[Bioperl-l] Query about SLAC.pm module

[Albert Vilella]

[CCing to the bioperl ml]

Sorry, there were some bits left in the pod header referring to PAML
objects that aren't quite true.
I've updated now the PODs. The Hyphy executions return hashes:

If you run the SLAC test in t/Hyphy.t you will se that the $results
are something like:

DB<3> x 2 $results
0  HASH(0x8df3110)
   'E[NS Sites]' => ARRAY(0x8e6cff4)
   'E[S Sites]' => ARRAY(0x8e6ceb0)
   'Observed NS Changes' => ARRAY(0x8e7b380)
   'Observed S Changes' => ARRAY(0x8e7b344)
   'Observed S. Prop.' => ARRAY(0x8e6d018)
   'P{S geq. observed}' => ARRAY(0x8e6d360)
   'P{S leq. observed}' => ARRAY(0x8e6d33c)
   'P{S}' => ARRAY(0x8e6d03c)
   'Scaled dN-dS' => ARRAY(0x8e6d384)
   'dN' => ARRAY(0x8e6d084)
   'dN-dS' => ARRAY(0x8e6d0a8)
   'dS' => ARRAY(0x8e6d060)
  DB<4> x $rc

which correspond to the csv file that hyphy produces.

Cheers,

    Albert.

On Dec 3, 2007 10:04 AM, Johan Nilsson <johan.nilsson at sh.se> wrote:
>
> Dear Dr. Vilella,
>
> Please allow me to introduce myself. My name is Johan Nilsson and I am a
> postdoctoral researcher in bioinformatics.
>
> I was  planning to perform a large-scale analysis for positively selected
> protein coding genes using any appropriate method from the Hyphy package,
> and I thought your bioperl wrappers 'SLAC.pm', 'FEL.pm' etc. should be very
> useful for this.
>
> IF I interpreted the documents of e.g. the SLAC module correctly, running
> $slac->run($aln,$tree) will return a
> Bio::Tools::Phylo::PAML object. However, when I try to retrieve any results
> from the obtained hashref (running my script on the test files provided
> with bioperl ...t/hyphy1.tree and ...t/hyphy1.fasta), the script complains
> that it is not blessed (e.g. 'Can't call method "get_seqs" on unblessed
> reference').
>
> I am fairly new to bioperl, so please appologise if this question was a
> stupid one :)
>
> Thanks in advance!
>
> Yours Sincerely
> /Johan
>
> --
> Johan Nilsson, Ph.D.
> School of Life Sciences
> Södertörns University College
> S-141 89 Huddinge, Sweden
> E-mail: johan.nilsson at sh.se
> Phone: +46 8 608 47 05, +46 70 456 10 51
>
>