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# Copyright 2017 by Kozo Nishida. 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.
"""Code to work with the KEGG Gene database.
Functions:
- parse - Returns an iterator giving Record objects.
Classes:
- Record - A representation of a KEGG Gene.
"""
from Bio.KEGG import _default_wrap, _wrap_kegg, _write_kegg
# Set up line wrapping rules (see Bio.KEGG._wrap_kegg)
name_wrap = [0, "", (" ", "$", 1, 1), ("-", "$", 1, 1)]
id_wrap = _default_wrap
class Record:
"""Holds info from a KEGG Gene record.
Attributes:
- entry The entry identifier.
- name A list of the gene names.
- definition The definition for the gene.
- orthology A list of 2-tuples: (orthology id, role)
- organism A tuple: (organism id, organism)
- position The position for the gene
- motif A list of 2-tuples: (database, list of link ids)
- dblinks A list of 2-tuples: (database, list of link ids)
"""
def __init__(self):
"""Initialize new record."""
self.entry = ""
self.name = []
self.definition = ""
self.orthology = []
self.organism = ""
self.position = ""
self.motif = []
self.dblinks = []
def __str__(self):
"""Return a string representation of this Record."""
return self._entry() + self._name() + self._dblinks() + "///"
def _entry(self):
return _write_kegg("ENTRY", [self.entry])
def _name(self):
return _write_kegg(
"NAME", [_wrap_kegg(l, wrap_rule=name_wrap) for l in self.name]
)
def _definition(self):
return _write_kegg("DEFINITION", [self.definition])
def _dblinks(self):
s = []
for entry in self.dblinks:
s.append(entry[0] + ": " + " ".join(entry[1]))
return _write_kegg("DBLINKS", [_wrap_kegg(l, wrap_rule=id_wrap(9)) for l in s])
def parse(handle):
"""Parse a KEGG Gene file, returning Record objects.
This is an iterator function, typically used in a for loop. For
example, using one of the example KEGG files in the Biopython
test suite,
>>> with open("KEGG/gene.sample") as handle:
... for record in parse(handle):
... print("%s %s" % (record.entry, record.name[0]))
...
b1174 minE
b1175 minD
"""
record = Record()
for line in handle:
if line[:3] == "///":
yield record
record = Record()
continue
if line[:12] != " ":
keyword = line[:12]
data = line[12:].strip()
if keyword == "ENTRY ":
words = data.split()
record.entry = words[0]
elif keyword == "NAME ":
data = data.strip(";")
record.name.append(data)
elif keyword == "DEFINITION ":
record.definition = data
elif keyword == "ORTHOLOGY ":
id, name = data.split(" ")
orthology = (id, name)
record.orthology.append(orthology)
elif keyword == "ORGANISM ":
id, name = data.split(" ")
organism = (id, name)
record.organism = organism
elif keyword == "POSITION ":
record.position = data
elif keyword == "MOTIF ":
key, values = data.split(": ")
values = values.split()
row = (key, values)
record.motif.append(row)
elif keyword == "DBLINKS ":
if ":" in data:
key, values = data.split(": ")
values = values.split()
row = (key, values)
record.dblinks.append(row)
else:
row = record.dblinks[-1]
key, values = row
values.extend(data.split())
row = key, values
record.dblinks[-1] = row
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
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