CODEWITHSUNDEEP
pythonfor-loop
accidental_coder
accidental_coder

Reputation: 69

Python: Reading multiple files and storing the output for a particular file

I have a thousand .xvg files in a directory which I need to read and store an output for each of them. Currently I have a python code which works for only one file. Could you please suggest how do I read all files at once and get an output and store it for every file separately?

    f = open('/home/abc/xyz/coord/coord_1.xvg')
    dat = f.readlines()
    dat1 = dat[22:len(dat)]
    dat2=[]

    for k in dat1:
        dat2.append(k.split())

    for k in dat2:
        if float(k[1])>=9.5:
            print('P')
            break
        elif float(k[1])<=5.9:
            print('R')
            break
        else:
            print('N')

Upvotes: 0

Views: 130

Answers (1)

DarrylG
DarrylG

Reputation: 17156

Here's a version but used as much as code as possible to make it easier to follow.

import os

def process_files():
  " Will process all files in folder using your code "
  for file in os.listdir("."): # '.' correspond to the current  directory
                               # You can specify whatever directory, 
                               #such as /usr/accidental_coder/working
    if file.endswith(".xvg"):
        # Find found
        # Output will be with same name but with .txt suffix
        with open(os.path.join(".", file), 'r') as infile, \
          open(os.path.join(".", file.replace('.xvg', '.txt')), 'w') as ofile:

          # Using your original code
          # left alone so you could know how to change if desired
          # (note: your can be shortened)
          dat = infile.readlines()
          dat1 = dat[22:len(dat)]
          dat2=[]

          for k in dat1:
              dat2.append(k.split())
          for k in dat2:
              if float(k[1])>=9.5:
                  ofile.write('P\n')
                  break
              elif float(k[1])<=5.9:
                  ofile.write('R\n')
                  break
              else:
                  ofile.write('N\n')

process_files()

Refactoring Your Code for Better Performance

Seems you just process the 23'rd line in each file

import os

def process_files():
  for file in os.listdir("."):
    # Examples of getting files from directories
    # https://stackoverflow.com/questions/3964681/find-all-files-in-a-directory-with-extension-txt-in-python
    if file.endswith(".xvg"):
        with open(os.path.join(".", file), 'r') as infile, \
          open(os.path.join(".", file.replace('.xvg', '.txt')), 'w') as ofile:

          # Skip first 22 lines
          for _ in range(22):
            next(infile)

          # use data on 23rd line
          data = next(infile)  
          k = data.split()

          if float(k[1])>=9.5:
              ofile.write('P\n')
          elif float(k[1])<=5.9:
              ofile.write('R\n')
          else:
              ofile.write('N\n')

process_files()

Upvotes: 1

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