sam*_*man 5 python regex pandas
I don't exactly know how to describe the issue I'm having, so I'll just show it. I have 2 data tables, and I'm using regex to search through and extract values in those tables based on if it matches with the correct word. I'll put the whole script for reference.
import re
import os
import pandas as pd
import numpy as np
os.chdir('C:/Users/Sams PC/Desktop')
f=open('test5.txt', 'w')
NHSQC=pd.read_csv('NHSQC.txt', sep='\s+', header=None)
NHSQC.columns=['Column_1','Column_2','Column_3']
HNCA=pd.read_csv('HNCA.txt', sep='\s+', header=None)
HNCA.columns=['Column_1','Column_2','Column_3','Column_4']
x=re.findall('[A-Z][0-9][0-9][A-Z]-[H][N]',str(NHSQC))
y=re.findall('[A-Z][0-9][0-9][A-Z]-[C][A]-[H][N]',str(HNCA))
print (NHSQC)
print (HNCA)
print(x)
print (y)
data=[]
label=[]
for i in range (0,6):
if x[i] in str(NHSQC):
data2=NHSQC.set_index('Column_1',drop=False)
data3=(data2.loc[str(x[i]), 'Column_2':'Column_3'])
data.extend(list(data3))
a=[x[i]]
label.extend(a)
label.extend(a)
if y[i] in str(HNCA):
data2=HNCA.set_index('Column_1',drop=False)
data3=(data2.loc[str(y[i]),'Column_3'])
data.append(data3)
a=[y[i]]
label.extend(a)
else:
print('Not Found')
else:
print('Not Found')
data6=[label,data]
matrix=data6
data5=np.transpose(matrix)
print(data5)
f.write(str(data5))
f.close()
This script, does exactly what I want it to do, and it works as intended when I run my test data files, but fails when I run my actual data files. I don't know how to explain the issue, so I'll just show it. This is the output:
Column_1 Column_2 Column_3
0 S31N-HN 114.424 7.390
1 Y32N-HN 121.981 7.468
2 Q33N-HN 120.740 8.578
3 A34N-HN 118.317 7.561
4 G35N-HN 106.764 7.870
.. ... ... ...
89 R170N-HN 118.078 7.992
90 S171N-HN 110.960 7.930
91 R172N-HN 119.112 7.268
92 999_XN-HN 116.703 8.096
93 1000_XN-HN 117.530 8.040
[94 rows x 3 columns]
Column_1 Column_2 Column_3 Column_4
0 Assignment w1 w2 w3
1 S31N-A30CA-S31HN 114.424 54.808 7.393
2 S31N-A30CA-S31HN 126.854 53.005 9.277
3 S31N-CA-HN 114.424 61.717 7.391
4 S31N-HA-HN 126.864 59.633 9.287
.. ... ... ... ...
173 R170N-CA-HN 118.016 60.302 7.999
174 S171N-R170CA-S171HN 110.960 60.239 7.932
175 S171N-CA-HN 110.960 60.946 7.931
176 R172N-S171CA-R172HN 119.112 60.895 7.264
177 R172N-CA-HN 119.112 55.093 7.265
[178 rows x 4 columns]
['S31N-HN', 'Y32N-HN', 'Q33N-HN', 'A34N-HN', 'G35N-HN']
['S31N-CA-HN']
Traceback (most recent call last):
File "test.py", line 29, in <module>
if y[i] in str(HNCA):
IndexError: list index out of range
As you can see, there is an issue because my regex for y isn't finding all the values. Furthermore, there is an issue with how many my x regex is finding (only 5 instead of the hundreds it should be). Initially I thought this was just a display thing (it wasn't displaying the hundreds of matches since it would take too long), and I also thought the ... in the middle of it printing my table was also for display purposes. However, if I copy part of my HNCA.txt data and save it as a separate file, it fixes the issue.
[94 rows x 3 columns]
Column_1 Column_2 Column_3 Column_4
0 Assignment w1 w2 w3
1 S31N-A30CA-S31HN 114.424 54.808 7.393
2 S31N-A30CA-S31HN 126.854 53.005 9.277
3 S31N-CA-HN 114.424 61.717 7.391
4 S31N-HA-HN 126.864 59.633 9.287
5 Y32N-S31CA-Y32HN 121.981 61.674 7.467
6 Y32N-CA-HN 121.981 60.789 7.469
7 Q33N-Y32CA-Q33HN 120.770 60.775 8.582
8 Q33N-CA-HN 120.701 58.706 8.585
9 A34N-Q33CA-A34HN 118.317 58.740 7.559
10 A34N-CA-HN 118.317 52.260 7.565
11 G35N-A34CA-G35HN 106.764 52.195 7.868
12 G35N-CA-HN 106.764 46.507 7.868
13 R36N-G35CA-R36HN 117.833 46.414 8.111
14 R36N-CA-HN 117.833 54.858 8.112
15 G37N-R36CA-G37HN 110.365 54.808 8.482
16 G37N-CA-HN 110.365 44.901 8.484
17 I55N-CA-HN 118.132 65.360 7.935
18 Y56N-I55CA-Y56HN 123.025 65.464 8.088
19 Y56N-CA-HN 123.025 62.195 8.082
20 A57N-Y56CA-A57HN 120.470 62.159 7.978
21 A57N-CA-HN 120.447 55.522 7.980
22 S72N-K71CA-S72HN 117.239 55.390 8.368
23 S72N-CA-HN 117.259 58.583 8.362
24 C73N-S72CA-C73HN 128.142 58.569 9.690
25 C73N-CA-HN 128.142 61.410 9.677
26 G74N-C73CA-G74HN 116.187 61.439 9.439
27 G74N-CA-HN 116.194 46.528 9.437
28 H75N-G74CA-H75HN 122.640 46.307 9.642
29 H75N-CA-HN 122.621 56.784 9.644
30 C76N-H75CA-C76HN 122.775 56.741 7.152
31 C76N-CA-HN 122.738 57.527 7.146
32 R77N-C76CA-R77HN 120.104 57.532 8.724
33 R77N-CA-HN 120.135 59.674 8.731
['S31N-HN', 'Y32N-HN', 'Q33N-HN', 'A34N-HN', 'G35N-HN']
['S31N-CA-HN', 'Y32N-CA-HN', 'Q33N-CA-HN', 'A34N-CA-HN', 'G35N-CA-HN', 'R36N-CA-HN', 'G37N-CA-HN', 'I55N-CA-HN', 'Y56N-CA-HN', 'A57N-CA-HN', 'S72N-CA-HN', 'C73N-CA-HN', 'G74N-CA-HN', 'H75N-CA-HN', 'C76N-CA-HN', 'R77N-CA-HN']
[['S31N-HN' '114.42399999999999']
I won't post the whole output, but as you can see, now it finds all the proper matches. Its also now displaying the entire table, instead of doing ... and only showing the top and bottom halves. I don't exactly understand where this issue is arising from though. Why is it displaying only the top and bottom half of my table, but if I copy and paste it to another file, it displays the entire thing. Why does regex not search through the entire table even if it isn't displayed (based on the fact it shows the top and bottom half, makes me think the entire table is there, but again its not showing it because its trying to simplify the display, but why would whats being displayed effect what regex is searching)?