[Tutor] Pandas Problem?
Flynn, Stephen (Life & Pensions)
Steve.Flynn at capita.co.uk
Tue Sep 24 09:16:17 EDT 2019
You're trying to open a file named 'ligand_file', as evidenced by:
FileNotFoundError: [Errno 2] File b'ligand_file' does not exist:
b'ligand_file'
However, ligand_file is the name of the variable which contains the name of the file you want to open. Remove the quotes from 'ligand_file' in your read_table statement.
S.
-----Original Message-----
From: Tutor <tutor-bounces+steve.flynn=capita.co.uk at python.org> On Behalf Of Stephen P. Molnar
Sent: 24 September 2019 13:11
To: Python Tutor <tutor at python.org>
Subject: [Tutor] Pandas Problem?
I am using the Spyder3 IDE with Python 3.7.3 and have encountered, what to me at least, is a rather strange problem.
The code, at this point is:
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Apr 8 15:17:07 2017
@author: comp
"""
#import numpy as np
#import matplotlib.pyplot as plt
import pandas as pd
name = input("Enter Molecule ID: ")
print(name)
ligand_file = name+'_apo-1acl.RMSD'
print('Ligand file = ',ligand_file)
data = pd.read_table('ligand_file',skiprows = 7)
print(data)
The input file, in this example, 17-3_apo-1acl.RMSD is:
RMSD TABLE
__________
_____________________________________________________________________
| | | | | |
Rank | Sub- | Run | Binding | Cluster | Reference | Grep
| Rank | | Energy | RMSD | RMSD | Pattern
_____|______|______|___________|_________|_________________|___________
1 1 8 -7.23 0.00 93.07 RANKING
1 2 9 -6.79 1.39 92.64 RANKING
2 1 16 -7.18 0.00 93.19 RANKING
3 1 2 -6.93 0.00 93.38 RANKING
3 2 17 -6.84 0.23 93.45 RANKING
4 1 15 -6.55 0.00 91.83 RANKING
4 2 7 -6.34 0.33 91.77 RANKING
5 1 5 -6.41 0.00 93.05 RANKING
6 1 3 -6.36 0.00 92.84 RANKING
6 2 10 -6.28 0.47 92.92 RANKING
6 3 6 -6.27 0.43 92.82 RANKING
6 4 18 -6.25 0.32 92.88 RANKING
6 5 13 -6.24 0.96 92.75 RANKING
6 6 1 -6.24 0.87 92.60 RANKING
6 7 14 -6.21 0.51 92.90 RANKING
6 8 11 -6.14 0.98 92.78 RANKING
6 9 20 -6.11 0.71 92.67 RANKING
6 10 19 -6.01 1.36 93.00 RANKING
7 1 12 -6.30 0.00 93.28 RANKING
8 1 4 -5.85 0.00 92.97 RANKING
_______________________________________________________________________
The output at this point is:
Enter Molecule ID: 17-3
17-3
Ligand file = 17-3_apo-1acl.RMSD
Traceback (most recent call last):
File "<ipython-input-3-48de0a8fd907>", line 1, in <module> runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.',
wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable')
File
"/usr/local/lib/python3.7/dist-packages/spyder_kernels/customize/spydercustomize.py",
line 827, in runfile
execfile(filename, namespace)
File
"/usr/local/lib/python3.7/dist-packages/spyder_kernels/customize/spydercustomize.py",
line 110, in execfile
exec(compile(f.read(), filename, 'exec'), namespace)
File
"/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.",
line 23, in <module>
data = pd.read_table('ligand_file',skiprows = 7)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py",
line 685, in parser_f
return _read(filepath_or_buffer, kwds)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py",
line 457, in _read
parser = TextFileReader(fp_or_buf, **kwds)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py",
line 895, in __init__
self._make_engine(self.engine)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py",
line 1135, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "/usr/local/lib/python3.7/dist-packages/pandas/io/parsers.py",
line 1917, in __init__
self._reader = parsers.TextReader(src, **kwds)
File "pandas/_libs/parsers.pyx", line 382, in pandas._libs.parsers.TextReader.__cinit__
File "pandas/_libs/parsers.pyx", line 689, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] File b'ligand_file' does not exist:
b'ligand_file'
However, if I change the data = line to:
data = pd.read_table('13-7_apo-1acl.RMSD',skiprows = 7)
The output is:
runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/RMSDTable_3.py.',
wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable')
Enter Molecule ID: 13-7
13-7
Ligand file = 13-7_apo-1acl.RMSD
_____|______|______|___________|_________|_________________|___________
0 1 1 8 -7.23 0.00 9...
1 1 2 9 -6.79 1.39 9...
2 2 1 16 -7.18 0.00 9...
3 3 1 2 -6.93 0.00 9...
4 3 2 17 -6.84 0.23 9...
5 4 1 15 -6.55 0.00 9...
6 4 2 7 -6.34 0.33 9...
7 5 1 5 -6.41 0.00 9...
8 6 1 3 -6.36 0.00 9...
9 6 2 10 -6.28 0.47 9...
10 6 3 6 -6.27 0.43 9...
11 6 4 18 -6.25 0.32 9...
12 6 5 13 -6.24 0.96 9...
13 6 6 1 -6.24 0.87 9...
14 6 7 14 -6.21 0.51 9...
15 6 8 11 -6.14 0.98 9...
16 6 9 20 -6.11 0.71 9...
17 6 10 19 -6.01 1.36 9...
18 7 1 12 -6.30 0.00 9...
19 8 1 4 -5.85 0.00 9...
20 ______________________________________________...
I have used the ligand_file = line in other Python script that has worked without any errors.
Google has not been a solution in his case. Pointers towards wolutions to this problem will be much appreciated.
Thanks in advance.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
http://www.Molecular-Modeling.net Multivariate and stochastic
614.312.7528 (c)
Skype: smolnar1
_______________________________________________
Tutor maillist - Tutor at python.org
To unsubscribe or change subscription options:
https://mail.python.org/mailman/listinfo/tutor
This message has been scanned by Capita systems, but if you believe it to be spam, please send it to spam at forcepoint.com.
Messages sent to spam at forcepoint.com are queued for email analysis by Forcepoint Threat Lab.
This email is security checked and subject to the disclaimer on web-page: http://www.capita.co.uk/email-disclaimer.aspx
More information about the Tutor
mailing list