struct_renum_to_seq2.py

#!/usr/bin/env python
'''
Created on Jan 18, 2013

@author: lunt
'''
import sys

import Bio.pairwise2 as PW


def printall(alignments):
	print "one set"
	for a in alignments:
		sys.stderr.write( PW.format_alignment(*a) )
		sys.stderr.write('\n')


def main():
	
	seq1 = "AAAABBBAAAACCCCCCCCCCCCCCAAAABBBAAAA"
	seq2 = "AABBBAAAACCCCAAAABBBAA"


	breaks = set([11])
	
	nogaps = lambda x,y: -2000 -y #There really should not be inserts with respect to the database sequence.
	specificgaps = lambda x,y: (-2 -y) if x in breaks else (-2000 -y) #This makes it very expensive to open a gap anywhere but in the middle of the CCs


	alignments = PW.align.globalmc(seq1,seq2,1,-1,nogaps,specificgaps)

	printall(alignments)

	

	breaks = set([3])
	#now, it should break after the first B in seq2, if it doesnt: there is a problem
	alignments = PW.align.globalmc(seq1,seq2,1,-1,nogaps,specificgaps)
	printall(alignments)



if __name__ == '__main__':
	main()