ant dna

gistfile1.txt

example map for
strenght: .AG. GC.. ...A ..GC | AC.. GT.. T.TC ....
size:     CG.. .... ...C ..T. | ..AC .... ...C ..A.

ant 1: TTTC AAAG GGGG GAGC TGTA AGGA TTCT CCAG 
ant 2: CCGC GGGC AGGT TTAC TACT TGGA TACC ACTC 

Then we match each gene in strength and size against the ant unless it's a '.'
If we have match the score is increased. If we have a similarity (A<->G or C<->T)
the score is not changed and otherwise it's decreased.

For a fully working example script that works with strings:

http://gist.github.com/164135


example output:
CCGT TGTA GTAC GACT CCAA GCTT GCGT GTTG 
size:      1 
strength:  0 
weight:   -2 
ATCT GGGT GGAC GCAC TTTA TTGG CGCC GCTG 
size:      2 
strength:  0 
weight:   -3 
GCAG ACTA CCAT TGTA CCAC CCCC ACGT CAGG 
size:      0 
strength: -2 
weight:    4 
CAGA CCTT CTCC TTAC CCGA CCTA CCAG TATT 
size:      0 
strength:  2 
weight:    5 
GTTG TGTC TTGT CTAA TTCC CGAA TAGC CTTC 
size:      1 
strength:  0 
weight:   -2 
TAGT ACTG TCAT TTTG TTCG GTAA TTCG GACT 
size:     -2 
strength:  3 
weight:    3 
ACCA GCAA GCCG ATAC CCCT CTTA TCTG TGGA 
size:     -2 
strength:  5 
weight:    3 
AAAC CTCG TGGA TCTC TTAG ATAA ACAA CGCA 
size:      1 
strength:  0 
weight:    1 
AGCT CTCG CAAC AGTT TAGC CCTC ATGG CCTA 
size:      3 
strength: -4 
weight:    3 
GCTT CCCC CCAC CATT TACG CTAG TAGA TGGC 
size:      1 
strength:  2 
weight:   -6 
GCAA GTCT AAAA CATC GTGC GCAA ATAC TCAC 
size:      3 
strength:  0 
weight:    2