[Bioperl-l] Form validating and Bio::Seq objects..

Simon Andrews simon.andrews at bbsrc.ac.uk
Tue Jul 15 05:48:18 EDT 2008


On 15 Jul 2008, at 10:24, Samantha Thompson wrote:

> Thanks for this it was helpful.
>
> I have two related questions:
>
> 1)      From the HTML <form> to cgi script the sequence text is  
> sent as a string variable. As such, can Bio::SeqIO be initialised  
> with a variable rather than a file? (I had been using the sequence  
> to directly initialise a Bio::Seq object, although this wouldn’t  
> take into account someone pasting multiple FASTA sequences into the  
> text box).

You can use IO::Scalar to make your variable act like a filehandle  
and then pass that to SeqIO.

Simon.


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