# 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.
# Patched by Brad Chapman.
# Chris Wroe added modifications for work in myGrid
"""
This module provides code to work with the WWW version of BLAST
provided by the NCBI.
http://www.ncbi.nlm.nih.gov/BLAST/
Classes:
BlastParser Parses output from WWW blast.
_Scanner Scans output from NCBI's BLAST WWW server.
Functions:
blast Do a BLAST search against the WWW page. (Deprecated)
blasturl Do a BLAST search against the stable blasturl. (Deprecated)
qblast Do a BLAST search using the QBLAST API.
"""
import string
import re
import sgmllib
try:
import cStringIO as StringIO
except ImportError:
import StringIO
from Bio.ParserSupport import *
class BlastParser(AbstractParser):
"""Parses WWW BLAST data into a Record.Blast object.
"""
def __init__(self):
"""__init__(self)"""
import NCBIStandalone
self._scanner = _Scanner()
self._consumer = SGMLStrippingConsumer(NCBIStandalone._BlastConsumer())
def parse(self, handle):
"""parse(self, handle)"""
self._scanner.feed(handle, self._consumer)
return self._consumer.data
class _Scanner:
"""Scan BLAST output from NCBI's web server at:
http://www.ncbi.nlm.nih.gov/BLAST/
Tested with BLAST v2.0.10
Methods:
feed Feed data into the scanner.
"""
def feed(self, handle, consumer):
"""S.feed(handle, consumer)
Feed in a BLAST report for scanning. handle is a file-like
object that contains the BLAST report. consumer is a Consumer
object that will receive events as the report is scanned.
"""
from Bio import File
# This stuff appears in 2.0.12.
#
#
#
# BLAST Search Results
#
# 
# BLAST Formatted information
#
#
#
#
#