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

Ulas Karaoz UKaraoz at lbl.gov
Thu Aug 14 20:03:51 EDT 2008


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;
}


More information about the Bioperl-l mailing list