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

Smithies, Russell Russell.Smithies at agresearch.co.nz
Mon Feb 25 18:23:06 EST 2008


I solved the problem :-)
The contig lines in our .ace files have a lower-case 'c' in the contig name instead of upper-case so weren't being found by this regex in ace.pm line 142:
	(/^CO Contig(\d+) (\d+) (\d+) (\d+) (\w+)/) && do { # New contig found!

e.g:
	CO contig00001 711 12 6 U 
instead of:
	CO Contig00001 711 12 6 U

Our contigs were generated with Newbler version 1.1.01.20. so might be something to watch out for in future.


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 








> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-
> bio.org] On Behalf Of Smithies, Russell
> Sent: Tuesday, 26 February 2008 11:13 a.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Bio::Assembly::IO problems
> 
> 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
>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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