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Des.py

# 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)
"""


00018 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, line=None):
        self.sunid = ''
        self.nodetype = ''
        self.sccs = ''
        self.name = ''
        self.description =''
        if line:
            self._process(line)
        
00044     def _process(self, line):
        """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

        line = line.rstrip()  # no trailing whitespace
        columns = line.split("\t")  # separate the tab-delineated cols
        if len(columns) != 5:
            raise ValueError, "I don't understand the format of %s" % line
        
        sunid, self.nodetype, self.sccs, self.name, self.description = columns
        if self.name=='-': self.name =''
        self.sunid = int(sunid)


    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"


def parse(handle):
    """Iterates over a DES file, returning a Des record for each line
    in the file.

    Arguments:
        handle -- file-like object
    """
    for line in handle:
        yield Record(line)


00092 class Iterator:
    """Iterates over a DES file.
    """
00095     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.
                  
        """
        import warnings
        warnings.warn("Bio.SCOP.Des.Iterator is deprecated. Please use Bio.SCOP.Des.parse() instead.", DeprecationWarning)
        from types import FileType, InstanceType
        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

00113     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:
    def __init__(self):
        import warnings
        warnings.warn("""Bio.SCOP.Des.Parser is deprecated.
        Instead of

        parser = Des.Parser()
        record = parser.parse(entry)

        please use

        record = Des.Record(entry)
        """, DeprecationWarning)

    def parse(self, entry):
        """Returns a Des Record """
        return Record(entry)

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