[Bioperl-l] pairwise_kaks.PLS: verbose rquired by PAML

Stefan Kirov stefan.kirov at bms.com
Wed Jan 9 14:54:07 EST 2008


Jason,
Even this last fix I still had problems with bp_pairwise_kaks.pl. It
turns out, verbose needs to be set on by default for codeml in order for
the sequences to appear in mlc file.\
That being said, we need instead of:
    $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new
        (-verbose => $verbose,
         -params => { 'runmode' => -2,
                      'seqtype' => 1,
                  }
         );
this:

    $kaks_factory = Bio::Tools::Run::Phylo::PAML::Codeml->new
        (-verbose => $verbose,
         -params => { 'runmode' => -2,
                      'seqtype' => 1,
                      'verbose' => 1,
                  }
         );

verbose can 2 as well.... Just got this clarification from Ziheng. He
also offers to change the output so it becomes easier for us. I plan to
ask him to put the sequence in the mlc header by default.
Stefan



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