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90 lines
2.9 KiB
Python
90 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 DEScription file.
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The file format is described in the scop
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"release notes.":http://scop.berkeley.edu/release-notes-1.55.html
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The latest DES file can be found
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"elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/
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"Release 1.55":http://scop.berkeley.edu/parse/des.cla.scop.txt_1.55 (July 2001)
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"""
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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
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- nodetype - One of 'cl' (class), 'cf' (fold), 'sf' (superfamily),
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'fa' (family), 'dm' (protein), 'sp' (species), 'px' (domain).
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Additional node types may be added.
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- sccs - SCOP concise classification strings. e.g. b.1.2.1
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- name - The SCOP ID (sid) for domains (e.g. d1anu1), currently empty for other node types
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- description - e.g. "All beta proteins","Fibronectin type III",
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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.nodetype = ""
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self.sccs = ""
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self.name = ""
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self.description = ""
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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 DES records (PRIVATE).
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Records consist of 5 tab deliminated fields,
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sunid, node type, sccs, node name, node description.
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"""
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# For example ::
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#
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# 21953 px b.1.2.1 d1dan.1 1dan T:,U:91-106
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# 48724 cl b - All beta proteins
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# 48725 cf b.1 - Immunoglobulin-like beta-sandwich
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# 49265 sf b.1.2 - Fibronectin type III
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# 49266 fa b.1.2.1 - Fibronectin type III
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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) != 5:
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raise ValueError(f"I don't understand the format of {line}")
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sunid, self.nodetype, self.sccs, self.name, self.description = columns
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if self.name == "-":
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self.name = ""
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self.sunid = int(sunid)
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def __str__(self):
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"""Represent the SCOP description record as a tab-separated string."""
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s = []
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s.append(self.sunid)
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s.append(self.nodetype)
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s.append(self.sccs)
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if self.name:
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s.append(self.name)
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else:
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s.append("-")
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s.append(self.description)
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return "\t".join(map(str, s)) + "\n"
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def parse(handle):
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"""Iterate over a DES file as a Des record 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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