[Bioperl-l] Automating a fasta sequence submission

Sean Davis sdavis2 at mail.nih.gov
Tue Jul 6 07:29:26 EDT 2004


It sounds like you should probably begin by looking at the SeqIO HowTO
(http://bioperl.org/HOWTOs/html/SeqIO.html).  This will show you how to read
in fasta format files and begin to work with the resulting seq objects.

As for 2-4, if you are using a standard online tool, there may be access
through bioperl, but maybe not.  If not, this will involve constructing a
URL that describes the "input" to the webpage and will likely involve
parsing the HTML output unless there is a "batch" option.  What are you
planning on using, if I may ask?


On 7/6/04 6:53 AM, "Stuart Gillies" <gillies82 at hotmail.com> 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
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