Fwd: [Bioperl-l] need BLAT parse code

[Jason Stajich]

Begin forwarded message:

> From: neeti somaiya <neetisomaiya at gmail.com>
> Date: November 29, 2005 1:27:27 AM EST
> To: Jason Stajich <jason.stajich at duke.edu>
> Subject: Re: [Bioperl-l] need BLAT parse code
>
> I use the following code :
>
> open(FH,"output.psl");
> while(<FH>)
> {
>     if( /^psLayout/ )
>     {
>           for( 1..4 ) { <> }
>       }
>      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;
>
>
>       print $t_start;
>       print "\n";
>       print $t_end;
>
> }
>
> for output.psl file :
>
> 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
> ---------------------------------------------------------------------- 
> ---------------------------------------------------------------------- 
> -------------------
> 27025   0       0       0       0       0       0       0        
> +       query_sequence3 27025   0       27025    
> database_sequence3      57701691        132995  160020  1        
> 27025,  0,      132995,
> ~
>
>
> It gave me output :
>
> Q
> Q
>
> 132995
> 160020
>
> What is the Q? Cant I obtain the coordinates (132995, 160020) alone?
>
> Please let me know.
> Thanks.
>
> On 11/28/05, Jason Stajich <jason.stajich at duke.edu> wrote:
> 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
>
>
>
>
>
> -- 
> -Neeti
> Even my blood says, B positive

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