[Bioperl-l] bioperl-run 1.5.1 RC1 up

[George Hartzell]

Here's another patch for Primer3.pm.  Without the first section one
ends up with an entry in the hash who's key is the empty string and
who's value is the empty string.  Without the second section, one ends
up w/out an input_options section.

I've been running both against an older copy of -run in a real app for
a while, so I think that they're ok.

g.


*** Bio/Tools/Run/Primer3.pm.orig	Tue Mar  1 18:26:31 2005
--- Bio/Tools/Run/Primer3.pm	Sun Jun 12 18:17:55 2005
***************
*** 437,442 ****
--- 437,443 ----
  			print OUT $_;
  		}
  		chomp;
+ 		next if ($_ eq "="); # skip over the boulderio record terminator.
  		my ($return, $value) = split('=',$_);
  		$self->{'results'}->{$return} = $value;
  	}
***************
*** 452,457 ****
--- 453,462 ----
  	$self->{results_obj} = new Bio::Tools::Primer3;
  	$self->{results_obj}->_set_variable('results', $self->{results});
  	$self->{results_obj}->_set_variable('seqobject', $self->{seqobject});
+ 	# Bio::Tools::Primer3::_separate needs a hash of the primer3 arguments,
+ 	# with the arg as the key and the value as the value (surprise!).
+ 	my %input_hash = map {split '='} @{$self->{'primer3_input'}};
+ 	$self->{results_obj}->_set_variable('input_options', \%input_hash);
  	$self->{results_separated}= $self->{results_obj}->_separate();
  	return $self->{results_obj};
  }