Unwanted white spaces resulting into distorted column

user_3286747 0
Viewed 74

I am trying to import a list of chemicals from a txt file which is spaced (not tabbed).

enter image description here

NO FORMULA NAME CAS No A B C D TMIN TMAX code ngas@TMIN ngas@25 C ngas@TMAX
1 CBrClF2 bromochlorodifluoromethane 353-59-3 -0.0799 4.9660E-01 -6.3021E-05 -9.0961E-09 200 1500 2 96.65 142.14 572.33
2 CBrCl2F bromodichlorofluoromethane 353-58-2 4.0684 4.1343E-01 1.6576E-05 -3.4388E-08 200 1500 2 87.14 127.90 545.46
3 CBrCl3 bromotrichloromethane 75-62-7 7.3767 3.5056E-01 6.9163E-05 -4.9571E-08 200 1500 2 79.86 116.73 521.53
4 CBrF3 bromotrifluoromethane 75-63-8 -9.5253 6.5020E-01 -3.4459E-04 1.0987E-07 230 1500 1,2 123.13 156.61 561.26
5 CBr2F2 dibromodifluoromethane 75-61-6 2.8167 4.9405E-01 -1.2627E-05 -2.8629E-08 200 1500 2 100.89 148.24 618.87
6 CBr4 carbon tetrabromide 558-13-4 10.6812 3.2869E-01 1.0739E-04 -6.0788E-08 200 1500 2 80.23 116.62 540.18
7 CClF3 chlorotrifluoromethane 75-72-9 13.8075 4.7487E-01 -1.3368E-04 2.2485E-08 230 1500 1,2 116.23 144.10 501.22
8 CClN cyanogen chloride 506-77-4 0.8665 3.6619E-01 -2.9975E-05 -1.3191E-08 200 1500 2 72.80 107.03 438.19

When I import with pandas

df = pd.read_csv('trial1.txt', sep='\s')

I get:

enter image description here

For first 5 compounds (index 0-4) name is correctly in Name column but for 6th (index 5) and 8th (index 7) compounds - their name is divided because of space and it goes to CAS. Causing CAS column value to go under No column and values and so on subsequently.

Is there a way to eliminate this issue ? Thank you

pandas dataframe csv python string
2 Answers

I would suggest you put some work on the 'trial1.txt' file before loading it to df. The following code will result to what you finally want to get:

with open ('trial1.txt') as f:
    l=f.readlines()

l=[i.split() for i in l]
target=len(l[1])
for i in range(1,len(l)):
    if len(l[i])>target:
        l[i][2]=l[i][2]+' '+l[i][3]
        l[i].pop(3)
l=['#'.join(k) for k in l] #supposing that there is no '#' in your entire file, otherwise use some other rare symbol that doesn't eist in your file
l=[i+'\n' for i in l]
 
with open ('trial2.txt', 'w') as f:
    f.writelines(l)

df = pd.read_csv('trial2.txt', sep='#', index_col=0)
user_82285580

Try this:

You basically have to strip out the spaces between words in the name column. So here I first read the file and then strip out the spaces in the NAME column using re.sub.

In this code, I am assuming that words are separated by atleast 5 letters on either sides. You can change that number {5} as you deem fit.

import re
with open('trial1.txt', 'r') as f:
    lines = f.readlines()
l = [re.sub(r"([a-z]{5,})\s([a-z]{5,})", r"\1\2", line) for line in lines] 
df = pd.read_csv(io.StringIO('\n'.join(l)), delim_whitespace=True)

Prints:

NO  FORMULA NAME                        CAS          No     A       B            C              D       TMIN    TMAX    code    ngas@TMIN   ngas@25 C.1 ngas@TMAX
1   CBrClF2 bromochlorodifluoromethane  353-59-3    -0.0799 0.49660 -0.000063   -9.096100e-09   200     1500    2       96.65   142.14      572.33  NaN NaN
2   CBrCl2F bromodichlorofluoromethane  353-58-2    4.0684  0.41343  0.000017   -3.438800e-08   200     1500    2       87.14   127.90      545.46  NaN NaN
3   CBrCl3  bromotrichloromethane       75-62-7     7.3767  0.35056  0.000069   -4.957100e-08   200     1500    2       79.86   116.73      521.53  NaN NaN
4   CBrF3   bromotrifluoromethane       75-63-8     -9.5253 0.65020 -0.000345    1.098700e-07   230     1500    1,2     123.13  156.61      561.26  NaN NaN
5   CBr2F2  dibromodifluoromethane      75-61-6     2.8167  0.49405 -0.000013   -2.862900e-08   200     1500    2       100.89  148.24      618.87  NaN NaN
6   CBr4    carbontetrabromide          558-13-4    10.6812 0.32869  0.000107   -6.078800e-08   200     1500    2       80.23   116.62      540.18  NaN NaN
7   CClF3   chlorotrifluoromethane      75-72-9     13.8075 0.47487 -0.000134    2.248500e-08   230     1500    1,2     116.23  144.10      501.22  NaN NaN
8   CClN    cyanogenchloride            506-77-4    0.8665  0.36619 -0.000030   -1.319100e-08   200     1500    2       72.80   107.03      438.19  NaN NaN
user_136288830
Related