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107 lines
2.9 KiB
Python
107 lines
2.9 KiB
Python
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
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# This file is part of the Biopython distribution and governed by your
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# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
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# Please see the LICENSE file that should have been included as part of this
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# package.
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"""Handle the SCOP HIErarchy files.
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The SCOP Hierarchy files describe the SCOP hierarchy in terms of SCOP
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unique identifiers (sunid).
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The file format is described in the SCOP `release notes
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<http://scop.berkeley.edu/release-notes-1.55.html>`_.
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The latest HIE file can be found `elsewhere at SCOP
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<http://scop.mrc-lmb.cam.ac.uk/scop/parse/>`_.
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`Release 1.55 <http://scop.berkeley.edu/parse/dir.hie.scop.txt_1.55>`_
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(July 2001).
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"""
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# TODO - Update the above URLs
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class Record:
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"""Holds information for one node in the SCOP hierarchy.
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Attributes:
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- sunid - SCOP unique identifiers of this node
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- parent - Parents sunid
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- children - Sequence of children sunids
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"""
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def __init__(self, line=None):
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"""Initialize the class."""
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self.sunid = ""
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self.parent = ""
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self.children = []
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if line:
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self._process(line)
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def _process(self, line):
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"""Parse HIE records (PRIVATE).
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Records consist of 3 tab deliminated fields; node's sunid,
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parent's sunid, and a list of children's sunids.
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"""
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# For example ::
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#
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# 0 - 46456,48724,51349,53931,56572,56835,56992,57942
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# 21953 49268 -
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# 49267 49266 49268,49269
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line = line.rstrip() # no trailing whitespace
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columns = line.split("\t") # separate the tab-delineated cols
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if len(columns) != 3:
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raise ValueError(f"I don't understand the format of {line}")
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sunid, parent, children = columns
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if sunid == "-":
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self.sunid = ""
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else:
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self.sunid = int(sunid)
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if parent == "-":
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self.parent = ""
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else:
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self.parent = int(parent)
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if children == "-":
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self.children = ()
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else:
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children = children.split(",")
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self.children = [int(x) for x in children]
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def __str__(self):
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"""Represent the SCOP hierarchy record as a string."""
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s = []
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s.append(str(self.sunid))
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if self.parent:
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s.append(str(self.parent))
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else:
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if self.sunid != 0:
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s.append("0")
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else:
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s.append("-")
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if self.children:
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s.append(",".join(str(x) for x in self.children))
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else:
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s.append("-")
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return "\t".join(s) + "\n"
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def parse(handle):
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"""Iterate over a HIE file as Hie records for each line.
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Arguments:
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- handle - file-like object.
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"""
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for line in handle:
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if line.startswith("#"):
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continue
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yield Record(line)
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