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# Copyright 1999 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.
import os
import types
import string
from types import *
from Bio import File
from Bio import ParserSupport
from Bio import Gobase
tests = [ 'G405967.htm', 'G423945.htm', 'P2661406.htm', 'S4323016.htm' ]
# 'ps00488.txt', 'ps00546.txt' ]
record_parser = Gobase.RecordParser()
def print_list( list ):
for item in list:
print "testing %s" % item
def print_sequence_record( data ):
print 'modlecule type %s ' % data.molecule_type
print 'is plasmid %s ' % data.is_plasmid
print 'shape %s' % data.shape
# submission_date
# update_date
print 'Entrez Record %s' % data.entrez_record
print 'Genbank accession %s' % data.genbank_accession
def print_gene_record( data ):
print 'Gene class is %s' % data.gene_class
print 'Plasmid encoded is %s' % data.is_plasmid
print 'Partial gene %s' % data.is_partial_gene
print 'Pseudo %s' % data.is_pseudo_gene
print 'Transpliced gene %s' % data.is_transpliced_gene
print 'Chloroplast origin %s' % data.chloroplast_origin
print 'Contains intron %s' % data.contains_intron
print 'ORF %s' % data.orf
print 'Included in an intron %s' % data.included_in_intron
# published_info
print 'Genbank accession %s' % data.genbank_accession
print 'Entrez record %s' % data.entrez_record
print 'Product type %s' % data.product_type
print 'Product class %s' % data.product_class
def print_protein_record( data ):
print 'Product class is %s ' % data.product_class
print 'Gene class is %s ' % data.gene_class
print 'Partial protein %s ' % data.is_partial_protein
print 'Plasmid %s' % data.is_plasmid
print 'Function %s ' % data.function
print 'Entrez record %s' % data.entrez_record
for test in tests:
print "testing %s" % test
datafile = os.path.join( 'Gobase', test )
src_handle = open( datafile )
data = record_parser.parse( src_handle )
segments = string.split( str( data.__class__ ), '.' )
klass = segments[ len( segments ) - 1 ]
print klass
if( klass == 'SequenceRecord' ):
print_sequence_record( data )
elif( klass == 'GeneRecord' ):
print_gene_record( data )
elif( klass == 'ProteinRecord' ):
print_protein_record( data )
print data.species_name
print data.taxon_division
print '\n'
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