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

Sergei Ryazansky dr.hogart at gmail.com
Wed Apr 30 11:42:41 EDT 2008



------- 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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