On 09/14/2010 11:33 AM, Keith Goodman wrote:
On Tue, Sep 14, 2010 at 9:25 AM, kee chen<[email protected]> wrote:
Dear All,
Suppose I have a list group some kind like DNA sequence:
1 ATGCATGCAATTGGCC
2 ATGCATGCAATTGGCCATCD
3 CATGCAATTGGCCCCCCCCC
......
100000 CATGCAAATTGGCCCCCCCCC
the string length of each item is not sure and may get change/update later,
then how can I store above in a numpy array (include the ID) and easy to get
the single value?
for example
1. ATGCATGCAATTGGCC
I want get the first T then I use something like array[1][1], means
A[T]G...... and if I want to update the 3rd postion I can use array[1][2]
= T to set the AT[G]C... to AT[T]C...?
How about using a python list:
array = ['ATGC', 'CATGA', 'A']
array[0][1]
'T'
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Variable length is incompatible with numpy:
'NumPy arrays have a fixed size at creation, unlike Python lists (which
can grow dynamically).'
http://docs.scipy.org/doc/numpy/user/whatisnumpy.html
So you have to allocate the space for the largest sequence - although
you can try using Scipy's sparse matrix (where nucleotides/amino acids
are coded in numbers starting at 1 such that zeros code the empty areas.
If lists (or dictionaries) don't work for you, you might want to explore
bioinformatics packages like 'pygr' (http://code.google.com/p/pygr/) and
Biopython (http://biopython.org/wiki/Main_Page) or try more general
approaches such hdf5 and pytables.
Bruce
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