[Bioperl-l] StandAloneBlast -> bl2seq case

[Peter Schattner]

Marcel van Batenburg wrote:

> Dear Peter,
>
> I attached the input and  output of my script (with some debug info), and
> the perl script using the StandAloneBlast. I think the problem lies in
> BPbl2seq.pm but I am not sure.
> I am looking forward to your reply.
>

Hello Marcel

I received your files.  I attempted to reproduce your problem, but was unable to
because I couldn't understand clearly enough what you wanted to do in order to fix
the bugs in your script.  I could fix a few - eg that you probably mean $len1 and
not the undefined $length in line 26.  However other bugs, such as what you were
trying to do when you set the array reference @$string to the string 'aactcgggga'
I couldn't figure out.  As a result I couldn't reach the point in the program
where you were getting the error message from StandAloneBlast.  I suggest you run
your script with the -w warnings switch and the "use strict" pragma.  That should
help you find your bugs and resolve them.

Without being able to reproduce the problem, I'm not positve what StandAloneBlast
or BPbl2seq is unhappy about.  But my guess judging from the error message is that
since there are only 10 nt in the one sequence, the Blast program reported that
there were no "hits" and BPbl2seq is simply relaying that fact.

Good luck

Peter

PS  If you wish to continue to discuss this topic, we should probably continue
"off-line".  I attempted to reply only to you (rather than to the entire bioperl
list), however I received the following message from your mail-server:

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