[Bioperl-l] Automating a fasta sequence submission

pdavid at netvisao.pt pdavid at netvisao.pt
Tue Jul 6 07:48:58 EDT 2004


To read through the text file, you can use Bio::Seq


If you read the synopsis, you'll see how to get each sequence from the
file into a variable. To do the rest, if it's something that Bioperl won't
do (check the tutorial at
http://www.bioperl.org/Core/Latest/bptutorial.html) I would use the
WWW::Mechanize module to feed the sequences into the website. It's not
hard to use, if you look at the examples and then at the module itself:


Good luck,
Paulo Almeida

> 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.

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