[Bioperl-l] What is the relationship between primer3 moduleandrun-primer3 module?

[Wiersma, Paul]

The bug that Wenwu referred should only occur when reading a Primer3 output file;  the Bio::Tools::Run::Primer3->run method takes the results and directly transfers them to a Bio::Tools::Primer3 object without an intermediate file.  A Data::Dumper look at the Bio::Tools::Primer3 object shows the keys and results for PRIMER_SEQUENCE_ID and SEQUENCE in 'results' and then again in the 'results_by_number' hash but only in the '0' hash.

All of this doesn't really matter for Li's original concern.  If you want to include the id of sequence along with the primer3 results just take it from the seq object (i.e. $seq->display_id() ).  Since you are in a loop taking one sequence at a time this $seq will be the one that was sent to primer3.

PAW

Paul A. Wiersma
Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada
Summerland, BC
wiersmap at agr.gc.ca
 
 



-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Cui, Wenwu (NIH/NCI) [F]
Sent: Wednesday, May 10, 2006 6:46 PM
To: chen li; bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] What is the relationship between primer3 moduleandrun-primer3 module?

1. Bio::Tools::Primer3 is already included in Bio::Tools::Run::Primer3 module so that you can parse the result file.
 
2. There is a bug in Bio::Toos::Primer3.pm line 264 as I mentioned. Once fixed, it can output 
 
3. primer3.exe is called in the Bio::Tools::Run::Primer3  "run" function, please read the function definition.