[Bioperl-l] combining a CGI filehandle with SeqIO

[Jamie Hatfield (AGCoL)]

Not a bioperl problem exactly.  Just a output buffering issue.

Just out of curiosity, why do you use FileHandle instead of just an
open?  Is that more correct or just OO?

:
:
> # output filehandle, same as $o destination
> my $fh = FileHandle->new(">>${fastafile}.html") or die "No 
> append: $!";
> flock($fh, LOCK_SH) 				or die "No LOCK_SH: $!";

autoflush $fh 1;

> # initialize HTML doc
> print $fh $q->start_html(-title  => 'test page',
> 			 -author => 'nkuipers at uvic.ca',);
:
:


----------------------------------------------------------------------
Jamie Hatfield                              Room 541H, Marley Building
Systems Programmer                          University of Arizona
Arizona Genomics Computational              Tucson, AZ  85721
  Laboratory (AGCoL)                        (520) 626-9598

> -----Original Message-----
> From: bioperl-l-bounces at bioperl.org 
> [mailto:bioperl-l-bounces at bioperl.org] On Behalf Of nkuipers
> Sent: Friday, February 07, 2003 11:35 AM
> To: bioperl-l at bioperl.org
> Subject: [Bioperl-l] combining a CGI filehandle with SeqIO
> 
> 
> Hello,
> 
> I have written a script to convert a fasta flat file to an 
> html version of the 
> same.  The CGI object writes to the same filehandle as the 
> SeqIO object, with 
> a shared lock.  For some reason (maybe a Perl thing?) every 
> CGI event is 
> ignored until the SeqIO iteration is finished.  So I end up 
> getting a bunch of 
> fasta sequences followed by all the html that should precede, 
> be dispersed 
> through, and end the document.  Does anyone know what's up?  
> The script is 
> small, and as follows:
> 
> #!/usr/bin/perl
> 
> use strict;
> use warnings;
> 
> =pod
> 	author: nkuipers at uvic.ca
> 	written: 02/05/03
> 	updated: 02/07/03
> 	usage: perl FastatoHTML fastafile
> 
> 	OS: Red Hat Linux 8.0
> 	Perl: 5.8.0
> 	bioperl: 1.2
> =cut
> 
> use lib "/home/nkuipers/lib";
> use Bio::SeqIO;
> use CGI::Pretty ":html13";
> use FileHandle;
> use Fcntl ":flock";
> 
> # input file
> my $fastafile = shift;
> 
> # input reader
> my $i = Bio::SeqIO->new(-file => $fastafile);
> 
> # output writers
> my $q = CGI::Pretty->new;
> my $o = Bio::SeqIO->new(-file   => ">>${fastafile}.html",
> 			-format => 'Fasta');
> 
> # output filehandle, same as $o destination
> my $fh = FileHandle->new(">>${fastafile}.html") or die "No 
> append: $!";
> flock($fh, LOCK_SH) 				or die "No LOCK_SH: $!";
> 
> # initialize HTML doc
> print $fh $q->start_html(-title  => 'test page',
> 			 -author => 'nkuipers at uvic.ca',);
> 
> # iterate through the input sequences
> while (my $seqobj = $i->next_seq)
> {
> 	$o->write_seq($seqobj);
> 	print $fh $q->br,$q->hr,$q->br;
> }
> 
> # end HTML doc and clean up
> print $fh $q->end_html;
> $fh->close;
> 
> __END__
> 
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