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

[Samantha Thompson]

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).

2)      Is there a definition of the FASTA format anywhere set in stone? .. is the initial line/title always between a > and a single newline char? Can there be white space before the ‘>’ for example.

 

Thanks,

 

ST

 

From: dave at davemessina.com [mailto:dave at davemessina.com] On Behalf Of Dave Messina
Sent: 15 July 2008 08:08
To: Samantha Thompson
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] Form validating and Bio::Seq objects..

 

Hi Samantha,

 

Bio::SeqIO will strip out whitespace and newlines when it reads in a sequence, but it won't validate the alphabet for you -- you'll need to do that on your own.

 

This topic came up on this mailing list recently, and Arshad Mohammed came up with some draft code to do this. See here:

 

http://www.nabble.com/Format-Validator-td17444139.html

 

 

Dave