[Bioperl-l] error loading sequence

Munirul Islam ba6450 at wayne.edu
Tue Jul 24 20:10:04 EDT 2007


Thanks.  That worked nicely.  I need your suggestion to load codeml control data from a file.  Consider the following code:

-------------------------------------------------------------
my $codeml_null = Bio::Tools::Run::Phylo::PAML::Codeml->new(-save_tempfiles => 1,
-params =>	{'noisy' => 9,
		 'verbose' => 2,
		 'runmode' => 0,
		 'seqtype' => 1,
		 'CodonFreq' => 2,
		 'aaDist' => 0,
		 'model' => 2,
		 'NSsites' => 2,
		 'icode' => 0	});
-------------------------------------------------------------

Tried to modify it by passing a hash reference after loading data from a file.:

-------------------------------------------------------------
my $codeml_null = Bio::Tools::Run::Phylo::PAML::Codeml->new(-save_tempfiles => 1,
-params => \%hashlist );
-------------------------------------------------------------

Still that didn't work.  Your suggestions pls.

Munir

---- Original message ----
>Date: Tue, 24 Jul 2007 23:39:33 +0100
>From: Sendu Bala <bix at sendu.me.uk>  
>Subject: Re: [Bioperl-l] error loading sequence  
>To: Munirul Islam <ba6450 at wayne.edu>
>Cc: bioperl-l at lists.open-bio.org
>
>Munirul Islam wrote:
>> Hello everyone:
>> 
>> I am having problem loading a sequence file from within a directory.  
>> 
>> #############################################################
>> $dirname = "rundir";
>> opendir (DIR, $dirname) || die("can't open $dirname");
>>       
>> while (defined($file = readdir(DIR))) {
>>     next if $file =~ /^\.\.?$/;		# skip . and ..
>>     $abs_path = File::Spec->rel2abs( $file ) ;
>>     
>>     # gives a file not found exception for the following code
>
>This isn't a Bioperl problem. You're using the wrong File::Spec method. 
>You want File::Spec->catfile($dirname, $file).


More information about the Bioperl-l mailing list