ValueError: could not convert string to float: id

Question

I'm running the following python script:

#!/usr/bin/python

import os,sys
from scipy import stats
import numpy as np

f=open('data2.txt', 'r').readlines()
N=len(f)-1
for i in range(0,N):
    w=f[i].split()
    l1=w[1:8]
    l2=w[8:15]
    list1=[float(x) for x in l1]
    list2=[float(x) for x in l2]
    result=stats.ttest_ind(list1,list2)
    print result[1]

However I got the errors like:

ValueError: could not convert string to float: id

I'm confused by this. When I try this for only one line in interactive section, instead of for loop using script:

>>> from scipy import stats
>>> import numpy as np
>>> f=open('data2.txt','r').readlines()
>>> w=f[1].split()
>>> l1=w[1:8]
>>> l2=w[8:15]
>>> list1=[float(x) for x in l1]
>>> list1
[5.3209183842, 4.6422726719, 4.3788135547, 5.9299061614, 5.9331108706, 5.0287087832, 4.57...]

It works well.

Can anyone explain a little bit about this? Thank you.

Solution 1

Obviously some of your lines don't have valid float data, specifically some line have text id which can't be converted to float.

When you try it in interactive prompt you are trying only first line, so best way is to print the line where you are getting this error and you will know the wrong line e.g.

#!/usr/bin/python

import os,sys
from scipy import stats
import numpy as np

f=open('data2.txt', 'r').readlines()
N=len(f)-1
for i in range(0,N):
    w=f[i].split()
    l1=w[1:8]
    l2=w[8:15]
    try:
        list1=[float(x) for x in l1]
        list2=[float(x) for x in l2]
    except ValueError,e:
        print "error",e,"on line",i
    result=stats.ttest_ind(list1,list2)
    print result[1]

Solution 2

My error was very simple: the text file containing the data had some space (so not visible) character on the last line.

As an output of grep, I had 45  instead of just 45. 

Solution 3

This error is pretty verbose:

ValueError: could not convert string to float: id

Somewhere in your text file, a line has the word id in it, which can't really be converted to a number.

Your test code works because the word id isn't present in line 2.

---

If you want to catch that line, try this code. I cleaned your code up a tad:

#!/usr/bin/python

import os, sys
from scipy import stats
import numpy as np

for index, line in enumerate(open('data2.txt', 'r').readlines()):
    w = line.split(' ')
    l1 = w[1:8]
    l2 = w[8:15]

    try:
        list1 = map(float, l1)
        list2 = map(float, l2)
    except ValueError:
        print 'Line {i} is corrupt!'.format(i = index)'
        break

    result = stats.ttest_ind(list1, list2)
    print result[1]

Solution 4

Perhaps your numbers aren't actually numbers, but letters masquerading as numbers?

In my case, the font I was using meant that "l" and "1" looked very similar. I had a string like 'l1919' which I thought was '11919' and that messed things up.

Solution 5

For a Pandas dataframe with a column of numbers with commas, use this:

df["Numbers"] = [float(str(i).replace(",", "")) for i in df["Numbers"]]

So values like 4,200.42 would be converted to 4200.42 as a float.

Bonus 1: This is fast.

Bonus 2: More space efficient if saving that dataframe in something like Apache Parquet format.

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