Pandas read_csv wrong columns
I am trying to read a data file that looks like this (for the first 4 lines) using pandas.read_csv.
num NED IAU z N det TOF type alph.4 alph1 alph5 alph10 alph15 alph20 alph50 dSIbydnu DWORRY UVNONE
1 ESO473-G007 J001605-234 0.06401 19.51 det 8.59 u -0.432 -0.428 -0.413 -0.402 -0.395 -0.389 -0.369 0.017 53.53 UV
2 PKS0023-26 J0025-2602 0.32162 18.36 det 7.95 a -0.272 -0.437 -0.726 -0.849 -0.919 -0.972 -1.135 -0.414 53.57 UV
3 NGC0315 0055+30 0.01648 18.84 det 7.41 a -0.248 -0.306 -0.379 -0.398 -0.406 -0.411 -0.417 -0.119 53.60 UV
I type data = pandas.read_csv('radio.dat',sep=' ', header=0)
, but when I do print data
, I get 3 row headers and then the column names start 3 columns down from where they should start and I get an additional 3 NaN columns:
num NED IAU z N det ...
1 ESO473-G007 J001605-234 NaN 0.06401 19.51 det NaN 8.59 ...
2 PKS0023-26 J0025-2602 NaN 0.32162 18.36 det NaN 7.95 ...
3 NGC0315 0055+30 NaN 0.01648 18.84 det NaN 7.41 ...
num should be a column heading with 1 2 3 ..., NED for the next column, IAU for the next, and NaNs shouldn't even be there.
I tried setting index_col = 0, but it gives me this error:
File "C:\Python27\lib\site-packages\pandas\io\parsers.py", line 1184, in read
values = data.pop(self.index_col[i])
IndexError: list index out of range
Setting index_col = False gives
File "C:\Python27\lib\site-packages\pandas\io\parsers.py", line 1164, in read
data = self._reader.read(nrows)
File "pandas\parser.pyx", line 758, in pandas.parser.TextReader.read (pandas\parser.c:7411)
File "pandas\parser.pyx", line 780, in pandas.parser.TextReader._read_low_memory (pandas\parser.c:7651)
File "pandas\parser.pyx", line 855, in pandas.parser.TextReader._read_rows (pandas\parser.c:8484)
File "pandas\parser.pyx", line 936, in pandas.parser.TextReader._convert_column_data (pandas\parser.c:9490)
File "pandas\parser.pyx", line 1208, in pandas.parser.TextReader._get_column_name (pandas\parser.c:13172)
IndexError: list index out of range
How do I read this file correctly?
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You have varying number of spaces in your csv usage sep='\s+'
to handle this
In [128]:
t="""num NED IAU z N det TOF type alph.4 alph1 alph5 alph10 alph15 alph20 alph50 dSIbydnu DWORRY UVNONE
1 ESO473-G007 J001605-234 0.06401 19.51 det 8.59 u -0.432 -0.428 -0.413 -0.402 -0.395 -0.389 -0.369 0.017 53.53 UV
2 PKS0023-26 J0025-2602 0.32162 18.36 det 7.95 a -0.272 -0.437 -0.726 -0.849 -0.919 -0.972 -1.135 -0.414 53.57 UV
3 NGC0315 0055+30 0.01648 18.84 det 7.41 a -0.248 -0.306 -0.379 -0.398 -0.406 -0.411 -0.417 -0.119 53.60 UV"""
data = pd.read_csv(io.StringIO(t),sep='\s+', header=0)
data
Out[128]:
num NED IAU z N det TOF type alph.4 \
0 1 ESO473-G007 J001605-234 0.06401 19.51 det 8.59 u -0.432
1 2 PKS0023-26 J0025-2602 0.32162 18.36 det 7.95 a -0.272
2 3 NGC0315 0055+30 0.01648 18.84 det 7.41 a -0.248
alph1 alph5 alph10 alph15 alph20 alph50 dSIbydnu DWORRY UVNONE
0 -0.428 -0.413 -0.402 -0.395 -0.389 -0.369 0.017 53.53 UV
1 -0.437 -0.726 -0.849 -0.919 -0.972 -1.135 -0.414 53.57 UV
2 -0.306 -0.379 -0.398 -0.406 -0.411 -0.417 -0.119 53.60 UV
So here:
alph50 dSIbydnu DWORRY
you have two spaces between those columns and between your data.
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