On Fri, Oct 4, 2019 at 7:31 PM Stephen P. Molnar <s.molnar@sbcglobal.net> wrote:
I have a snippet of code
#!/usr/bin/env python3 # -*- coding: utf-8 -*- """
Created on Tue Sep 24 07:51:11 2019
""" import numpy as np
files = []
data = np.genfromtxt(files, usecols=(3), dtype=None, skip_header=8, skip_footer=1, encoding=None)
print(data)
If file is a single file the code generates the data that I want. However I have a list of files that I want to process. According to numpy.genfromtxt fname can be a "File, filename, list, or generator to read." If I use [13-7a_apo-1acl.RMSD 13-7_apo-1acl.RMSD 14-7_apo-1acl.RMSD 15-7_apo-1acl.RMSD 17-7_apo-1acl.RMSD ] get the error:
Hi Stephen, As far as I know genfromtxt is designed to read the contents of a single file. Consider this quote from the docs for the first parameter: "The strings in a list or produced by a generator are treated as lines." And the general description of the function says "Load data from a text file, with missing values handled as specified." ("a text file", singular) So if I understand correctly the list case is there so that you can pass `f.readlines()` or equivalent into genfromtxt. From a higher-level standpoint, how would reading multiple files behave if the files have different structure, and what type and shape should the function return in that case? If one file can be read just fine then I suggest looping over them to read each, one after the other. You can then tell python what to do with each returned array and so it doesn't have to guess. Regards, András
runfile('/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/Test/DeltaGTable_s.py', wdir='/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/Test', current_namespace=True) Traceback (most recent call last):
File "/home/comp/Apps/Models/1-PhosphorusLigands/CombinedLigands/MOL/Docking/Results/RMSDTable/Test/DeltaGTable_s.py", line 12, in <module> data = np.genfromtxt(files, usecols=(3), dtype=None, skip_header=8, skip_footer=1, encoding=None)
File "/home/comp/Apps/Miniconda3/lib/python3.7/site-packages/numpy/lib/npyio.py", line 1762, in genfromtxt next(fhd)
StopIteration
I have tried very combination of search terms that I can think of in order to find an example of how to make this work without success.
How can I make this work?
Thanks in advance.
-- Stephen P. Molnar, Ph.D. www.molecular-modeling.net 614.312.7528 (c) Skype: smolnar1
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