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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 HIErarchy files, which describe the SCOP hierarchy in
terms of SCOP unique identifiers (sunid).
The file format is described in the scop
"release notes.":http://scop.berkeley.edu/release-notes-1.55.html
The latest HIE file can be found
"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/
"Release 1.55":http://scop.berkeley.edu/parse/dir.hie.scop.txt_1.55 (July 2001)
"""
from types import *
class Record:
"""Holds information for one node in the SCOP hierarchy.
sunid -- SCOP unique identifiers of this node
parent -- Parents sunid
children -- Sequence of childrens sunids
"""
def __init__(self):
self.sunid = ''
self.parent = ''
self.children = []
def __str__(self):
s = []
s.append(str(self.sunid))
if self.parent:
s.append(str(self.parent))
else:
if self.sunid != 0:
s.append('0')
else:
s.append('-')
if self.children :
child_str = map(str, self.children)
s.append(",".join(child_str))
else:
s.append('-')
return "\t".join(s) + "\n"
class Iterator:
"""Iterates over a HIE file.
"""
def __init__(self, handle, parser=None):
"""Create an object that iterates over a HIE file.
handle -- file-like object.
parser -- an optional Parser object to change 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 HIE 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 HIE records.
Records consist of 3 tab deliminated fields; node's sunid,
parent's sunid, and a list of children's sunids.
"""
#For example ::
#
#0 - 46456,48724,51349,53931,56572,56835,56992,57942
#21953 49268 -
#49267 49266 49268,49269
def parse(self, entry):
"""Returns a Hie Record """
entry = entry.rstrip() # no trailing whitespace
columns = entry.split('\t') # separate the tab-delineated cols
if len(columns) != 3:
raise SyntaxError, "I don't understand the format of %s" % entry
rec = Record()
rec.sunid, rec.parent, children = columns
if rec.sunid =='-' : rec.sunid = ''
if rec.parent =='-' : rec.parent = ''
else : rec.parent = int( rec.parent )
if children =='-' :
rec.children = ()
else :
rec.children = children.split(',')
rec.children = map ( int, rec.children )
rec.sunid = int(rec.sunid)
return rec
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