLA:HLA00489 length 263
|
|
HLA:HLA00490 length 94
|
|
HLA:HLA00491 length 94
|
|
HLA:HLA00492 length 80
|
|
HLA:HLA00493 length 175
|
|
HLA:HLA01083 length 188
|
|
|
|
"""
|
|
super().__init__(source, fmt="Pir")
|
|
# Skip any text before the first record (e.g. blank lines, comments)
|
|
for line in self.stream:
|
|
if line[0] == ">":
|
|
self._line = line
|
|
break
|
|
else:
|
|
self._line = None # Premature end of file, or just empty?
|
|
|
|
def __next__(self):
|
|
"""Iterate over the records in the PIR file."""
|
|
line = self._line
|
|
if line is None:
|
|
raise StopIteration
|
|
|
|
pir_type = line[1:3]
|
|
if pir_type not in _pir_mol_type or line[3] != ";":
|
|
raise ValueError(
|
|
"Records should start with '>XX;' where XX is a valid sequence type"
|
|
)
|
|
|
|
identifier = line[4:].strip()
|
|
description = self.stream.readline()
|
|
if description == "":
|
|
raise StopIteration
|
|
else:
|
|
description = description.strip()
|
|
|
|
lines = []
|
|
for line in self.stream:
|
|
if line[0] == ">":
|
|
self._line = line
|
|
break
|
|
# Remove trailing whitespace, and any internal spaces
|
|
lines.append(line.rstrip().replace(" ", ""))
|
|
else:
|
|
self._line = None
|
|
seq = "".join(lines)
|
|
if seq[-1] != "*":
|
|
# Note the * terminator is present on nucleotide sequences too,
|
|
# it is not a stop codon!
|
|
raise ValueError("Sequences in PIR files should include a * terminator!")
|
|
|
|
# Return the record and then continue...
|
|
record = SeqRecord(
|
|
Seq(seq[:-1]), id=identifier, name=identifier, description=description
|
|
)
|
|
record.annotations["PIR-type"] = pir_type
|
|
if _pir_mol_type[pir_type]:
|
|
record.annotations["molecule_type"] = _pir_mol_type[pir_type]
|
|
return record
|
|
|
|
|
|
class PirWriter(SequenceWriter):
|
|
"""Class to write PIR format files."""
|
|
|
|
modes = "t"
|
|
|
|
def __init__(self, handle, wrap=60, record2title=None, code=None):
|
|
"""Create a PIR writer.
|
|
|
|
Arguments:
|
|
- handle - Handle to an output file, e.g. as returned
|
|
by open(filename, "w")
|
|
- wrap - Optional line length used to wrap sequence lines.
|
|
Defaults to wrapping the sequence at 60 characters
|
|
Use zero (or None) for no wrapping, giving a single
|
|
long line for the sequence.
|
|
- record2title - Optional function to return the text to be
|
|
used for the title line of each record. By default
|
|
a combination of the record.id, record.name and
|
|
record.description is used.
|
|
- code - Optional sequence code must be one of P1, F1,
|
|
D1, DL, DC, RL, RC, N3 and XX. By default None is used,
|
|
which means auto detection based on the molecule type
|
|
in the record annotation.
|
|
|
|
You can either use::
|
|
|
|
handle = open(filename, "w")
|
|
writer = PirWriter(handle)
|
|
writer.write_file(myRecords)
|
|
handle.close()
|
|
|
|
Or, follow the sequential file writer system, for example::
|
|
|
|
handle = open(filename, "w")
|
|
writer = PirWriter(handle)
|
|
...
|
|
Multiple writer.write_record() and/or writer.write_records() calls
|
|
...
|
|
handle.close()
|
|
|
|
"""
|
|
super().__init__(handle)
|
|
self.wrap = None
|
|
if wrap:
|
|
if wrap < 1:
|
|
raise ValueError("wrap should be None, 0, or a positive integer")
|
|
self.wrap = wrap
|
|
self.record2title = record2title
|
|
self.code = code
|
|
|
|
def write_record(self, record):
|
|
"""Write a single PIR record to the file."""
|
|
if self.record2title:
|
|
title = self.clean(self.record2title(record))
|
|
else:
|
|
title = self.clean(record.id)
|
|
|
|
if record.name and record.description:
|
|
description = self.clean(record.name + " - " + record.description)
|
|
elif record.name and not record.description:
|
|
description = self.clean(record.name)
|
|
else:
|
|
description = self.clean(record.description)
|
|
|
|
if self.code:
|
|
code = self.code
|
|
else:
|
|
molecule_type = record.annotations.get("molecule_type")
|
|
if molecule_type is None:
|
|
code = "XX"
|
|
elif "DNA" in molecule_type:
|
|
code = "D1"
|
|
elif "RNA" in molecule_type:
|
|
code = "RL"
|
|
elif "protein" in molecule_type:
|
|
code = "P1"
|
|
else:
|
|
code = "XX"
|
|
|
|
if code not in _pir_mol_type:
|
|
raise TypeError(
|
|
"Sequence code must be one of " + _pir_mol_type.keys() + "."
|
|
)
|
|
assert "\n" not in title
|
|
assert "\r" not in description
|
|
|
|
self.handle.write(f">{code};{title}\n{description}\n")
|
|
|
|
data = _get_seq_string(record) # Catches sequence being None
|
|
|
|
assert "\n" not in data
|
|
assert "\r" not in data
|
|
|
|
if self.wrap:
|
|
line = ""
|
|
for i in range(0, len(data), self.wrap):
|
|
line += data[i : i + self.wrap] + "\n"
|
|
line = line[:-1] + "*\n"
|
|
self.handle.write(line)
|
|
else:
|
|
self.handle.write(data + "*\n")
|
|
|
|
|
|
if __name__ == "__main__":
|
|
from Bio._utils import run_doctest
|
|
|
|
run_doctest(verbose=0)
|