[Bioperl-l] need BLAT parse code

[Jason Stajich]

Bio::SearchIO::psl can parse psl output.

or more simply:

while(<>) {
   if( /^psLayout/ ) { # if there is a header
   for( 1..4 ) { <> }  # take next 4 lines to skip the header
   }
  my @line = split;
  my ( $matches,$mismatches,$rep_matches,$n_count,
             $q_num_insert,$q_base_insert,
             $t_num_insert, $t_base_insert,
             $strand, $q_name, $q_length, $q_start,
             $q_end, $t_name, $t_length,$t_start, $t_end, $block_count,
             $block_sizes,  $q_starts,      $t_starts
             ) = split;

  #  query aln vals are  $q_start, and $q_end values
  # hit aln vals are $t_start, $t_end
}

On Nov 28, 2005, at 8:06 AM, neeti somaiya wrote:

> Hi,
>
> I am using BLAT in a project.I am having simple .psl output files  
> after
> running BLAT of a gene sequences against full chromosomal
> sequences.Doesanyone have a simple BLAT parse code. I am only
> interested in obtaining the
> alignment start and end positions on the target.
> --
> -Neeti
> Even my blood says, B positive
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
Duke University
http://www.duke.edu/~jes12