[Bioperl-l] RE: :Tools::Genemark.pm

[Fiers, M.W.E.J.]

Hi all,

as I started discussing with jason;

the analysis_query method of both Genescan.pm and Genemark.pm do not seem to
be used in these modules. If I understand correctly, there should be a
PrimarySeq compatible object here pointing to the sequence which has been
analysed by the genepredictor. 

Genscan.pm put's the parsed out sequence name in $gene->seqname. Another
option would be to have an empty PrimarySeq object there (If I understand
Jason correctly) with display_id set. 

I'd prefer to put the name in $gene->seqname() and leave the analysis_query
empty.

Any thoughts?

Mark



m
On Mon, 18 Jun 2001, Fiers, M.W.E.J. wrote:
> Hi Jason,
>
> Following the definition of analysis subject as given in
AnalysisResult.pm,
> the analysis subject should contain the name of the matrix used for
> prediction.
>
> The sequence name should go into the analysis_query, but the definition
asks
> for a PrimarySeq compatible object here. Usually I do this after
> instantiating the module and have the module use the seq object to extract
> the predicted_cds's
>
Well the analysis_query object will have display_id already set
whenever it is instantiated (which will be outside of the parsing of the
result file) so basically we have to throw away the seqname
information from the report or we just set seqname for the gene object
the best we can do when making building the gene prediction objects...
i.e. we set $gene->seqname to be = analysis_query->display_id when
analysis_query is defined OR the parsed $seqname.  That way $gene->seqname
is never null.  I think this is how we set things in genscan, but I
haven't visited that code in a while.
> I am not sure how to solve this. Do you want the sequence name in there?
> Genscan.pm doesn't seem to use it either.
>
> I could change the .t file.
>
I'm happy to disable the test, but I think we can make this work - might
want to write a summary of this for the list to help decide - I'm sure
Hilmar has ideas.
> by the way, my apologies, since it seems to be rather obvious that I
didn;t
> bother to check if the tests wouls still run.
>
no worries.
> cheers
> Mark
>
>
>
>
> -----Original Message-----
>
> From: Jason Stajich
>
> To: Fiers, M.W.E.J.
>
> Sent: 6/18/01 3:21 PM
>
> Subject: Bio::Tools::Genemark.pm
>
>
>
> (on main-trunk)
>
>
>
> In you last checkin it looks like you have commented out the lines that
>
> set the seqname (lines 337-341) which is causing a test to fail in
>
> t/Genepred.t
>
>
>
> Can I uncomment these lines (which causes test to pass again) or you do
>
> you have another preferred fix?
>
>
>
> Thanks,
>
> Jason
>
>
>
> Jason Stajich
>
> jason@chg.mc.duke.edu
>
> Center for Human Genetics
>
> Duke University Medical Center
>
> http://www.chg.duke.edu/
>
>
>
>
Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center
http://www.chg.duke.edu/