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

[Florent Angly]

Sounds cool Mark! After all, UNIX is based on the notion on piping data 
from one program to another using filehandles.
Any chance that this could also work for compressed files like *.gz ?? I 
don't think that Bio::Root::Utilities::compress and uncompress can deal 
with filehandles, can it?
Florent

Mark A. Jensen wrote:
> 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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