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Copying files from one location of a server to another using python

Say I have a file that contains the different locations where some '.wav' files are present on a server. For example say the content of the text file location.txt containing the locations of the wav files is this
/home/user/test_audio_folder_1/audio1.wav
/home/user/test_audio_folder_2/audio2.wav
/home/user/test_audio_folder_3/audio3.wav
/home/user/test_audio_folder_4/audio4.wav
/home/user/test_audio_folder_5/audio5.wav
Now what I want to do is that I want to copy these files from different locations within the server to a particular directory within that server, for example say /home/user/final_audio_folder/ and this directory will contain all the audio files from audio1.wav to audio5.wav
I am trying to perform this task by using shutil, but the main problem with shutil that I am facing is that while copying the files, I need to name the file. I have written a demo version of what I am trying to do, but dont know how to scale it when I will be reading the paths of the '.wav' files from the txt file and copy them to my desired location using a loop.
My code for copying a single file goes as follows,
import shutil
original = r'/home/user/test_audio_folder_1/audio1.wav'
target=r'/home/user/final_audio_folder_1/final_audio1.wav'
shutil.copyfile(original,target)
Any suggestions will be really helpful. Thank you.

import shutil
i=0
with open(r'C:/Users/turing/Desktop/location.txt', "r") as infile:
for t in infile:
i+=1
x="audio"+str(i)+".wav"
t=t.rstrip('\n')
original= r'{}'.format(t)
target=r'C:/Users/turing/Desktop/audio_in/' + x
shutil.copyfile(original, target)

Use the built-in string's split() method within a for loop on the location.txt contents & split the name of the directory on the '/' character, then the last element in a new list would be your filename.

Run only if "if " statement is true.!

So I've a question, Like I'm reading the fits file and then i'm using the information from the header of the fits to define the other files which are related to the original fits file. But for some of the fits file, the other files (blaze_file, bis_file, ccf_table) are not available. And because of that my code gives the pretty obvious error that No Such file or directory.
import pandas as pd
import sys, os
import numpy as np
from glob import glob
from astropy.io import fits
PATH = os.path.join("home", "Desktop", "2d_spectra")
for filename in os.listdir(PATH):
if filename.endswith("_e2ds_A.fits"):
e2ds_hdu = fits.open(filename)
e2ds_header = e2ds_hdu[0].header
date = e2ds_header['DATE-OBS']
date2 = date = date[0:19]
blaze_file = e2ds_header['HIERARCH ESO DRS BLAZE FILE']
bis_file = glob('HARPS.' + date2 + '*_bis_G2_A.fits')
ccf_table = glob('HARPS.' + date2 + '*_ccf_G2_A.tbl')
if not all(file in os.listdir(PATH) for file in [blaze_file,bis_file,ccf_table]):
continue
So what i want to do is like, i want to make my code run only if all the files are available otherwise don't. But the problem is that, i'm defining the other files as variable inside the for loop as i'm using the header information. So how can i define them before the for loop???? and then use something like
So can anyone help me out of this?

The filenames returned by os.listdir() are always relative to the path given there.
In order to be used, they have to be joined with this path.
Example:
PATH = os.path.join("home", "Desktop", "2d_spectra")
for filename in os.listdir(PATH):
if filename.endswith("_e2ds_A.fits"):
filepath = os.path.join(PATH, filename)
e2ds_hdu = fits.open(filepath)
…
Let the filenames be ['a', 'b', 'a_ed2ds_A.fits', 'b_ed2ds_A.fits']. The code now excludes the two first names and then prepends the file path to the remaining two.
a_ed2ds_A.fits becomes /home/Desktop/2d_spectra/a_ed2ds_A.fits and
b_ed2ds_A.fits becomes /home/Desktop/2d_spectra/b_ed2ds_A.fits.
Now they can be accessed from everywhere, not just from the given file path.
I should become accustomed to reading a question in full before trying to answer it.
The problem I mentionned is a problem if you don't start the script from any path outside the said directory. Nevertheless, applying it will make your code much more consistent.
Your real problem, however, lies somewhere else: you examine a file and then, after checking its contents, want to read files whose names depend on informations from that first file.
There are several ways to accomplish your goal:
Just extend your loop with the proper tests.
Pseudo code:
for file in files:
if file.endswith("fits"):
open file
read date from header
create file names depending on date
if all files exist:
proceed
or
for file in files:
if file.endswith("fits"):
open file
read date from header
create file names depending on date
if not all files exist:
continue # actual keyword, no pseudo code!
proceed
Put some functionality into functions (variation of 1.)
Create a loop in a generator function which yields the "interesting information" of one fits file (or alternatively nothing) and have another loop run over them to actually work with the data.
If I am still missing some points or am not detailled enough, please let me know.

Since you have to read the fits file to know the other dependant files names, there's no way you can avoid reading the fit file first. The only thing you can do is test for the dependant files existance before trying to read them and skip the rest of the loop (using continue) if not.

Edit this line
e2ds_hdu = fits.open(filename)
And replace with
e2ds_hdu = fits.open(os.path.join(PATH, filename))

Errors with Glob while outputting file names

I am combining two questions here because they are related to each other.
Question 1: I am trying to use glob to open all the files in a folder but it is giving me "Syntax Error". I am using Python 3.xx. Has the syntax changed for Python 3.xx?
Error Message:
File "multiple_files.py", line 29
files = glob.glob(/src/xyz/rte/folder/)
SyntaxError: invalid syntax
Code:
import csv
import os
import glob
from pandas import DataFrame, read_csv
#extracting
files = glob.glob(/src/xyz/rte/folder/)
for fle in files:
with open (fle) as f:
print("output" + fle)
f_read.close()
Question 2: I want to read input files, append "output" to the names and print out the names of the files. How can I do that?
Example: Input file name would be - xyz.csv and the code should print output_xyz.csv .
Your help is appreciated.

Your first problem is that strings, including pathnames, need to be in quotes. This:
files = glob.glob(/src/xyz/rte/folder/)
… is trying to divide a bunch of variables together, but the leftmost and rightmost divisions are missing operands, so you've confused the parser. What you want is this:
files = glob.glob('/src/xyz/rte/folder/')
Your next problem is that this glob pattern doesn't have any globs in it, so the only thing it's going to match is the directory itself.
That's perfectly legal, but kind of useless.
And then you try to open each match as a text file. Which you can't do with a directory, hence the IsADirectoryError.
The answer here is less obvious, because it's not clear what you want.
Maybe you just wanted all of the files in that directory? In that case, you don't want glob.glob, you want listdir (or maybe scandir): os.listdir('/src/xyz/rte/folder/').
Maybe you wanted all of the files in that directory or any of its subdirectories? In that case, you could do it with rglob, but os.walk is probably clearer.
Maybe you did want all the files in that directory that match some pattern, so glob.glob is right—but in that case, you need to specify what that pattern is. For example, if you wanted all .csv files, that would be glob.glob('/src/xyz/rte/folder/*.csv').
Finally, you say "I want to read input files, append "output" to the names and print out the names of the files". Why do you want to read the files if you're not doing anything with the contents? You can do that, of course, but it seems pretty wasteful. If you just want to print out the filenames with output appended, that's easy:
for filename in os.listdir('/src/xyz/rte/folder/'):
print('output'+filename)

This works in http://pyfiddle.io:
Doku: https://docs.python.org/3/library/glob.html
import csv
import os
import glob
# create some files
for n in ["a","b","c","d"]:
with open('{}.txt'.format(n),"w") as f:
f.write(n)
print("\nFiles before")
# get all files
files = glob.glob("./*.*")
for fle in files:
print(fle) # print file
path,fileName = os.path.split(fle) # split name from path
# open file for read and second one for write with modified name
with open (fle) as f,open('{}{}output_{}'.format(path,os.sep, fileName),"w") as w:
content = f.read() # read all
w.write(content.upper()) # write all modified
# check files afterwards
print("\nFiles after")
files = glob.glob("./*.*") # pattern for all files
for fle in files:
print(fle)
Output:
Files before
./d.txt
./main.py
./c.txt
./b.txt
./a.txt
Files after
./d.txt
./output_c.txt
./output_d.txt
./main.py
./output_main.py
./c.txt
./b.txt
./output_b.txt
./a.txt
./output_a.txt
I am on windows and would use os.walk (Doku) instead.
for d,subdirs,files in os.walk("./"): # deconstruct returned aktDir, all subdirs, files
print("AktDir:", d)
print("Subdirs:", subdirs)
print("Files:", files)
Output:
AktDir: ./
Subdirs: []
Files: ['d.txt', 'output_c.txt', 'output_d.txt', 'main.py', 'output_main.py',
'c.txt', 'b.txt', 'output_b.txt', 'a.txt', 'output_a.txt']
It also recurses into subdirs.

Iterating through subdirectories to add unique strings to each file

My goal: To build a program that:
Opens a folder (provided by the user) from the user's computer
Iterates through that folder, opening each document in each subdirectory (named according to language codes; "AR," "EN," "ES," etc.)
Substitutes a string in for another string in each document. Crucially, the new string will change with each document (though the old string will not), according to the language code in the folder name.
My level of experience: Minimal; been learning python for a few months but this is the first program I'm building that's not paint-by-numbers. I'm building it to make a process at work faster. I'm sure I'm not building this as efficiently as possible; I've been throwing it together from my own knowledge and from reading stackexchange religiously while building it.
Research I've done on my own: I've been living in stackexchange the past few days, but I haven't found anyone doing quite what I'm doing (which was very surprising to me). I'm not sure if this is just because I lack the vocabulary to search (tried out a lot of search terms, but none of them totally match what I'm doing) or if this is just the wrong way of going about things.
The issue I'm running into:
I'm getting this error:
Traceback (most recent call last):
File "test5.py", line 52, in <module>
for f in os.listdir(src_dir):
OSError: [Errno 20] Not a directory: 'ExploringEduTubingEN(1).txt'
I'm not sure how to iterate through every file in the subdirectories and update a string within each file (not the file names) with a new and unique string. I thought I had it, but this error has totally thrown me off. Prior to this, I was getting an error for the same line that said "Not a file or directory: 'ExploringEduTubingEN(1).txt'" and it's surprising to me that the first error could request a file or a directory, and once I fixed that, it asked for just a directory; seems like it should've just asked for a directory at the beginning.
With no further ado, the code (placing at bottom because it's long to include context):
import os
ex=raw_input("Please provide an example PDF that we'll append a language code to. ")
#Asking for a PDF to which we'll iteratively append the language codes from below.
lst = ['_ar.pdf', '_cs.pdf', '_de.pdf', '_el.pdf', '_en_gb.pdf', '_es.pdf', '_es_419.pdf',
'_fr.pdf', '_id.pdf', '_it.pdf', '_ja.pdf', '_ko.pdf', '_nl.pdf', '_pl.pdf', '_pt_br.pdf', '_pt_pt.pdf', '_ro.pdf', '_ru.pdf',
'_sv.pdf', '_th.pdf', '_tr.pdf', '_vi.pdf', '_zh_tw.pdf', '_vn.pdf', '_zh_cn.pdf']
#list of language code PDF appending strings.
pdf_list=open('pdflist.txt','w+')
#creating a document to put this group of PDF filepaths in.
pdf2='pdflist.txt'
#making this an actual variable.
for word in lst:
pdf_list.write(ex + word + "\n")
#creating a version of the PDF example for every item in the language list, and then appending the language codes.
pdf_list.seek(0)
langlist=pdf_list.readlines()
#creating a list of the PDF paths so that I can use it below.
for i in langlist:
i=i.rstrip("\n")
#removing the line breaks.
pdf_list.close()
#closing the file after removing the line breaks.
file1=raw_input("Please provide the full filepath of the folder you'd like to convert. ")
#the folder provided by the user to iterate through.
folder1=os.listdir(file1)
#creating a list of the files within the folder
pdfpath1="example.pdf"
langfile="example2.pdf"
#setting variables for below
#my thought here is that i'd need to make the variable the initial folder, then make it a list, then iterate through the list.
for ogfile in folder1:
#want to iterate through all the files in the directory, including in subdirectories
src_dir=ogfile.split("/",6)
src_dir="/".join(src_dir[:6])
#goal here is to cut off the language code folder name and then join it again, w/o language code.
for f in os.listdir(src_dir):
f = os.path.join(src_dir, f)
#i admit this got a little convoluted–i'm trying to make sure the files put the right code in, I.E. that the document from the folder ending in "AR" gets the PDF that will now end in "AR"
#the perils of pulling from lots of different questions in stackexchange
with open(ogfile, 'r+') as f:
content = f.read()
f.seek(0)
f.truncate()
for langfile in langlist:
f.write(content.replace(pdfpath1, langfile))
#replacing the placeholder PDF link with the created PDF links from the beginning of the code
If you read this far, thanks. I've tried to provide as much information as possible, especially about my thought process. I'll keep trying things and reading, but I'd love to have more eyes on it.

You have to specify the full path to your directories/files. Use os.path.join to create a valid path to your file or directory (and platform-independent).
For replacing your string, simply modify your example string using the subfolder name. Assuming that ex as the format filename.pdf, you could use: newstring = ex[:-4] + '_' + str.lower(subfolder) + '.pdf'. That way, you do not have to specify the list of replacement strings nor loop through this list.
Solution
To iterate over your directory and replace the content of your files as you'd like, you can do the following:
# Get the name of the file: "example.pdf" (note the .pdf is assumed here)
ex=raw_input("Please provide an example PDF that we'll append a language code to. ")
# Get the folder to go through
folderpath=raw_input("Please provide the full filepath of the folder you'd like to convert. ")
# Get all subfolders and go through them (named: 'AR', 'DE', etc.)
subfolders=os.listdir(folderpath)
for subfolder in subfolders:
# Get the full path to the subfolder
fullsubfolder = os.path.join(folderpath,subfolder)
# If it is a directory, go through it
if os.path.isdir(fullsubfolder):
# Find all files in subdirectory and go through each of them
files = os.listdir(fullsubfolder)
for filename in files:
# Get full path to the file
fullfile = os.path.join(fullsubfolder, filename)
# If it is a file, process it (note: we do not check if it is a text file here)
if os.path.isfile(fullfile):
with open(fullfile, 'r+') as f:
content = f.read()
f.seek(0)
f.truncate()
# Create the replacing string based on the subdirectory name. Ex: 'example_ar.pdf'
newstring = ex[:-4] + '_' + str.lower(subfolder) + '.pdf'
f.write(content.replace(ex, newstring))
Note
Instead of asking the user to find write the folder, you could ask him to open the directory with a dialog box. See this question for more info: Use GUI to open directory in Python 3

how can I cat two files with a matching string in the filename?

So I have a directory with ~162K files. Half of these files have the file name "uniquenumber.fasta" and the other half of the files have the file name "uniquenumber.fasta letters". For example:
12345.fasta
12345.fasta Somebacterialtaxaname
67890.fasta
67890.fasta Someotherbacterialtaxaname
...for another many thousand "pairs"
I would like to cat together the two files that share the unique fasta number. It does not matter the order of the concatenation (i.e. which contents comes first in the newly created combined file). I have tried some renditions of grep in the command line and a few lousy python scripts but I feel like this is more of a trivial problem than I am making it. Suggestions?

Here's a solution in Python (it will work unchanged with both Python 2 and 3). This assumes that each file XXXXX.fasta has one and only one matching XXXXX.fasta stringofstuff file.
import glob
fastafiles = sorted(glob.glob("*.fasta"))
for fastafile in fastafiles:
number = fastafile.split(".")[0]
space_file = glob.glob(number + ".fasta *")
with open(fastafile, "a+") as fasta:
with open(space_file[0], "r") as fasta_space:
fasta.write("\n")
fasta.writelines(fasta_space.readlines())
Here's how it works: first, the names of all *.fasta files are put into a list (I sort the list, but it's not strictly necessary). Next, the filename is split on . and the first part (the number in the filename) is stored. Then, we search for the matching XXXXX.fasta something file and, assuming there's only one of them, we open the .fasta file in append mode and the .fasta something file in read mode. We write a newline to the end of the .fasta file, then read in the contents of the "space file" and write them to the end of the .fasta file. Since we use the with context manager, we don't need to specifically close the files when we're done.

There's probably many ways to achieve this, but the first that came to my head would be to use the unix command find.
http://en.wikipedia.org/wiki/Find#Execute_an_action
The find command will print the filename that follows the pattern you specify. Using the -name and -exec flags, you can specify what characters should be in the file name, or run an additional command to filter the output.
If I was solving this problem, I would probably cycle over all files in the directory, and run either a -name pattern or -exec pattern that would "find" the matching file. Then | the two file names to a cat and redirect that output to a new file, hopefully concatenating the two. Hope that helps!