Question

I have a .csv file containing 3 columns of data. I need to create a new output file that includes a specific set of data from the first and third column from the original file. The third column contains decimal values, and I believe in such a case I have use the float() feature of python. I have tried the following code:

in_file = open("filename.csv", "r")

out_file = open("output.csv", "w")

while True:

    line = in_file.readline()
    if (line == ''): 
        break
    line = line.strip() 
    items = line.split(',') 
    gi_name = items[0] 
    if (gi_name.startswith("_"))
        continue
    p_value = float(items[2]) 
    if (p_value > 0.05):
        continue
    out_file.write(','.join([gene_name, str(p_value)]))
in_file.close()
out_file.close()

when I run the above, I recieve the following error:

Error: invalid literal for float(): 0.000001

the value 0.0000001 is the first value in my data set for the third column, and I guess the code cannot read beyond that set but I’m not sure why. I am new to python, and don’t really understand why I am getting this error or how to fix it. I have tried other modifications for how to input the float(), but without success. Does anyone know how I might be able to fix this?

Answer 1

From what you’ve posted, it’s not clear whether there is something subtly wrong with the string you’re trying to pass to float() (because it looks perfectly reasonable). Try adding a debug print statement:

print(repr(items[2]))
p_value = float(items[2])

Then you can determine exactly what is being passed to float(). The call to repr() will make even normally invisible characters visible. Add the result to your question and we will be able to comment further.