[Bioperl-l] Help needed urgently

Phillip SanMiguel pmiguel at purdue.edu
Wed Nov 15 22:53:02 EST 2006


Chris Fields wrote:
>> 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.
>>
>>
>>
>>     

[..base segment documentation elided...]
>>
>>
>> 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?
>
>   
Chris,
    I'm pretty sure that the Base Segment tag (BS) is not the one Sayali 
wants. At least that is my reading of Sayali's wanting to get the 
consensus sequence and the traces names used in the assembly. I write 
this because of an email sent me by David Gordon in 2001 included here 
without his permission:

> Phrap writes BS lines which
> indicate, for each consensus position, which read phrap uses at that
> position to become the consensus.  These BS ("base segments") are 
> manipulated by Consed when there are changes to the assembly, such as
> joins, tears, removing reads, or changing the consensus.
Which is basically what Sayali quoted from the documentation from phrap. 
But it is not consistent with "trace names used in the assembly".
-- 
Phillip



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