[Bioperl-l] Bio::Assembly::IO problems

Chris Fields cjfields at uiuc.edu
Mon Feb 25 18:01:42 EST 2008


Russell,

Using the test data from the bioperl installation appears to work, but  
I wouldn't be surprised if this is a bug.  Can you file this as a bug  
along with some test data?

http://bugzilla.open-bio.org/

chris

On Feb 25, 2008, at 4:12 PM, Smithies, Russell wrote:

> Is the Bio::Assembly::IO stuff working?
> I want to parse some .ace files but keep getting errors:
>
> 	[smithiesr at impala ace_phrap]$ perl 454_read_ace.pl
> 	Can't call method "get_consensus_sequence" on an undefined value  
> at /usr/lib/perl5/site_perl/5.8.8/Bio/Assembly/IO/ace.pm line 169,  
> <GEN0> line 20.
>
> My code is:
>
> 	#!perl -w
>
> 	use Bio::Assembly::IO;
> 	use Data::Dumper;
>
> 	my $in = "454Contigs.ace";
>
> 	$io = new Bio::Assembly::IO(-file=>$in,-format=>"ace");
> 	$ass = $io->next_assembly;
>
> 	print Dumper $ass;
> 	exit;
>
> 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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