[Bioperl-l] Help needed urgently

[Chris Fields]

> I wish to fetch consensus sequence and the names of the trace  
> (chromat)
> files used in the assembly from the .ace file
>
> For this purpose, I am using Bio::Assembly::IO. But I am unable to  
> find the
> appropriate methods which would enable me to fetch this information.
>
>
>
> Note:
>
> The BS line (base segment) in the .ace file indicates which read  
> phrap has
> chosen to be the consensus at a particular position.
>
> For example:
>
> BS 1 515 K26-572c gives
>
> BS <padded start consensus position> <padded end consensus  
> position> <read
> name> respectively.
>
>
>
> How do I retrieve this information contig wise?
>
> Kindly help.
>
> Regards,
>
> Sayali D Salodkar

It looks like the relevant part of the Bio::Assembly::IO::ace parser  
responsible for parsing this is commented out:

	# Loading base segments definitions (Base Segment field)
#	/^BS (\d+) (\d+) (\S+)/ && do {
#	    if (exists($self->{'contigs'}[$contig]{'reads'}{$3} 
{'segments'})) {
#		$self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} .= " " . $1 .  
" " . $2;
#	    } else { $self->{'contigs'}[$contig]{'reads'}{$3}{'segments'} =  
$1 . " " . $2 }
#	};

I'm not sure why to be honest as I'm not very familiar with the  
Bio::Assembly.  Have you tried removing the comments to see what  
happens?

You could file a bug report noting this using Bugzilla:

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

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign