[Bioperl-l] Re: [Bioperl-guts-l] BPlite questions

James Wasmuth james.wasmuth at ed.ac.uk
Thu Sep 2 11:29:36 EDT 2004


it is probably better if you use the Bio::SearchIO module. THere is a 
HOWTO section: http://bioperl.org/HOWTOs/SearchIO/use.html

re; strand, it depends on the BLAST search you are performing but 
something along the lines of $hsp->query->strand will return '1' for 
positve frame or '-1' for negative frame.
so my

my $blast_frame = ($hsp->query->frame + 1) * $hsp->query->strand;


Jinal Jhaveri wrote:

>Hi All, 
>While running BPlite for parsing a blast report, I am getting following 
>warnings? What does this mean
>-------------------- WARNING ---------------------
>MSG: Query frame (-3) did not match strand of query (1)
>Also, how do I detect whether the query matches the target on +ve strand or 
>the -ve strand? I tried to use the $hsp->strand but I think it doesn't give 
>me the correct result as it doesn't tells me whether the query matches it on 
>+ve or -ve strand
>thank you
>Bioperl-guts-l mailing list
>Bioperl-guts-l at portal.open-bio.org

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