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# Copyright 2001 by Katharine Lindner. 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.
"""Parser for SAF (Simple Alignment Format).
http://www.embl-heidelberg.de/predictprotein/Dexa/optin_safDes.html
"""
# standard library
import string
import array
import os
import re
import sgmllib
import urlparse
# XML from python 2.0
from xml.sax import handler
from xml.sax.handler import ContentHandler
# Martel
import Martel
from Martel import RecordReader
from Martel import Dispatch
from Bio.ParserSupport import EventGenerator
from Bio.ParserSupport import AbstractConsumer
from Bio import File
from Bio.Align.Generic import Alignment
import Bio.Alphabet
import saf_format
import Record
class Iterator:
"""Iterator interface to move over a file of Saf entries one at a time.
"""
def __init__(self, handle, parser = None):
"""Initialize the iterator.
Arguments:
o handle - A handle with Saf entries to iterate through.
o parser - An optional parser to pass the entries through before
returning them. If None, then the raw entry will be returned.
"""
self.handle = File.UndoHandle( handle )
self._reader = RecordReader.Everything( self.handle )
self._parser = parser
def next(self):
"""Return the next Saf record from the handle.
Will return None if we ran out of records.
"""
data = self._reader.next()
if self._parser is not None:
if data:
dumpfile = open( 'dump', 'w' )
dumpfile.write( data )
dumpfile.close()
return self._parser.parse(File.StringHandle(data))
return data
def __iter__(self):
return iter(self.next, None)
class _Scanner:
"""Start up Martel to do the scanning of the file.
This initialzes the Martel based parser and connects it to a handler
that will generate events for a Feature Consumer.
"""
def __init__(self, debug = 0):
"""Initialize the scanner by setting up our caches.
Creating the parser takes a long time, so we want to cache it
to reduce parsing time.
Arguments:
o debug - The level of debugging that the parser should
display. Level 0 is no debugging, Level 2 displays the most
debugging info (but is much slower). See Martel documentation
for more info on this.
"""
# a listing of all tags we are interested in scanning for
# in the MartelParser
self.interest_tags = [ 'candidate_line', 'saf_record' ]
# make a parser that returns only the tags we are interested in
expression = Martel.select_names( saf_format.saf_record, self.interest_tags)
self._parser = expression.make_parser(debug_level = debug)
def feed(self, handle, consumer):
"""Feed a set of data into the scanner.
Arguments:
o handle - A handle with the information to parse.
o consumer - The consumer that should be informed of events.
"""
consumer.set_interest_tags( self.interest_tags )
self._parser.setContentHandler( consumer )
# self._parser.setErrorHandler(handle.ErrorHandler())
self._parser.parseFile(handle)
class _RecordConsumer( Dispatch.Dispatcher ):
"""Create a Saf Record object from scanner generated information.
"""
def __init__(self ):
Dispatch.Dispatcher.__init__( self )
self.data = Record.Record()
self._refresh()
def _refresh( self ):
self._sequences = {}
self._names = {}
self._history = []
self._guide = ''
self._ref_length = 0
self._ordinal = 0
def set_interest_tags( self, interest_tags ):
self.interest_tags = interest_tags
def startDocument(self):
self.data = Record.Record()
self._refresh()
def start_candidate_line(self, name, attrs):
self.save_characters()
def end_candidate_line(self, candidate_lines ):
candidate_line = self.get_characters()
name = candidate_line.split( ' ' )[ 0 ]
sequence = candidate_line[ len( name ): ]
name = name.strip()
sequence = sequence.replace( " ", "" )
if( self._guide == '' ):
self._guide = name
self._ref_length = len( sequence )
elif( name == self._guide ):
history = []
self._ref_length = len( sequence )
try:
self._history.index( name )
except ValueError:
self._names[ self._ordinal ] = name
self._ordinal = self._ordinal + 1
self._history.append( name )
sequence = sequence.strip()
try:
sequence = self._sequences[ name ] + sequence
except KeyError:
pass
self._sequences[ name ] = sequence
def start_saf_record( self, sequence, attrs ):
self._sequences = {}
def end_saf_record( self, saf_record ):
ordinals = self._names.keys()
ordinals.sort()
for ordinal in ordinals:
name = self._names[ ordinal ]
sequence = self._sequences[ name ]
self.data.alignment.add_sequence( name, sequence )
self._refresh()
class RecordParser:
"""Parse Saf files into Record objects
"""
def __init__(self, debug_level = 0):
"""Initialize the parser.
Arguments:
o debug_level - An optional argument that specifies the amount of
debugging information Martel should spit out. By default we have
no debugging info (the fastest way to do things), but if you want
you can set this as high as two and see exactly where a parse fails.
"""
self._scanner = _Scanner(debug_level)
def parse(self, handle):
"""Parse the specified handle into a SAF record.
"""
self._consumer = _RecordConsumer()
self._scanner.feed(handle, self._consumer)
return self._consumer.data
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