--- biopython-1.44/Bio/SeqUtils/__init__.py.old 2007-09-14 09:38:35.000000000 -0400 +++ biopython-1.44/Bio/SeqUtils/__init__.py 2007-12-17 11:07:27.000000000 -0500 @@ -7,8 +7,7 @@ # license. Please see the LICENSE file that should have been included # as part of this package. -import os, sys, getopt, re, time -from string import maketrans +import re, time from Bio import SeqIO from Bio import Translate from Bio.Seq import Seq @@ -277,8 +276,9 @@ nice looking 6 frame translation with GC content - code from xbbtools similar to DNA Striders six-frame translation """ - comp = complement(seq) - anti = reverse(comp) + from Bio.Seq import reverse_complement + anti = reverse_complement(seq) + comp = anti[::-1] length = len(seq) frames = {} for i in range(0,3): @@ -399,6 +399,7 @@ # {{{ if __name__ == '__main__': + import sys, getopt # crude command line options to use most functions directly on a FASTA file options = {'apply_on_multi_fasta':0, 'quick':0,