[Bioperl-l] Fwd: Re: alignment by TCoffee as a subroutine

Chris Fields cjfields at uiuc.edu
Wed Apr 30 12:25:06 EDT 2008


Sergei,

I agree with Sendu; we can't diagnose this unless we either have the  
entire script of a minimal version of it demonstrating the bug.

The best way to handle this is to file a bug report, attaching  
relevant data using the 'Create a new attachment' link (including  
either the full script or a shortened one which demonstrates the bug).  
Otherwise we're just shooting in the dark trying to diagnose the  
problem.

http://bugzilla.open-bio.org/

chris

On Apr 30, 2008, at 10:42 AM, Sergei Ryazansky wrote:

>
>
> ------- Forwarded message -------
> From: "Sergei Ryazansky" <dr.hogart at gmail.com>
> To: "Sendu Bala" <bix at sendu.me.uk>
> Cc:
> Subject: Re: [Bioperl-l] alignment by TCoffee as a subroutine
> Date: Wed, 30 Apr 2008 19:40:26 +0400
>
>> What do you do with the output of &align? The thing you are doing  
>> with that output is most likely the cause of your script  
>> terminating, which is why &sub4 and &sub5 run when you don't run  
>> &align (have no output that causes the problem).
>
> please sea my answer to Sebastien Moretti - there are description of
> another similar problem. The only thing that I did there with output  
> is
> printing to file. Nevetheless the problem was the same.
>
>> # don't do anything with the output of align() - does &sub4 still  
>> run?
>
> please sea above.
>
>> # add some print statements after you call align(), and then after  
>> every further block of code in your script to see exactly where the  
>> script terminates
>> # reduce your script down to a minimal script that shows the  
>> problem (with the help of the previous step) and show us that
>
> all tests with individual bloks was performed earlier. the results  
> is ok.
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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