[Bioperl-l] Re: [Bioperl-guts-l] (no subject)

[Jason Stajich]

On Tue, 22 Oct 2002, Sally Li wrote:

>
> Hi, there,
>
> I have trouble with aligment format change. My codes is
>
>
>
> use Bio::AlignIO;
> use Bio::SimpleAlign;
>
> #my $inputFileName="/export/people/tang/perlproj1/fordan/pepp.fasta";
> my $inputFileName="./pepp.fasta";
> my $in=Bio::AlignIO->newFh(-file=>$inputFileName, '-format'=>'fasta');
> my $out=Bio::AlignIO->newFh( -file=>">outAln", '-format'=>'clustalw');
>
You have to get the alignments out from the reader.

my $aln;
while( defined($aln = <$in>) ) {
   print $out $aln
}

>
> The error msgs like:
>
> Can't call method "isa" without a package or object reference at /usr/local/lib/perl5/site_perl/5.8.0/Bio/AlignIO/clustalw.pm line 180.
>
> The bioperl works fine for other objs.
>
>
>
> Any help is appreciated.
>
>
>
> Sally.
>
>
>
>
>
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu