[Bioperl-l] sequence object with no sequence data

Roy Chaudhuri roy at colibase.bham.ac.uk
Wed Sep 13 10:26:25 EDT 2006


Hi Nath.

Just a couple more suggestions to add to Hilmar's advice. If you mean 
what I think you do by a "slice", then you may want to look at 
Bio::SeqUtils->trunc_with_features

I don't think it will work correctly without any sequence data, maybe 
you can try creating a sequence consisting of just Ns, by calling 
something like $seq->seq('N'x$seq->length)

As for working with centiMorgan coordinates, couldn't you just multiply 
all your values by a fixed amount (100, say) to give you integer 
coordinates? It might even be possible to hack Bio::Graphics, to convert 
these pseudo-coordinates back into their original format if you want to 
draw a scale etc.

Roy.
--
Dr. Roy Chaudhuri
Bioinformatics Research Fellow
Division of Immunity and Infection
University of Birmingham, U.K.

http://xbase.bham.ac.uk

> Interesting. No, you can't - length and also feature positions are  
> measured in basepairs.
> 
> Having said that, I'm not sure off the top of my head at which places  
> and whether at all it is checked that the positions are actually  
> integers. So, so long as you make sure that you never ask the system  
> for translating to basepair coordinates, providing cM could be worth  
> a try if you're in an adventurous mood. I.e., make the length long  
> enough that your highest cM number is still lower, and never ask for  
> subsequences. Also, the system may check that for features the start  
> is greater or equal to 1, so you may have to translate the  
> coordinates by adding 1 if some of your markers are at <1cM.
> 
> 	-hilmar
> 
> On Sep 13, 2006, at 9:26 AM, Nathan Haigh wrote:
> 
>> Hilmar Lapp wrote:
>>> Yes you can, just make sure you set the length. I'm not sure though
>>> what you mean by taking slices of it.
>>>
>>>     -hilmar
>> One more related quick question:
>>
>> Is it possible to have a sequence length measured in different  
>> units so
>> that decimals could be used? In particular, I'm thinking of  
>> centimorgans
>> as units and I'd also like to be able to draw these sequences using
>> Bio::Graphics.
>>
>> Thanks
>> Nath
>>
> 


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