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# Copyright 2001 by Tarjei Mikkelsen. All rights reserved.
# Copyright 2007 by Michiel de Hoon. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""
This module provides code to work with the KEGG Ligand/Compound database.
Functions:
parse - Returns an iterator giving Record objects.
Classes:
Record - A representation of a KEGG Ligand/Compound.
"""
# other Biopython stuff
from Bio.KEGG import _write_kegg
from Bio.KEGG import _wrap_kegg
# Set up line wrapping rules (see Bio.KEGG._wrap_kegg)
name_wrap = [0, "",
(" ","$",1,1),
("-","$",1,1)]
id_wrap = lambda indent : [indent, "",
(" ","",1,0)]
struct_wrap = lambda indent : [indent, "",
(" ","",1,1)]
class Record(object):
"""Holds info from a KEGG Ligand/Compound record.
Members:
entry The entry identifier.
name A list of the compund names.
formula The chemical formula for the compound
mass The molecular weight for the compound
pathway A list of 3-tuples: (database, id, pathway)
enzyme A list of 2-tuples: (enzyme id, role)
structures A list of 2-tuples: (database, list of struct ids)
dblinks A list of 2-tuples: (database, list of link ids)
"""
def __init__(self):
"""__init___(self)
Create a new Record.
"""
self.entry = ""
self.name = []
self.formula = ""
self.mass = ""
self.pathway = []
self.enzyme = []
self.structures = []
self.dblinks = []
def __str__(self):
"""__str__(self)
Returns a string representation of this Record.
"""
return self._entry() + \
self._name() + \
self._formula() + \
self._mass() + \
self._pathway() + \
self._enzyme() + \
self._structures() + \
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 _formula(self):
return _write_kegg("FORMULA",
[self.formula])
def _mass(self):
return _write_kegg("MASS",
[self.mass])
def _pathway(self):
s = []
for entry in self.pathway:
s.append(entry[0] + ": " + entry[1] + " " + entry[2])
return _write_kegg("PATHWAY",
[_wrap_kegg(l, wrap_rule = id_wrap(16)) \
for l in s])
def _enzyme(self):
s = ""
for entry in self.enzyme:
if entry[1]:
t = entry[0] + " (" + entry[1] + ")"
else:
t = entry[0]
s = s + t.ljust(16)
return _write_kegg("ENZYME",
[_wrap_kegg(s, wrap_rule = id_wrap(0))])
def _structures(self):
s = []
for entry in self.structures:
s.append(entry[0] + ": " + " ".join(entry[1]) + " ")
return _write_kegg("STRUCTURES",
[_wrap_kegg(l, wrap_rule = struct_wrap(5)) \
for l in s])
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 Ligan/Compound 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,
>>> handle = open("KEGG/compound.sample")
>>> for record in parse(handle):
... print record.entry, record.name[0]
...
C00023 Iron
C00017 Protein
C00099 beta-Alanine
C00294 Inosine
C00298 Trypsin
C00348 Undecaprenyl phosphate
C00349 2-Methyl-3-oxopropanoate
C01386 NH2Mec
"""
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=="ENZYME ":
while data:
column = data[:16]
data = data[16:]
if '(' in column:
entry = column.split()
enzyme = (entry[0], entry[1][1:-1])
else:
enzyme = (column.strip(), "")
record.enzyme.append(enzyme)
elif keyword=="PATHWAY ":
if data[:5]=='PATH:':
path, map, name = data.split(None,2)
pathway = (path[:-1], map, name)
record.pathway.append(pathway)
else:
pathway = record.pathway[-1]
path, map, name = pathway
name = name + " " + data
pathway = path, map, name
record.pathway[-1] = pathway
elif keyword=="FORMULA ":
record.formula = data
elif keyword=="MASS ":
record.mass = data
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
def _test():
"""Run the Bio.KEGG.Compound module's doctests.
This will try and locate the unit tests directory, and run the doctests
from there in order that the relative paths used in the examples work.
"""
import doctest
import os
if os.path.isdir(os.path.join("..","..","..","Tests")):
print "Running doctests..."
cur_dir = os.path.abspath(os.curdir)
os.chdir(os.path.join("..","..","..","Tests"))
doctest.testmod()
os.chdir(cur_dir)
del cur_dir
print "Done"
if __name__ == "__main__":
_test()
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