[Bioperl-l] what am I doing wrong with $alignio->next_aln

[Albert Vilella]

Quick guess, can you try changing:

>   my $alignio = new Bio::AlignIO('-format' => 'fasta',
>                               -interleaved => 0,
>                               -file   => $tempfile); 
> 

to:

>   my $alignio = new Bio::AlignIO('-format' => 'fasta',
>                               -file   => $tempfile); 
> 

the "interleaved" bit is for phylip file format... not sure if that is
really the problem here.

if you don't get a proper $aln object after:

my $aln = $alignio->next_aln;

then you should double-check the place where you are getting the
alignment files from.

To be sure it is not a bioperl-run/PAML problem, you can run the test:

cd /where/bioperl/and/bioperl-run/are/placed/
perl t/PAML.t

should give you 18 ok's,

    Albert.

El dt 06 de 12 del 2005 a les 13:24 -0800, en/na Alisha Holloway va
escriure:
> I'm trying to run PAML through BioPerl.  I get this error message
> 
> 
> -------------------- WARNING ---------------------
> MSG: must have supplied a valid alignment file in order to run codeml
> ---------------------------------------------------
> 
> because I'm not getting a return value from "my $aln =
> $alignio->next_aln".  I just can't quite figure out why.  Here's the
> code bit.  Any help would be greatly appreciated.  I have a feeling
> this has to do with the input file, but the format of the file is
> fine.  Is there something about the path that I'm missing?
> 
> 
> 
> 
> if($sepfiles[$x] =~ /.fa$/){
>     my $tempfile = './tempfiles/'.$sepfiles[$x];
>     print "Datafile is - $allfiles[$a], $tempfile\n";
>        ##my $tempfile= shift @ARGV; ## to load infile on command line
>   my $alignio = new Bio::AlignIO('-format' => 'fasta',
>                               -interleaved => 0,
>                               -file   => $tempfile); 
>                                     
>         my $aln = $alignio->next_aln;
>    my $codeml = new Bio::Tools::Run::Phylo::PAML::Codeml();
>        #$codeml->no_param_checks(1);  
>        $codeml->set_parameter('runmode',0);
>    $codeml->set_parameter('seqtype',1);
>    $codeml->set_parameter('CodonFreq',2);
>        $codeml->set_parameter('model', 1);
>        $codeml->set_parameter('NSsites', 0);
>        $codeml->set_parameter('fix_omega', 0);
> $codeml->set_parameter('omega',0.4);
>    $codeml->set_parameter('fix_kappa', 0);
> $codeml->set_parameter('kappa',2);
>      $codeml->set_parameter('cleandata',1);
>   
>         print $codeml->executable(), " is codeml\n";
> 
>        $codeml->alignment($aln);  ## it gets to here and tries to use
> $aln and gives the warning
> 
> 
> Thanks,
> 
> 
> Alisha
> 
> 
> 
> 
> -- 
> Alisha Holloway
> 
> Postdoctoral Fellow
> Section of Evolution & Ecology
> 3347 Storer Hall
> University of California
> Davis, CA  95616
> 
> 530-754-9551 Office
> 512-297-3958 Cell
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