[Bioperl-l] a PerlIO layer for Bio::SeqIO

[Smithies, Russell]

In a Statistics seminar I attended recently, the presenter pointed out that Statisticians aren't boring people, they just get excited by boring things.
I think the same applies to Bioinformaticians and Perl programmers  ;-)

--Russell

> -----Original Message-----
> From: Mark A. Jensen [mailto:maj at fortinbras.us]
> Sent: Friday, 23 October 2009 12:04 p.m.
> To: Smithies, Russell; 'BioPerl List'
> Subject: Re: [Bioperl-l] a PerlIO layer for Bio::SeqIO
> 
> Because it's fun! Also:
> 
> use CGI;
> use PerlIO::via::SeqIO;
> use strict;
> use warnings;
> my $q = new CGI;
> my ($seqfh, $dup);
> open($seqfh, "<:via(SeqIO)", 'test.fas');
> open(STDOUT, ">:via(SeqIO::fasta)");
> 
> my $s = <$seqfh>;
> 
> print (
>     $q->start_html,
>     "Copy the desired format from the boxes below:<br><br>",
>     $q->div({-style=>"border:solid 1px black"},
>      $q->h3("FASTA\n"),
>      $q->pre($s))
>     );
> (tied *STDOUT)->set_write_format('embl');
> print (
>     $q->div({-style=>"border:solid 1px black"},
>      $q->h3("EMBL"),
>      $q->pre($s))
>     );
> (tied *STDOUT)->set_write_format('gcg');
> print (
>     $q->div({-style=>"border:solid 1px black"},
>      $q->h3("GCG"),
>      $q->pre($s)),
>     $q->end_html
>     );
> 1;
> 
> ----- Original Message -----
> From: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
> To: "'Mark A. Jensen'" <maj at fortinbras.us>; "'BioPerl List'"
> <bioperl-l at bioperl.org>
> Sent: Thursday, October 22, 2009 6:57 PM
> Subject: RE: [Bioperl-l] a PerlIO layer for Bio::SeqIO
> 
> 
> Why anyone would want to do it this way is the only thing that's bugging me
> ;-)
> Maybe I'm a bit dense this morning but what's the advantage?
> 
> --Russell
> (I need more coffee)
> 
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen
> > Sent: Friday, 23 October 2009 11:24 a.m.
> > To: BioPerl List
> > Subject: [Bioperl-l] a PerlIO layer for Bio::SeqIO
> >
> > Hi All:
> >
> > Have you ever wanted to do this?
> >
> >  open($f, "<:via(SeqIO)", "my.fas");
> >  open($g, ">:via(SeqIO::embl)", "my.fas.embl");
> >  while (<$f>) { print $g $_; }
> >
> > Or this?
> >
> >  open($f, "<:via(SeqIO)", "my.fas");
> >  open(STDOUT, ">:via(SeqIO::fasta)");
> >  $seq = <$f>;
> >  print "The following is an example of FASTA format:", $seq;
> >
> > Or even this?
> >
> >  (tied *STDOUT)->set_write_format('gcg');
> >  print "While this is an example of GCG:", $seq;
> >
> > Now you can, and much more. See
> > http://search.cpan.org/search?query=PerlIO::via::SeqIO
> >
> > Send me the bugs.
> > cheers,
> > MAJ
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
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