[Bioperl-l] How to format an alignment to occur over several lines instead of one line

[Jason Stajich]

Parsing with Bio::SearchIO and converting the HSPs to Bio::SimpleAlign
objects with the $hsp->get_aln method and then writing it Bio::AlignIO is
one option.  See the SearchIO HOWTO.

Or if you want to look at them, what about just in the original BLAST
report format?  Bio::SearchIO::Writer::TextResultWriter or
HTMLResultWriter will also do this for you.

-jason
On Tue, 25 May 2004 omid at rogers.com wrote:

> Hello All,
>
> I have parsed alignments from a blast report using the BPlite module.
> However the alignment is in the form of:
>
> 1 aaaaaaaaaaaaaaaaaaaaaaaaaa....aaaaaaaa 1000
>   ||||||||||||||||||||||||||....||||||||
> 1 aaaaaaaaaaaaaaaaaaaaaaaaaa....aaaaaaaa 1000
>
> depending on the size of the alignment this could be quite long.
>
> How can get the alignment to occur over several line so that it is easier to view ie..
>
> aaaaaaaa
> ||||||||
> aaaaaaaa
>
> aaaaaaaa
> ||||||||
> aaaaaaaa
>
> is there a module in bioperl that would assist in accomplishing such tasks.
>
> Thanks
> Omid
>
>
>
>
>
>
>
>
> 1
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu