[Bioperl-l] Automating a fasta sequence submission
heikki at ebi.ac.uk
Tue Jul 6 07:49:38 EDT 2004
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:
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.
When you do not what to do, check the FAQ:
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
> 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!
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
______ _/ _/_____________________________________________________
_/ _/ 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
More information about the Bioperl-l