[Numpy-discussion] Create numpy array from a list error

Gökhan Sever gokhansever@gmail....
Wed Sep 23 11:34:31 CDT 2009


On Wed, Sep 23, 2009 at 9:06 AM, Dave Wood <davejwood@gmail.com> wrote:

> Hi all,
>
> I've got a fairly large (but not huge, 58mb) tab seperated text file, with
> approximately 200 columns and 56k rows of numbers and strings.
>
> Here's a snippet of my code to create a numpy matrix from the data file...
>
> ####
>
> data = map(lambda x : x.strip().split('\t'), sys.stdin.readlines())
> data = array(data)
>
> ###
>
> It causes the following error:
>
> data = array(data)
>   ValueError: setting an array element with a sequence
>
> If I take the 1st 40,000 lines of the file, it works fine.
> If I take the last 40,000 lines of the file, it also works fine, so it
> isn't a problem with the file.
>
> I've found a few other posts complaining of the same problem, but none of
> their fixes work.
>
> It seems like a memory problem to me. This was reinforced when I tried to
> break the dataset into 3 chunks and stack the resulting arrays - I got an
> error message saying "memory error".
> Also, I don't really understand why reading in this 57mb txt file is taking
> up ~2gb's of RAM.
>
> Any advice? Thanks in advance
>
> Dave
>
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>
One more reply,

You try to read mixed data (strings and numbers) into an array, that might
be causing the problem. In my example, after skipping the meta-header all I
have is numbers.

Additionally, when you are reading chunk of data if one of the column
elements truncated or overflows its section NumPy complains with that
ValueError.

-- 
Gökhan
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