[Bioperl-l] Bio::Assembly::IO problems reading .ace files

[Smithies, Russell]

Thanx Chris,
I'm only writing a simple .ace viewer to display assembled contigs in a
Bio::Graphics::Panel so I'll parse the coords from the .ace files
"manually".
Unless anyone else has a better idea ?
(and some example code ;-)

Russell



> -----Original Message-----
> From: Chris Fields [mailto:cjfields at uiuc.edu]
> Sent: Tuesday, 4 December 2007 3:16 p.m.
> To: Smithies, Russell
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio::Assembly::IO problems reading .ace files
> 
> This seems similar to the 'too many open filehandles issue' documented
> here:
> 
> http://bugzilla.open-bio.org/show_bug.cgi?id=2320
> 
> It unfortunately is due to having an open DB_File for every contig,
> and is a problem with the Bio::Assembly implementation that isn't
> easily fixed.  Changing the open filehandle limit using ulimit is the
> only known fix:
> 
> ulimit -n 10000
> 
> chris
> 
> On Dec 3, 2007, at 6:49 PM, Smithies, Russell wrote:
> 
> > Hi all,
> >
> > It' trying to read .ace files but keep getting an error that I don't
> > know the cause of.
> > Really basic example code:
> >
> > 	#!/usr/local/bin/perl -w
> >
> > 	use lib "/data/home/smithiesr/bioperl-live";
> > 	use Bio::Assembly::IO;
> > 	use Data::Dumper;
> >
> > 	$ace = "CLP0001001240-cE15_20030319.ace";
> >
> > 	$io = new Bio::Assembly::IO(-file=>$ace,-format=>"ace");
> > 	$assembly = $io->next_assembly;
> >
> > 	foreach $contig ($assembly->all_contigs) {
> >      		print Dumper $contig;
> > 	}
> >
> > Gives this error;
> > 	[smithiesr at impala ace_phrap]$ perl bp_read_ace.pl
> > 	Can't call method "get_consensus_sequence" on an undefined value
> > at /data/home/smithiesr/bioperl-live/Bio/Assembly/IO/ace.pm line
170,
> > <GEN0> line 42.
> >
> > Which relates to this bit in ace.pm:
> > 	# Loading contig qualities... (Base Quality field)
> > 	/^BQ/ && do {
> > 	    my $consensus = $contigOBJ->get_consensus_sequence()->seq();
> >
> > Is this caused by a dud ace file or a problem with
> > Bio::Assembly::IO:ace
> > or is the Contig object not getting created?
> > Any ideas?
> >
> > Thanx,
> >
> > Russell Smithies
> >
> > Bioinformatics Software Developer
> > T +64 3 489 9085
> > E  russell.smithies at agresearch.co.nz
> >
> > Invermay  Research Centre
> > Puddle Alley,
> > Mosgiel,
> > New Zealand
> > T  +64 3 489 3809
> > F  +64 3 489 9174
> > www.agresearch.co.nz
> >
> > =
> >
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> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 

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