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

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Feb 25 17:12:39 EST 2008


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 


=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================



More information about the Bioperl-l mailing list