Re: [Pytables-users] sorting a table

[Francesc A. <fa...@py...>]

A Wednesday 28 April 2010 20:22:52 Ernesto escrigué:
> Hi Francesc, thank you for your reply.
> 
> > The first column contains an integer. Now I'd like to sort my table
> >  according to numbers of the first column. Is there a way to perform this
> >  action?
> >
> > Yes.  The simplest way is by setting the `sortby` parameter to true in
> > the `Table.copy()` method.  This triggers an on-disk sorting operation,
> > so you don't have to be afraid of your available memory.  You will need
> > the Pro version for getting this capability.
> 
> It means that I can sort a table using the Pro version only. No other
>  solutions are available?

I haven't said that no other solutions are available.  Only that the Pro venue 
is the simplest (and certainly a powerful one ;-)  If you want to go Pro, you 
may want to use plain NumPy for doing this.

>  Working with my simple table I found a strange
>  behaviour that probably is due to my limited experience with pytables. The
>  description of the table is:
> /newgroup/table (Table(729036,), shuffle, zlib(1)) 'A table'
>   description := {
>   "position": Int32Col(shape=(), dflt=0, pos=0),
>   "read": StringCol(itemsize=1, shape=(), dflt='', pos=1),
>   "qual": Int32Col(shape=(), dflt=0, pos=2),
>   "strand": StringCol(itemsize=1, shape=(), dflt='', pos=3)}
>   byteorder := 'little'
>   chunkshape := (819,)
> Next I iterate over a subset using the command:
> for row in table.where('(qual > 1) & (qual < 10)'):
> 	print row
> It works correctly and I get expected results.
> Then I use the following command:
> results=[row for row in table.where('(qual > 1) & (qual < 10)')]
> it works but I get a list containing the same value.
> I report the first five rows obtained using both procedures:
> - procedure 1:
> (167809, 'C', 8, '-')
> (167810, 'G', 9, '-')
> (167812, 'C', 5, '-')
> (167823, 'T', 9, '-')
> (1015856, 'G', 5, '-')
> - procedure 2:
> [(1041269, 'G', 39, '-'), (1041269, 'G', 39, '-'), (1041269, 'G', 39, '-'),
>  (1041269, 'G', 39, '-'), (1041269, 'G', 39, '-')]
> 
> Where is the error?

No, it is not, but it is a common pitfall for beginners.  See:

http://sourceforge.net/mailarchive/forum.php?thread_name=200905141759.16731.faltet%40pytables.org&forum_name=pytables-
users

Anyway, I've decided to avoid this behaviour in 2.2 series.  For details, see:

http://pytables.org/trac/ticket/252

Ciao,

-- 
Francesc Alted