Alexey Morozov | 25 Jul 07:35 2013
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Re: Why reading from generic object?

Thanks. It's a shame to miss such mistakes.

2013/7/25 longbow leo <longbow0 <at> gmail.com>

> 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.
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l <at> lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
>

--

-- 
Alexey Morozov,
LIN SB RAS, bioinformatics group.
Irkutsk, Russia.

Gmane