in reply to Re^2: Primer3 - BioPerl
in thread Primer3 - BioPerl

It can be confusing sometimes:). You seem to be using BioPerl, so, yes, you want to write your script according to the documentation for Bio::Tools::Primer3, which is part of the BioPerl distribution. The code that you posted, however, was written according to the documentation for BioPerl-Run, which is a different distribution altogether. You were going by Bio::Tools::Run::Primer3 instead of Bio::Tools::Primer3, which is the module that you want to use.

Update: You need to install primer3

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Re^4: Primer3 - BioPerl
by blarsen20 (Initiate) on Feb 07, 2012 at 16:14 UTC

    Ah yes, this was mentioned to me earlier this morning as well! Shame, I actually had never heard it mentioned before! :: facepalm ::

    Much appreciated! Also should help now that it's been moved to a server and off windows! Joy! Haha
[reply]
Re^4: Primer3 - BioPerl
by Anonymous Monk on Feb 08, 2012 at 15:14 UTC

    For some reason it didn't really put my reply yesterday... But yeah, someone actually mentioned that yesterday! Never knew we had to download two separate packages. :: facepalm :: So, I have it running but receive an error (see the "UPDATE" in the main post).

    The error I get as soon when dumping the results data structure via:

     my $results = $primer3->run;
print Dumper($results);

    [download]

    is "'PRIMER_ERROR' => 'thermodynamic approach chosen, but path to thermodynamic parameters not specified'". Not sure as to why this is, especially since it looks like that is not the default and I never passed anything in like that...hmm. Trying to modify it still, but got that error multiple times yesterday.

[reply]
[d/l]
      I'm getting this same error on my mac osx build. Any luck solving this issue? 
      Primer3/eprimer3 issue:
Error: thermodynamic approach chosen, but path to thermodynamic parame
+ters not specified

      [download]
      From: http://www.mcardle.wisc.edu/mprime/help/primer3/primer3_manual.htm#globalTags

      PRIMER_THERMODYNAMIC_PARAMETERS_PATH (string; default ./primer3_config)

      This tag specifies the path to the directory that contains all the parameter files used by the thermodynamic approach. In Linux, there are two default locations that are tested if this tag is not defined: ./primer3_config/ and /opt/primer3_config/. For Windows, there is only one default location: .\primer3_config\.

      I put the primer3_config in my PATH in bin and still cannot solve this issue:

      I even did 

      export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/pri
+mer3-2.3.2/src

      [download]
      and 
      export PRIMER_THERMODYNAMIC_PARAMETERS_PATH=/Users/jared/Downloads/pri
+mer3-2.3.2/src/primer3_config

      [download]
      to no avail.
[reply]
[d/l]
[select]
        Try copying the src/primer3_config file from the primer3 build directory to /opt/primer3_config - it should look in there by default according to the docs (http://www.mcardle.wisc.edu/mprime/help/primer3/primer3_manual.htm)
[reply]

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