[Bioperl-l] Bio::SeqIO::phd_comment objet

Jean-Marc FRIGERIO Frigerio at pierroton.inra.fr
Tue Aug 28 03:12:22 EDT 2007


Hi,

The Bio::SeqIO::phd module says, speaking about the COMMENT section of a phd 
file:
 # this should be an actual object to assist in serialization
  # but I don't have time for this now."

The doc says ( http://www.bioperl.org/wiki/Core_1.5.1_1.5.2_delta)

   This really needs a "phred_comments" object of some sort so that it will be 
serializable. Then when java clients get this object they will be able to 
deserialize it. 

I volunteer to do this,  but need your opinion.

Do we really need an object (Bio::phd_comment ? Bio::SeqIO::phd_comment ? 
Bio::phd_header ? other ?).

Or adding  few  Bio::Seq::SeqWithQuality subs in the Bio::SeqIO::phd module 
would suffice ? What are the constraints of serialization/deserialization of 
the java clients ?
I was thinking of just adding get/setter for all the comments
chromat_file(), abi_thumbprint(), etc.

touch() for the timestamp
attribute() for new unknown comments
write_comment().

others ?

		-- jmf

-- 
Jean-Marc Frigerio,
UMR BIOGECO   69, route d'Arcachon, 33612 CESTAS France
Tel : +33(0) 557 122 829   Fax : +33(0) 557 122 881
Frigerio at pierroton.inra.fr   http://www.pierroton.inra.fr/biogeco/index.html


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