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# Copyright 1999 by Jeffrey Chang. 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.
"""
This module provides code to work with the keywlist.txt file from
SwissProt.
http://www.expasy.ch/sprot/sprot-top.html
Classes:
ListParser Parses a keywlist.txt file into a list of keywords.
_Scanner Scans the keywlist.txt file.
_ListConsumer Consumes keywlist data to a list.
Functions:
extract_keywords Return the keywords from a keywlist.txt file.
"""
from types import *
from Bio import File
from Bio.ParserSupport import *
class ListParser(AbstractParser):
"""Parses keywlist.txt data into a list of keywords.
"""
def __init__(self):
self._scanner = _Scanner()
self._consumer = _ListConsumer()
def parse(self, handle):
self._scanner.feed(handle, self._consumer)
return self._consumer.keywords
class _Scanner:
"""Scan the keywlist.txt file included with the SwissProt distribution.
Tested with:
Release 37
Release 38
"""
def feed(self, handle, consumer):
"""feed(self, handle, consumer)
Feed in the keywlist.txt file for scanning. handle is a file-like
object that contains keyword information. consumer is a
Consumer object that will receive events as the report is scanned.
"""
if isinstance(handle, File.UndoHandle):
uhandle = handle
else:
uhandle = File.UndoHandle(handle)
self._scan_header(uhandle, consumer)
self._scan_keywords(uhandle, consumer)
self._scan_footer(uhandle, consumer)
def _scan_header(self, uhandle, consumer):
consumer.start_header()
read_and_call(uhandle, consumer.noevent, start='----')
read_and_call(uhandle, consumer.noevent, blank=1)
read_and_call(uhandle, consumer.noevent, contains="SWISS-PROT")
read_and_call(uhandle, consumer.noevent, contains="Release")
read_and_call(uhandle, consumer.noevent, blank=1)
read_and_call(uhandle, consumer.noevent, start='----')
read_and_call(uhandle, consumer.noevent, blank=1)
read_and_call(uhandle, consumer.noevent, start='List of keywords')
read_and_call(uhandle, consumer.noevent, blank=1)
read_and_call(uhandle, consumer.noevent, start='----')
while 1:
if attempt_read_and_call(uhandle, consumer.noevent, start='----'):
break
read_and_call(uhandle, consumer.noevent, blank=0)
read_and_call(uhandle, consumer.noevent, start='Document name')
read_and_call(uhandle, consumer.noevent, start='----')
read_and_call(uhandle, consumer.noevent, blank=1)
consumer.end_header()
def _scan_keywords(self, uhandle, consumer):
consumer.start_keywords()
# SwissProt38 starts with lines:
# Keyword
# ______________________________________
#
# Check and see if it's release 38, and parse it.
if attempt_read_and_call(uhandle, consumer.noevent, start='Keyword'):
read_and_call(uhandle, consumer.noevent, start='____')
while 1:
if not attempt_read_and_call(uhandle, consumer.keyword, blank=0):
break
read_and_call(uhandle, consumer.noevent, blank=1)
consumer.end_keywords()
def _scan_footer(self, uhandle, consumer):
consumer.start_footer()
read_and_call(uhandle, consumer.noevent, start='----')
while 1:
if attempt_read_and_call(uhandle, consumer.noevent, start='----'):
break
read_and_call(uhandle, consumer.copyright, blank=0)
consumer.end_footer()
class _ListConsumer(AbstractConsumer):
"""Consumer that converts a keywlist.txt file into a list of keywords.
Members:
keywords List of keywords.
"""
def __init__(self):
self.keywords = None
def start_keywords(self):
self.keywords = []
def keyword(self, line):
self.keywords.append(string.rstrip(line))
def extract_keywords(keywlist_handle):
"""extract_keywords(keywlist_handle) -> list of keywords
Return the keywords from a keywlist.txt file.
"""
if type(keywlist_handle) is not FileType and \
type(keywlist_handle) is not InstanceType:
raise ValueError, "I expected a file handle or file-like object"
return ListParser().parse(keywlist_handle)
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