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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.
from Bio.SeqFeature import Reference
from Bio.Seq import MutableSeq
"""Hold Kabat data in a straightforward format.
classes:
o Record - All of the information in a Kabat record.
o KabatReference - hold reference data for a record.
o Annotation - Hold the information in a Feature Table.
"""
class KabatReference( Reference ):
def __init__( self ):
Reference.__init__( self )
def print_kabat_reference( self ):
print self.authors
print self.journal
print self.pubmed_id
class Record:
"""Hold Kabat information in a format similar to the original record.
The Record class is meant to make data easy to get to when you are
just interested in looking at Kabat data.
Attributes:
kabatid - id of the sequence in the Kabat database
creation_date
date_last_mod - date of last modification
definition - definition of sequence
species
nucleic_acid_refs - references to nucleic acid sequence
amino_acid_refs - references to amino acid sequence
annotation
nucleotide_sequence_name
amino_acid_sequence_name
nucleotide_sequence
amino_acid_sequence
"""
def __init__(self):
self.kabatid = ''
self.creation_date = ''
self.date_last_mod = ''
self.definition = ''
self.species = ''
self.nucleotide_sequence_name = ''
self.amino_acid_sequence_name = ''
self.nucleotide_refs = []
self.amino_acid_refs = []
self.annotation = {}
self.nucleotide_sequence = MutableSeq( "" )
self.amino_acid_sequence = MutableSeq( "" )
def print_kabat( self ):
print 'Kabat id: %s' % self.kabatid
print 'Creation date: %s' % self.creation_date
print 'Last modification: %s' % self.date_last_mod
print self.definition
print 'Species; %s' % self.species
print self.nucleotide_sequence_name
print self.amino_acid_sequence_name
for ref in self.amino_acid_refs:
ref.print_kabat_reference()
for ref in self.nucleotide_refs:
ref.print_kabat_reference()
ks = self.annotation.keys()
ks.sort()
for key in ks:
val = self.annotation[ key ]
print '%s: %s' % ( key, val )
dna_seq = self.nucleotide_sequence.tostring()
print_seq( dna_seq )
amino_seq = self.amino_acid_sequence.tostring()
print_seq( amino_seq )
def print_seq( seq ):
print ""
for j in range( 0, len( seq ), 80 ):
print seq[ j: j + 80 ]
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