[Bioperl-l] parsing blat data

Charles Hauser chauser at duke.edu
Thu Jun 17 08:49:25 EDT 2004


I'd like to grab the Q name && HSP count (block count) from some blat

The docs for SearchIO suggest I can parse blat (.psl) data similar to
blast but not certain what method 

psLayout version 3
match   mis-    rep.    N's     Q gap   Q gap   T gap   T gap   strand  Q               Q       Q        Q       T               T       T       T       block   blockSizes      qStarts  tStarts
        match   match           count   bases   count   bases           name            size    start    end     name            size    start   end     count

   my $in = new Bio::SearchIO(-format => 'blat', 
                               -fh   => \*FH);

    while( my $result = $in->next_result ) {


There is also Bio/Tools/Blat.pm, which (I don't believe) has a method to
return values.


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