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

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Dec 3 19:49:21 EST 2007

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?


Russell Smithies

Bioinformatics Software Developer
T +64 3 489 9085
E  russell.smithies at agresearch.co.nz

Invermay  Research Centre
Puddle Alley, 
New Zealand
T  +64 3 489 3809   
F  +64 3 489 9174  

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