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# Copyright 2001 by Gavin E. Crooks. 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.
""" Handle the SCOP DEScription file.
The file format is described in the scop
"release notes.":http://scop.berkeley.edu/release-notes-1.55.html
The latest DES file can be found
"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/
"Release 1.55":http://scop.berkeley.edu/parse/des.cla.scop.txt_1.55 (July 2001)
"""
from types import *
class Record:
"""Holds information for one node in the SCOP hierarchy.
sunid -- SCOP unique identifiers
nodetype -- One of 'cl' (class), 'cf' (fold), 'sf' (superfamily),
'fa' (family), 'dm' (protein), 'sp' (species),
'px' (domain). Additional node types may be added.
sccs -- SCOP concise classification strings. e.g. b.1.2.1
name -- The SCOP ID (sid) for domains (e.g. d1anu1),
currently empty for other node types
description -- e.g. "All beta proteins","Fibronectin type III",
"""
def __init__(self):
self.sunid = ''
self.nodetype = ''
self.sccs = ''
self.name = ''
self.description =''
def __str__(self):
s = []
s.append(self.sunid)
s.append(self.nodetype)
s.append(self.sccs)
if self.name :
s.append(self.name)
else :
s.append("-")
s.append(self.description)
return "\t".join(map(str,s)) + "\n"
class Iterator:
"""Iterates over a DES file.
"""
def __init__(self, handle, parser=None):
"""Create an object that iterates over a DES file.
handle -- file-like object.
parser -- an optional Parser object to chang the results into
another form. If set to None, then the raw contents
of the file will be returned.
"""
if type(handle) is not FileType and type(handle) is not InstanceType:
raise TypeError, "I expected a file handle or file-like object"
self._handle = handle
self._parser = parser
def next(self):
"""Retrieve the next DES record."""
while 1:
line = self._handle.readline()
if not line: return None
if line[0] !='#': break # Not a comment line
if self._parser is not None :
return self._parser.parse(line)
return line
def __iter__(self):
return iter(self.next, None)
class Parser:
"""Parses DES records.
Records consist of 5 tab deliminated fields,
sunid, node type, sccs, node name, node description.
"""
#For example ::
#
#21953 px b.1.2.1 d1dan.1 1dan T:,U:91-106
#48724 cl b - All beta proteins
#48725 cf b.1 - Immunoglobulin-like beta-sandwich
#49265 sf b.1.2 - Fibronectin type III
#49266 fa b.1.2.1 - Fibronectin type III
def parse(self, entry):
"""Returns a Des Record """
entry = entry.rstrip() # no trailing whitespace
columns = entry.split("\t") # separate the tab-delineated cols
if len(columns) != 5:
raise SyntaxError, "I don't understand the format of %s" % entry
rec = Record()
rec.sunid, rec.nodetype, rec.sccs, rec.name, rec.description = columns
if rec.name == '-' : rec.name =''
rec.sunid = int(rec.sunid)
return rec
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