[Bioperl-l] Raw Blast Alignment

Simon K. Chan simon_sask at yahoo.com
Tue May 9 04:06:04 EDT 2006


Hi Fellow Bioperl-ers,

bioperl-live/examples/searchio/rawwriter.pl is
supposed to show the raw alignments using
Bio::SearchIO.  The script is written to parse a
PSI-BLAST report.  I found an old email in the archive
from Jason stating that this should parse other
flavors of blast reports as well.  

What do I need to do to make this script parse non-PSI
blast reports?  I tried to just specify a file and
that the -format is 'blast', but I get an error
stating that the object method 'raw_hit_data' is not
defined in Bio::Search::Hit::BlastHit.

Basically, I want to obtain the raw alignment because
I'd like to get the size of the gaps, not just the
number.

Any help will be much appreciated.
Many thanks


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