Spaces:
No application file
No application file
File size: 2,963 Bytes
b7731cd |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 |
# Copyright 2001 by Gavin E. Crooks. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Handle the SCOP HIErarchy files.
The SCOP Hierarchy files 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).
"""
# TODO - Update the above URLs
class Record:
"""Holds information for one node in the SCOP hierarchy.
Attributes:
- sunid - SCOP unique identifiers of this node
- parent - Parents sunid
- children - Sequence of children sunids
"""
def __init__(self, line=None):
"""Initialize the class."""
self.sunid = ""
self.parent = ""
self.children = []
if line:
self._process(line)
def _process(self, line):
"""Parse HIE records (PRIVATE).
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
line = line.rstrip() # no trailing whitespace
columns = line.split("\t") # separate the tab-delineated cols
if len(columns) != 3:
raise ValueError(f"I don't understand the format of {line}")
sunid, parent, children = columns
if sunid == "-":
self.sunid = ""
else:
self.sunid = int(sunid)
if parent == "-":
self.parent = ""
else:
self.parent = int(parent)
if children == "-":
self.children = ()
else:
children = children.split(",")
self.children = [int(x) for x in children]
def __str__(self):
"""Represent the SCOP hierarchy record as a string."""
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:
s.append(",".join(str(x) for x in self.children))
else:
s.append("-")
return "\t".join(s) + "\n"
def parse(handle):
"""Iterate over a HIE file as Hie records for each line.
Arguments:
- handle - file-like object.
"""
for line in handle:
if line.startswith("#"):
continue
yield Record(line)
|