longbow leo | 25 Jul 07:32 2013
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Re: Why reading from generic object?

Hi Alexey,

In the row:

my $seq=Bio::SeqIO->next_seq;

Here an object would be used, rather than the class.

The correct statement would be:

my $seq = $seqio->next_seq;

All the best,

Haizhou

On Thu, Jul 25, 2013 at 1:24 PM, Alexey Morozov <alexeymorozov1991 <at> gmail.com
> wrote:

> I've made this primitive script for joining seqs that are stored in lots of
> files (some of them in a genbank format) into a single fasta:
>
> my $out=Bio::SeqIO->new(-fh=>\*STDOUT, -format=>'fasta');
> foreach my $file ( <at> ARGV)
>     {
>     my $format=( $file~~m/.*\.gb$/ ?'genbank':'fasta');
>     my $seqio=Bio::SeqIO->new(-file=>"<$file", -format=>"$format");
>     my $seq=Bio::SeqIO->next_seq;
>     $out->write_seq($seq);
>     }
>
> It correctly tells a format, finds files and they're open for reading.
> There seems to be literally no place for the error, yet it throws:
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Sorry, you cannot read from a generic Bio::SeqIO object.
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472
> STACK: Bio::SeqIO::next_seq /usr/share/perl5/Bio/SeqIO.pm:506
> STACK: join_fa:13
> -----------------------------------------------------------
>
> Can someone please explain me where I messed up?
>
>
> --
> Alexey Morozov,
> LIN SB RAS, bioinformatics group.
> Irkutsk, Russia.
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>

Gmane