[Bioperl-l] need BLAT parse code

[Tamas Horvath]

what kind of blast output format do u use?

On 11/29/05, Jason Stajich <jason.stajich at duke.edu> wrote:>>>> 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>>> _______________________________________________> Bioperl-l mailing list> Bioperl-l at portal.open-bio.org> http://portal.open-bio.org/mailman/listinfo/bioperl-l>