[Bioperl-l] Error dereferencing sequence in SeqIO object

[Jennifer Krauel]

Well.  I made a very small fastq input file, stripped out all possible 
code, ran it in the debugger, and then it started working.  Now the 
original code and data files also work.  File it under "just keep trying 
stuff".

On Wednesday, November 12, 2014 6:01:01 PM UTC-6, Jennifer Krauel wrote:
>
> I'm having some trouble running a very basic bioperl script to transform a 
> fastq file into a fasta file.  When I try to dereference a sequence object 
> I get this error: "Can't call method "seq" without a package or object 
> reference..."
> It's boilerplate code, and the error is on the last line in the snippet 
> below:
>
> my $seq_in = Bio::SeqIO->new(
>                              -file   => "<$infile",
>                              -format => $infileformat,
>                              );
> my $i=0;
> while (my $this_seq = $seq_in->next_seq && $i < 100) 
>     { #while more sequences in fastq file
>     
>     $i++;
>     my $seqstring = $this_seq->seq();
> ...
>
> The counter is just to limit the number of reads while I'm testing the 
> code, I don't think it should be causing the problem. I tried to google the 
> error but didn't come up with anything useful except the suggestion that I 
> might not be working with a clean or up to date bio perl installation. 
>
> When I try to get the bioperl version using this code:
> perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"' 
> I get 1.005002102, which seems odd. 
>
> When I ask for the version number of SeqIO using 
> perl -MBio::SeqIO -e 'printf "%vd\n", $Bio::SeqIO::VERSION' 
> I get 49.46.48.48.53.48.48.50.49.48.50.
>
> I am using CloudBioLinux on AWS, with whatever standard installation that 
> provides (which is the whole point of using AWS). 
>
> Is there something bone-headed I am doing, or is this an issue I should 
> pursue with the Cloud folks?
>
> Thanks!
> Jennifer
>
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