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

Mark A. Jensen maj at fortinbras.us
Thu Oct 22 18:23:30 EDT 2009

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

Send me the bugs.

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