[Bioperl-l] error loading sequence
Munirul Islam
ba6450 at wayne.edu
Wed Jul 25 00:10:04 UTC 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).
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