[Pipet Devel] python data structure

Thomas.Sicheritz at molbio.uu.se Thomas.Sicheritz at molbio.uu.se
Mon Jan 11 08:19:00 EST 1999


Hej all python gurus ...

What python data type would you recommend for the class representation
of a nucleotide sequence ? 
- string, list or array (module) ?
I am not (yet) familiar with the performance questions of python types, but 
I got the impression that lists are very slow - and I have no idea how the
array module is implemented. (btw I used strings in Tcl)

J.W. Bizzaro writes:
> I wonder if DNA sequence analysis tools should be different programs from
> protein (or polypeptide) sequence analysis tools, or maybe a single
> program such as the sequence editor can switch between the two?  Of
> course they present some very different problems...but then again...?
> What do you guys think?

In case of an editor/viewer - I vote for different programs/implementations.
- Sequence analysis tools are just connected modules - e.g. the blast
module/parser/filter is only slightly different for DNA or protein
sequences.

my 2 cents ...
-thomas
-- 
Sicheritz Ponten Thomas E.  Department of Molecular Biology
blippblopp at linux.nu         BMC, Uppsala University
BMC:  +46 18 4714214        BOX 590 S-751 24 UPPSALA Sweden
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