[Bioperl-l] Automating a fasta sequence submission

[Heikki Lehvaslaiho]

Stuart,

Since you asking this question on bioperl mailing list, you must be 
contemplating on using bioperl on you problem.

What you need is a small program that loops over you sequences and calls a 
subrroutine to do the web form processing. 

You should be able to figure out from example scripts and this howto:
   http://bioperl.org/HOWTOs/html/SeqIO.html

how to do the first part.

Second part can be done with perl CPAN modules like LWP::Simple, 
LWP::UserAgent or WWW:Mechanize. There one solution to this within bioperl. 
see:

	http://bioperl.org/HOWTOs/html/SimpleWebAnalysis.html

Yours,
		-Heikki

When you do not what to do, check the FAQ:

	http://bio.perl.org/Core/Latest/faq.html

		-H


On Tuesday 06 Jul 2004 11:53, Stuart Gillies wrote:
> Hi, im pretty new to perl, and so i apologoes in advance for being a
> novice.
>
> i was hoping someone would help me woth a little task i have to do:
>
> I have a text file containing over 50 fasta sequences, i need a perl
> program to :
>
> 1- open the text file, reading through it, for each fasta sequence (the
> start is indicated by a > symbol) i need to do the following
> 2 - copy the sequence into an online submission form (similar to a blast
> submission form)
> 3 - hit the submit button
> 4 - retrieve the results from then following results page, preferably
> adding to a text file, so i end up with over 500 results on one text file.
>
> any help would be great
>
> stuart gillies
> university if liverpool
>
> _________________________________________________________________
> It's fast, it's easy and it's free. Get MSN Messenger today!
> http://www.msn.co.uk/messenger
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambridge, CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________