[Bioperl-l] Errors using Bio::Assembly

[Andy Nunberg]

I have tried the new Bio::Assembly module and I get a few errors...
using RH Linux 7.2 with Perl 5.6

first here is the script i am using...
use lib '/loginhome/anunberg/bioperl-1.2';
use strict;
use Bio::Assembly::IO;
use Bio::Assembly::ContigAnalysis;    
use Carp qw(cluck);
my $in=Bio::Assembly::IO->new(-file=>$ARGV[0], -format=>'ace');
my $assembly=$in->next_assembly;
my @contigs=$assembly->all_contigs;

foreach my $contig(@contigs){

	my $analysis=Bio::Assembly::ContigAnalysis->new(-contig=>$contig);
	my @hqd=$analysis->high_quality_discrepancies;
	my @ss=$analysis->single_strand;
	my @lcd=$analysis->low_consensus_quality;
	my $id=$contig->id;
	print "$id\t";
	print scalar @hqd."\t";
	print scalar @lcd."\n";
}

My first error is when calling the next_assembly method.  Some parsing
error occurs, I think.  I got mutlitiple warnings all the same
Argument "" isn't numeric in numeric comparison (<=>) at
/loginhome/anunberg/bioperl-1.2/Bio/SeqFeature/Collection.pm line 436,
<GEN0> line 54.
the lines correspond to the QA tag lines in the ace file.  Sometimes the
same complaint occurs one line above it if its blank, but not all blank
lines above the QA tag produce this warning

when using the method high_quality_discrepancies, i get this warning
Argument "" isn't numeric in numeric comparison (<=>) at
/loginhome/anunberg/bioperl-1.2/Bio/SeqFeature/Collection.pm line 436,
<GEN0> line 358.
which is a blank line at the end of the ace file.

I may be using the method wrong, but using an ace file where i know to have
a high quality descrepancie, i still get 0 .
The documentation is a little off for this method.  The description says
that a Bio::SeqFeature::Collection is returned, but the code and the
example has an array of Bio::SeqFeature::Generic objects being returned(if
i am reading the code correctly).  



the single_strand method gives me the following exception
------------- EXCEPTION Bio::Root::NotImplemented -------------
MSG: Abstract method
"Bio::Assembly::ContigAnalysis::_merge_overlapping_features" is not
implemented by package Bio::Assembly::ContigAnalysis.
This is not your fault - author of Bio::Assembly::ContigAnalysis should be
blamed!

STACK Bio::Root::RootI::throw_not_implemented
/loginhome/anunberg/bioperl-1.2/Bio/Root/RootI.pm:529
STACK Bio::Assembly::ContigAnalysis::_merge_overlapping_features
/loginhome/anunberg/bioperl-1.2/Bio/Assembly/ContigAnalysis.pm:476
STACK Bio::Assembly::ContigAnalysis::single_strand
/loginhome/anunberg/bioperl-1.2/Bio/Assembly/ContigAnalysis.pm:442
STACK toplevel ../testing_BioAssembly.pl:31

---------------------------------------------------------------

Thanks to anyone who can help.
Andy

*******************************************************************
Andy Nunberg, Ph.D
Computational Biologist
Orion Genomics, LLC 
(314) 615-6989
http://www.oriongenomics.com