Bioperl: Creating a SeqIO object

[Aaron J Mackey]

Sorry, my fault for not testing this.  Try this:

 my $seqs = $query->param('seq');
 tie *IN, 'IO::Scalar', \$seqs;
 my $inSeq = new Bio::SeqIO( -fh => \*IN, -format => 'fasta');

-Aaron

On Mon, 29 May 2000, gert thijs wrote:

> I tried to use this pseudo-filehandle, but I got the following error message:
> 
> "Not a GLOB reference at /users/sista/thijs/perl/lib/Bio/SeqIO.pm line 511."
> 
> Here's how I wrote it: 
> 
> my $seqs = $query->param('seq');
> my $fhs = new IO::Scalar \$seqs;
> my $inSeq = new Bio::SeqIO(-fh=>$fhs, -format=>'fasta');
> while ( $seqO = $inSeq->next_seq() ){
>   $seq = $seqO->seq();
>   if ( $seq =~ /[^ACGT]/ ) {
>     exec "echo 'There are non ACGT symbols in sequence $seqcount' >>
> /tmp/$filename.dump";
>   }else{
>     print $TMPFILE $seqO->display_id();
>     print $TMPFILE $seq;
>   }
>   ...
> }
> 
> 
> Gert
> 
> 
> 
> Aaron J Mackey wrote:
> > 
> > I think you might want to do something like this, using IO::Scalar to turn
> > your string into a pseudo-filehandle:
> > 
> > $seqs = param('seqs'); # grab your CGI form variable.
> > 
> > $fh = new IO::Scalar \$seqs;
> > 
> > $in = new Bio::SeqIO -fh => $fh, -format => 'Fasta';
> > 
> > while($seq = $in->next_seq()) {
> > 
> >         # do stuff with each $seq.
> > 
> > }
> > 
> > -Aaron
> > 
> > On Fri, 26 May 2000, gert thijs wrote:
> > 
> > > Hello,
> > >
> > > I hope this is not a stupid question, but I still haven't captured all the
> > > gory details of perl yet.
> > > I am developping a web interface where one can enter some DNA sequences that
> > > will be processed. Those DNA sequences should be in Fasta format. When I read
> > > the inputs of the web interface the sequences are stored as one long string in
> > > a variable $dnaseq. Now I am first writing this string to a file and then I
> > > use the filehandle to read the sequences into a new SeqIO object.
> > > But I was wondering if I can do this without writing $dnaseq to a file.
> > >
> > > tnx,
> > > Gert Thijs
> > >
> > >
> > 
> > --
> >  o ~   ~   ~   ~   ~   ~  o
> > / Aaron J Mackey           \
> > \  Dr. Pearson Laboratory  /
> >  \ University of Virginia  \
> >  /  (804) 924-2821          \
> >  \  amackey@virginia.edu    /
> >   o ~   ~   ~   ~   ~   ~  o
> 
> 

-- 
 o ~   ~   ~   ~   ~   ~  o
/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
 /  (804) 924-2821          \
 \  amackey@virginia.edu    /
  o ~   ~   ~   ~   ~   ~  o


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