[Bioperl-l] Bio::SearchIO

Janine Arloth janine.arloth at googlemail.com
Fri Mar 5 04:43:57 EST 2010


Hello,
using the example from http://www.bioperl.org/wiki/HOWTO:SearchIO -> Format msf I only got such an alignment:     

                 1                                                   50
test/1-85             ATGTGTGCAT ACATGTGTAA TCATCCTTGC TCCCCAGCAT CAGAGAATGA 
lcl|3013/20-104       ATGTGTGCAT ACATGTGTAA TCATCCTTGC TCCCCAGCAT CAGAGAATGA 


                      51                                                 100
test/1-85             TCTCTCCTTA TGGCCTTTTG TCTTTCTCCA AAGCA 
lcl|3013/20-104       TCTCTCCTTA TGGCCTTTTG TCTTTCTCCA AAGCA 



But I prefer this format:



Query  1    ATGTGTGCATACATGTGTAATCATCCTTGCTCCCCAGCATCAGAGAATGATCTCTCCTTA  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  20   ATGTGTGCATACATGTGTAATCATCCTTGCTCCCCAGCATCAGAGAATGATCTCTCCTTA  79

Query  61   TGGCCTTTTGTCTTTCTCCAAAGCA  85
            |||||||||||||||||||||||||
Sbjct  80   TGGCCTTTTGTCTTTCTCCAAAGCA  104


How can I get this?

Best Regards


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