[Bioperl-l] help with remote blast
barry.moore at genetics.utah.edu
Wed Sep 15 00:22:12 EDT 2004
A couple of suggestions for figuring it out yourself - both of which you
may have already done. First, on a module new to me I'll usually look
at the synopsis, description and methods to try to figure out what can
be done with this module. For instance on your problem with reading in
a fasta file. You'll want to use Bio::SeqIO (found here
http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html). Looking at
the doc page for that one the synopsis a description give a good idea of
what it does, and some example script of how to do it. But they don't
cover all that is possible. You had a problem with the module
"guessing" incorrectly that your sequence was protein. In the methods
you see that there is an method to set the alphabet. Accompanying that
is usage, a one line example, returns, args, throws etc. From that you
can deduce that if you add a line
$seqio->alphabet('dna') to the synopsis script you will force the parser
to interpret you seq as DNA.
The second suggestion is to check out script that are kept in the
examples and scripts directories of the bioperl-live CVS (found here
You can glean alot about usage from seeing how people use even seemingly
If you want to discuss this more, write back to the list or write me
Michael S. Robeson II wrote:
> I have been using perl for a while and have become somewhat
> comfortable with the language, though i have much to learn. However, I
> have been reading all of the bioperl documentation on remote BLAST in
> particular and... all I have to say is, "for the first time I have no
> idea what ya'll are talking about!" :-)
> I am new to the bioperl community and I have been trying my best, but
> the documentation is quit confusing to me.
> All, I am trying to do is set up a way in which I can automatically
> BLAST a set of sequences in a multi-sequence FASTA file. I have seen
> the "Read_all_Sequences" commands but every time I use them I get an
> error saying that nucleotide data is being submitted for protein data
> when in fact i am sending nucleotide data and the fact that the
> tutorial states that the default setting should be "nr"! I can not
> find any clear documentation or examples on the bioperl web site,
> tutorial, or perldocs that can even help me get started.
> I have setup and run all the tutorial scripts just fine. Problem is I
> have no idea how to modify the perl scripts w/o breaking them
> unlearning what I have learned from them. Are there any other external
> bioperl references or suggestions from the community?
> I do not want the answer, I really want to figure this out on my own.
> I think I just need a little nudge in the write direction to get me
> started. It's just that, from my limited experience reading the
> bioperl documentation, it is a world different from reading generic
> perl documentation. So, any help with the "Rules of Engagement" when
> reading this documentation would be a life saver!
> - Thanks for any help!
> - A totally lost bioperl newbie!
> - Mike
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
Dept. of Human Genetics
University of Utah
Salt Lake City, UT
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