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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.
import os
import string
from types import *
from Bio import File
from Bio import ParserSupport
from Bio import Fasta
from Bio import Alphabet
def title_to_ids(title):
"""Function to convert a title into the id, name, and description.
This is just a quick-n-dirty implementation, and is definately not meant
to handle every FASTA title line case.
"""
# first split the id information from the description
# the first item is the id info block, the rest is the description
all_info = string.split(title, " ")
id_info = all_info[0]
rest = all_info[1:]
descr = string.join(rest, " ")
# now extract the ids from the id block
# gi|5690369|gb|AF158246.1|AF158246
id_info_items = string.split(id_info, "|")
id = id_info_items[3] # the id with version info
name = id_info_items[4] # the id without version info
return id, name, descr
tests = [ 'lupine.nu', 'elderberry.nu', 'phlox.nu', 'centaurea.nu', \
'wisteria.nu', 'sweetpea.nu', 'lavender.nu' ]
record_parser = Fasta.RecordParser()
sequence_parser = Fasta.SequenceParser(Alphabet.generic_dna, title_to_ids)
for test in tests:
print "testing %s" % test
datafile = os.path.join( 'Nucleic', test )
src_handle = open( datafile )
data = record_parser.parse( src_handle )
print data
for test in tests:
print "testing %s" % test
datafile = os.path.join( 'Nucleic', test )
src_handle = open( datafile )
data = sequence_parser.parse( src_handle )
print data.id
print data.name
print data.description
print repr(data.seq)
tests = [ 'aster.pro', 'rosemary.pro', 'rose.pro', 'loveliesbleeding.pro' ]
sequence_parser = Fasta.SequenceParser(Alphabet.generic_protein, title_to_ids)
for test in tests:
print "testing %s" % test
datafile = os.path.join( 'Amino', test )
src_handle = open( datafile )
data = record_parser.parse( src_handle )
print data
for test in tests:
print "testing %s" % test
datafile = os.path.join( 'Amino', test )
src_handle = open( datafile )
data = sequence_parser.parse( src_handle )
print data.id
print data.name
print data.description
print repr(data.seq)
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