[Bioperl-l] Bio::SearchIO

Jason Stajich jason at bioperl.org
Tue Mar 9 15:49:06 EST 2010


SearchIO writer -> BLAST format. presumably something like 
Bio::SearchIO::Writer::TextResultWriter

Janine Arloth wrote, On 3/5/10 1:43 AM:
> 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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> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>    


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