[Bioperl-l] Newbie question on Bio::SeqIO

[Chris Fields]

Also, FASTQ parsing only works correctly if you are using BioPerl 1.6.1.  Not sure what version fink currently has.

chris

On Jan 26, 2011, at 4:30 PM, Adam Sjøgren wrote:

> On Wed, 26 Jan 2011 14:05:08 -0800 (PST), JayPea wrote:
> 
>> #!/usr/bin/perl
>> use Bio::Perl;
>> use Bio::SeqIO;
> 
>> my $seqio_obj = Bio::SeqIO->new(-file => "dna.fa",
>>                                -format => 'Fasta');
>> my $output = $seqio_obj->subseq(1,20);
> 
> Try replacing that line by these two:
> 
> my $seq=$seqio_obj->next_seq;
> my $output=$seq->subseq(1,20);
> 
>> print "$output\n";
> 
> See "perldoc Bio::SeqIO" :-)
> 
> 
> Also: Never forget to start your scripts with "use strict; use
> warnings;" - a great way to avoid typos and stuff.
> 
> 
>  Best regards,
> 
>    Adam
> 
> -- 
> "Här kommer rädslan, gamle vän                               Adam Sjøgren
>  När alla fjärilar i magen vaknar upp                   asjo at koldfront.dk
>  Viskar välkommen hem"
> 
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