fins and move files with path name with python3

Question

I am trying recreate python script from my perl script to find all files with common name model1_r.pdb and them move it to a new folder with newname of their previous existing folder. This is the python code I wrote;

import os, shutil, glob
# This program will list all pdb file named (model1_r.pdb) in a given directory.
# inpout: directory name 
# output: pdb files

source = input("enter filepath: ")

# build the command to look for model1_r.pdb
for file_path in glob.glob(os.path.join(source, '*model1_r.pdb')):
        new_dir = file_path.rsplit('/', 1)[1]
        find = os.system("find -type f -name \"model1_r.pdb\" ")
        print(filepath)
        destination = "/gs/gsfs0/users/kdhusia/dir_all_pdb/"
        #Move the files to new folder based with filepath folder name
        shutil.move(find, ios.path.join(destination, os.path.basename(filepath)))

Here is my perl script that works fine, but is slow

use strict;
use warnings;
use Data::Dumper;
use File::Basename;

# This program will list all pdb file named (model1_r.pdb) in a given directory.
# inpout: directory name 
# output: pdb files

my $dir = $ARGV[0] || undef;
die "a directory is required\n" unless $dir;

chomp $dir;

# build the command to look for model1_r.pdb
my $cmd = "find $dir -type f -name \"model1_r.pdb\" "; 
#my $cmd = "find $dir -type f -name \"*.pdb\" "; 
print $cmd, "\n";

my @output = `$cmd`;

my $DEST = "/gs/gsfs0/users/kdhusia/dcomplex_all";
for my $line (@output) {
   # remove CR from $line
   chomp $line;
   #print $line;
   # get pair-name from line
   my @pairs = split("\/", $line);
   #print Dumper(\@pairs);

   my $new_name = $pairs[2].".pdb";
   #print "new_name = $new_name\n";

   # copy model1_r.pdb to dinal destination
   # change the name of pdb to "pair-name.pdb"
   my $cmd = "cp $line $DEST/$new_name"; 
   # my $cmd = "./dcomplex $pdbfile A B "
   print "$cmd\n";

   # do the copy
   system($cmd);
}

I did the conversion using previous discussions at stack(Python: Moving files to folder based on filenames)

I am missing out something during the storing the filepath. Any comments would be highly appreciated.

What based your assumption on that python version will work faster than perl? — Polar Bear, Mar 11 '20 at 01:49

score 0 · Answer 1 · answered Mar 16 '20 at 15:10

Here is the reciprocal python3 code:

import os
import shutil
import glob
import argparse

# This program will list all pdb file named (model1_r.pdb) in a given directory.
# inpout: directory name 
# output: pdb files

parser = argparse.ArgumentParser()
parser.add_argument("file", help="filename is required", type=str)
args = parser.parse_args()

print (args.file)

dest = "/gs/gsfs0/users/.../dir_all_pdb/"
# build the command to look for model1_r.pdb
#for f in os.path.listdir(source):
for root, dirs, files in os.walk(args.file):
    for file in files:
        if file.endswith("l1_r.pdb"):
            #print (file)
            print ("moving ...")
            print(os.path.join(root, file)) # printing full pathname
            # extratc the name ofthe pair. position 6 identifies tha name of the pair 
            pair_name =  os.path.join(root, file).split("/")
            name = pair_name[6]

            # buildong final destination ful path name 
            f_name = dest + name+'.pdb'
            print ("to ...", f_name)           

            src = os.path.join(root, file)
            shutil.copy( src, f_name)

This takes path of directory to look for files name and then store it to the desination folder with the names of folder in which the file was found.

fins and move files with path name with python3

1 Answers1