[Bioperl-l] cigar string in GenericHSP

[Bob Freeman]

At 11:12 AM +0100 3/12/03, Marc Logghe wrote:
>Hi,
>I was only wondering, if you really would like to reproduce the original
>blast alignment, is the original homology string included in the cigar
>string ? If I recall well, the homology sequence is not included in the aln
>object and if you want to  add it explicitely, bioperl complains about the
>bad sequence.

true; the homology sequence is not included. also, trying to get the 
'match' sequence from $hsp->seq_str('match') doesn't work.

>Also, I was missing a writer method for blast alignments. I have written my
>own , but did not yet try to plug it in Bio::SearchIO::blast. If someone
>else would like to give it a try, I'll include the code I currently have
>($LINE_LEN is global and should be set to 60):

what about the reportwriter methods? am i missing something here?

on a separate note, it appears from code that I'm writing that using 
Bio::Tools::Run::StandAloneBlast to run local blast generates 
GenericHit and GenericHSP objects, not the Blast specific ones. E.g. 
print $hit->raw_hit_data throws an error. This method is present in 
Bio::Search::Hit::blast but not Bio::Search::GenericHit. Am I doing 
something wrong?

Bob

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