[Bioperl-l] CVS AND PAML

Albert Vilella avilella at gmail.com
Tue Apr 17 05:25:40 EDT 2007


hmmm, there are some perldoc links around your code snippet. can you post
the code again? what is the input data you are trying this with?

On 4/17/07, Luba Pardo <lubapardo at gmail.com> wrote:
>
> Dear all,
> I have two questions.
> 1.) I am trying to download some modules from Bioperl-run via CVS but I
> can
> not login.
>
> $ cvs -d :pserver:cvs at code.open-bio.org:/home/repository/bioperl login.
>
> The error I get is: time out, failed to connect to the server. I have
> no trouble to download other files and I installed bioperl modules via
> CPAN and it works.
>
> 2) The second question I have is that I am using the PAML:CODEML
> module to do phylogenetic analysis.
>
> I have used the example provided in the HOWTO:PAML (also given as
> example: pairwise_ka_ks.PL). The program does not crash but it returns
> and empty object. I think the problem is in the last part of the
> script because I manage to get sequences and also the alignment, but I
> can not get any ka, ks value. I am not sure whether there is a bug in
> the last part of the script.
>
> Does anyone have an idea?
>
> Thank you very much
>
> Luba Pardo
>
> $kaks_factory->alignment($dna_aln);
>
> # run the KaKs analysis
> my ($rc,$parser) = $kaks_factory->run();
> my $result = $parser->next_result;
> my $MLmatrix = $result->get_MLmatrix();
>
> my @otus = $result->get_seqs();
> # this gives us a mapping from the PAML order of sequences back to
> # the input order (since names get truncated)
> my @pos = map <http://www.perldoc.com/perl5.6/pod/func/map.html> {
>     my $c= 1;
>     foreach my $s ( @each ) {
>       last if( $s->display_id eq $_->display_id );
>       $c++;
>     }
>     $c;
>    } @otus;
>
> print <http://www.perldoc.com/perl5.6/pod/func/print.html> OUT join
> <http://www.perldoc.com/perl5.6/pod/func/join.html>("\t", qw
> <http://www.perldoc.com/perl5.6/pod/func/qw.html>(SEQ1 SEQ2 Ka Ks
> Ka/Ks PROT_PERCENTID CDNA_PERCENTID)),"\n";
> for( my $i = 0; $i < (scalar
> <http://www.perldoc.com/perl5.6/pod/func/scalar.html> @otus -1) ;
> $i++) {
>   for( my $j = $i+1; $j < (scalar
> <http://www.perldoc.com/perl5.6/pod/func/scalar.html> @otus); $j++ ) {
>     my $sub_aa_aln  = $aa_aln->select_noncont($pos[$i],$pos[$j]);
>     my $sub_dna_aln = $dna_aln->select_noncont($pos[$i],$pos[$j]);
>     print <http://www.perldoc.com/perl5.6/pod/func/print.html> OUT
> join <http://www.perldoc.com/perl5.6/pod/func/join.html>("\t",
> $otus[$i]->display_id,
>
> $otus[$j]->display_id,$MLmatrix->[$i]->[$j]->{'dN'},
>                          $MLmatrix->[$i]->[$j]->{'dS'},
>                          $MLmatrix->[$i]->[$j]->{'omega'},
>                          sprintf
> <http://www.perldoc.com/perl5.6/pod/func/sprintf.html
> >("%.2f",$sub_aa_aln->percentage_identity),
>                          sprintf
> <http://www.perldoc.com/perl5.6/pod/func/sprintf.html
> >("%.2f",$sub_dna_aln->percentage_identity),
>                          ), "\n";
>   }
> }
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