[Bioperl-l] Bio::Tools::FootPrinter

[Shawn Hoon]

Uhm yeah, I haven't played with this in a while. The parser is not bug 
free
as the output was not terribly amenable to parsing. For example, the 
same
motif represented by the same character 111111 for example has different
lengths for different instances. So what I took to be the 'motif' was 
the longest one
with that string of characters. Maybe if you have suggestions for 
fixing this
or sending an example output for this I can take a look.

cheers,

shawn


On Tuesday, November 4, 2003, at 4:07PM, ypeng at sfu.ca wrote:

> Hi all,
>
> Did anybody use this module to parse FootPrinter output? I am trying 
> to use
> it but encountered two problems:
>
> 1. Some shorter motifs also show up. Say, I specified the motif 
> size=14,
> "motifs" like "accg" also reported as features.
>
> 2. The parsed output is not the same as the FootPrinter HTML output.
>
> Any help will be appreciated.
>
>
> Fred Peng
>
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