A Tuesday 15 December 2009 17:31:46 Ernesto escrigué:
> thank you for your explanation and for your time. I'll try to use a
> combined approach.
> A very stupid question is the following:
>
> Normally I have to update each string of the vlarray (and in the table
> as well) adding a character at th
>I've been doing some benchmarks based on your requirements, and my
conclusion
>is that the implementation of variable length types in HDF5 is not
very
>efficient, specially with HDF5 1.8.x series (see [1]). So, you
should avoid
>using VLArrays for saving small arrays: they fit better in
A Monday 14 December 2009 14:25:48 Francesc Alted escrigué:
> A Saturday 12 December 2009 18:45:33 Ernesto escrigué:
> > Dear Francesc,
> >
> > thank you for your reply. I'll try to better explain my problem using
> > real examples of data and code.
>
> [clip]
>
> I've been doing some benchmarks
A Saturday 12 December 2009 18:45:33 Ernesto escrigué:
> Dear Francesc,
>
> thank you for your reply. I'll try to better explain my problem using
> real examples of data and code.
[clip]
I've been doing some benchmarks based on your requirements, and my conclusion
is that the implementation of va
Ernesto.
I agree, I think pytables would be a good solution for his full (with gaps)
multiple sequence alignment.
Regarding your problem, hopefully others with more experience can help with
optimization. Personally I've had troubles in similar situations where I
had large amounts of varia
Hi Richard,
>This looks, in part, a way to store a huge multiple sequence
alignment with
>a reference sequence (the first character in ( ) being the DNA base
in a
>reference DNA molecule, but due to the inequal lengths in each VLA,
it would
>seem that gaps are not stored, or stored else
I'm going to stab at understanding your problem. Correct me where
I'm wrong.
On Sat, Dec 12, 2009 at 12:45 PM, Ernesto wrote:
As I wrote I start with an input file. It contains a string of
variable length (10e7-10e8). This string consists of four different
characters (A,C,G,T), the bases of a
I'll join in the guessing game.
This looks, in part, a way to store a huge multiple sequence alignment with
a reference sequence (the first character in ( ) being the DNA base in a
reference DNA molecule, but due to the inequal lengths in each VLA, it would
seem that gaps are not stored, or stored
I'm going to stab at understanding your problem. Correct me where I'm wrong.
On Sat, Dec 12, 2009 at 12:45 PM, Ernesto wrote:
> As I wrote I start with an input file. It contains a string of
> variable length (10e7-10e8). This string consists of four different
> characters (A,C,G,T), the bases of
On Sat, Dec 12, 2009 at 9:45 AM, Ernesto wrote:
> Dear Francesc,
>
> thank you for your reply. I'll try to better explain my problem using
> real examples of data and code.
>
> As I wrote I start with an input file. It contains a string of
> variable length (10e7-10e8). This string consists of fou
Dear Francesc,
thank you for your reply. I'll try to better explain my problem using
real examples of data and code.
As I wrote I start with an input file. It contains a string of
variable length (10e7-10e8). This string consists of four different
characters (A,C,G,T), the bases of a DNA mo
Ciao Ernesto,
A Thursday 10 December 2009 21:19:00 Ernesto escrigué:
> Dear all,
>
> I'm new to pytables. I would use this package to store biological
> data. In practice I have 2 input files.
> The first consists in a long string of characters. The length is in
> the range 10e7-10e8. I have to r
Dear all,
I'm new to pytables. I would use this package to store biological
data. In practice I have 2 input files.
The first consists in a long string of characters. The length is in
the range 10e7-10e8. I have to read such file character by character
and store it in a table according to it
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