pandas read_csv: TypeError: 'sage.rings.integer.Integer' object is not iterable

[singlets]

Hello,

This is probably a trivial fix that is available in the sage groups, but I'm striking out searching for preparser / rings.integer / iterable posts. Maybe it is idiosyncratic to pandas?

I'm using pandas for some simple munging; python doesn't like the taste of what sage is passing as the skiprows argument.  (pd.read_csv() works fine from a terminal ipython session)

sage: import pandas as pd
sage: preparser(False)
sage: pd.read_csv('data/6226BB60.dat', skiprows=86)

Error in lines 2-2
Traceback (most recent call last):
  File "/mnt/home/HXupCDGU/.sagemathcloud/sage_server.py", line 668, in execute
    exec compile(block+'\n', '', 'single') in namespace, locals
  File "", line 1, in <module>
  File "/usr/local/sage/sage-5.12/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 400, in parser_f
    return _read(filepath_or_buffer, kwds)
  File "/usr/local/sage/sage-5.12/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 198, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
  File "/usr/local/sage/sage-5.12/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 475, in __init__
    self.options, self.engine = self._clean_options(options, engine)
  File "/usr/local/sage/sage-5.12/local/lib/python2.7/site-packages/pandas/io/parsers.py", line 562, in _clean_options
    skiprows = set() if skiprows is None else set(skiprows)
TypeError: 'sage.rings.integer.Integer' object is not iterable

Hints? 

Thanks,
Steve

31

[William Stein]

On Sat, Nov 23, 2013 at 5:13 PM, singlets <ssin...@coe.edu> wrote:
> Hello,
>
> This is probably a trivial fix that is available in the sage groups, but I'm
> striking out searching for preparser / rings.integer / iterable posts. Maybe
> it is idiosyncratic to pandas?
>
> I'm using pandas for some simple munging; python doesn't like the taste of
> what sage is passing as the skiprows argument. (pd.read_csv() works fine
> from a terminal ipython session)
>
> sage: import pandas as pd
> sage: preparser(False)
> sage: pd.read_csv('data/6226BB60.dat', skiprows=86)

Try int(86) instead of 86?`

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--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org

[Singleton, Steve]

>

> sage: import pandas as pd
> sage: preparser(False)
> sage: pd.read_csv('data/6226BB60.dat', skiprows=86)

Try int(86) instead of 86?

I'm an idiot...I tried Integer(86)...wrong direction. int() works fine.

Just out of curiosity, why doesn't preparser(False) work here? I'm probably misunderstanding how the preparser works.

Steve

[William Stein]

I'm surprised preparser(False) doesn't work. It's hard for me to
test without the data file...

>
> Steve

>
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> https://groups.google.com/d/msgid/sage-cloud/CANSCVnrC5ri1m6SX667wrwFMnSUpN5pS9nege15cdZtXgUy5zw%40mail.gmail.com.

[Singleton, Steve]

Actually, I think this is a glitch with pandas and sage. I get the error any time skiprows!=None in pandas.read_csv() under sage.

Probably not a front-burner issue, but if you think it's worth pursuing you're welcome to take a peek at

/mnt/home/HXupCDGU/fluorescence/*.TXT

Thanks,

Steve

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[Singleton, Steve]

I think I know the problem...

pandas.io.parsers.read_csv(): skiprows is either a list or an int.  Calling pandas.read.csv(skiprows=[1,2,3] or read.csv(skiprows=int(3) gives no error.  Looks like skiprows is making assumptions about types that are ok in iPython but not sage...

Thanks,

Steve