[Bioperl-l] Raw Blast Alignment

[Christopher Fields]

You need to read the SearchIO HOWTO, which gives several examples:

http://www.bioperl.org/wiki/HOWTO:SearchIO

Chris

---- Original message ----
>Date: Tue, 9 May 2006 01:06:04 -0700 (PDT)
>From: "Simon K. Chan" <simon_sask at yahoo.com>  
>Subject: [Bioperl-l] Raw Blast Alignment  
>To: bioperl-l at lists.open-bio.org
>
>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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