[Bioperl-l] sequence object with no sequence data
roy at colibase.bham.ac.uk
Wed Sep 13 14:26:25 UTC 2006
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
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.
Dr. Roy Chaudhuri
Bioinformatics Research Fellow
Division of Immunity and Infection
University of Birmingham, U.K.
> 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.
> 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.
>> 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
>> as units and I'd also like to be able to draw these sequences using
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