Can I parse CSV data separated by \t to vectors

asked 2013-08-10 04:46:38 +0100

Jaakko Seppälä
67 ●5 ●9 ●18

updated 2013-08-10 10:14:39 +0100

I have a CSV data as follows:

pcb138  pcb180  pcb52   pcb118  pcb
1.46    0.738   0.532   0.72    19.9959
0.64    0.664   0.03    0.236   6.0996
3.29    1.15    0.134   1.54    24.9655
3.94    1.33    0.466   1.94    37.4436
3.18    2.14    0.243   1.47    30.183
2.43    1.3     0.137   1.31    20.8036
3.94    3.49    0.208   0.876   41.3818
3.38    1.04    0.477   2.46    29.478
2.21    0.966   0.457   1.14    24.2387
2.49    1.59    0.298   1.18    26.3198
0.86    0.395   0.02    0.406   8.591
3.38    1.85    0.539   1.5     36.4229
7.39    4.42    0.707   3.55    66.4108

Is it possible to read that to vectors? I tried the following:

sage: import csv                           
sage: file='/home/jaakko/Downloads/pcb.dat'
sage: reader=csv.reader(open(file))        
sage: L=[]                                 
sage: for row in reader:^J    L.append(row)
....:     
sage: L[0][0]
'pcb138\tpcb180\tpcb52\tpcb118\tpcb'
sage: L[1][0]
'1'
sage: L[1][1]
'46\t'

What I would like to have is vectors of the form

pcb138=vector([1.46,0.64,...,7.39])

without those tabulators.

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answered 2013-08-10 06:29:58 +0100

Luca
890 ●6 ●21

Your data is not really cvs, since it is not comma separated. You could configure csv to properly parse it, but it is simpler to use native python. Here's a solution using a dictionary, instead of variables named pcb139, etc.

sage: data = map(lambda x: x.split('\t'), open(file).readlines())
sage: vects = {col[0] : vector(map(float, col[1:])) for col in zip(*data)}
sage: vects['pcb138']                                                     
(1.46, 0.64, 3.29, 3.94, 3.18, 2.43, 3.94, 3.38, 2.21, 2.49, 0.86, 3.38, 7.39)

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answered 2013-08-10 09:35:44 +0100

tmonteil
27423 ●31 ●204 ●517 http://wiki.sagemath.o...

If you want to use the csv module, you can specify that the delimiter is the tabulator as follows:

sage: reader=csv.reader(open(file), delimiter='\t')

then,

sage: L=[]
sage: for row in reader:                   
....:     L.append(row)
sage: L
[['pcb138', 'pcb180', 'pcb52', 'pcb118', 'pcb'],
 ['1.46', '0.738', '0.532', '0.72', '19.9959'],
 ['0.64', '0.664', '0.03', '0.236', '6.0996'],
 ['3.29', '1.15', '0.134', '1.54', '24.9655'],
 ['3.94', '1.33', '0.466', '1.94', '37.4436'],
 ['3.18', '2.14', '0.243', '1.47', '30.183'],
 ['2.43', '1.3', '', '0.137', '1.31', '20.8036'],
 ['3.94', '3.49', '0.208', '0.876', '41.3818'],
 ['3.38', '1.04', '0.477', '2.46', '29.478'],
 ['2.21', '0.966', '0.457', '1.14', '24.2387'],
 ['2.49', '1.59', '0.298', '1.18', '26.3198'],
 ['0.86', '0.395', '0.02', '0.406', '8.591'],
 ['3.38', '1.85', '0.539', '1.5', '', '36.4229'],
 ['7.39', '4.42', '0.707', '3.55', '66.4108']]
sage: L[1][0]
'1.46'

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