[Bioperl-l] RemoteBlast's save_output not saving properly for blasttable

Chris Fields cjfields at illinois.edu
Tue Aug 19 14:00:42 EDT 2008


Saving tabular BLAST to a file is working for me using bioperl-live.   
NCBI recently changed tabular BLAST output which broke parsing (there  
is an extra column now, can't remember what), but it is now fixed.

chris

On Aug 14, 2008, at 7:03 PM, Ulas Karaoz wrote:

> Hi,
>
> I found out that the save_output routine in RemoteBlast.pm doesn't  
> save the output properly into a file when the Blast output is a  
> hittable(blasttable). Might the reason be the fact that the tabular  
> output has a line that starts with a # while the parser is looking  
> for a line starting with just BLASTN, as in the section pasted below:
>
> if( $l =~ /^(?:[T]?BLAST[NPX])\s*.+$/i ||
> 			 $l =~/^RPS-BLAST\s*.+$/i ) {
> 			$seentop=1;
> }
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






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