I compare two text files and print out the results to a 3rd file. I am trying to make it so the script i'm running would iterate over all of the folders that have two text files in them, in the CWD of the script.
What i have so far:
import os
import glob
path = './'
for infile in glob.glob( os.path.join(path, '*.*') ):
print('current file is: ' + infile)
with open (f1+'.txt', 'r') as fin1, open(f2+'.txt', 'r') as fin2:
Would this be a good way to start the iteration process?
It's not the most clear code but it gets the job done. However, i'm pretty sure i need to take the logic out of the read / write methods but i'm not sure where to start.
What i'm basically trying to do is have a script iterate over all of the folders in its CWD, open each folder, compare the two text files inside, write a 3rd text file to the same folder, then move on to the next.
Another method i have tried is as follows:
import os
rootDir = 'C:\\Python27\\test'
for dirName, subdirList, fileList in os.walk(rootDir):
print('Found directory: %s' % dirName)
for fname in fileList:
print('\t%s' % fname)
And this outputs the following (to give you a better example of the file structure:
Found directory: C:\Python27\test
test.py
Found directory: C:\Python27\test\asdd
asd1.txt
asd2.txt
Found directory: C:\Python27\test\chro
ch1.txt
ch2.txt
Found directory: C:\Python27\test\hway
hw1.txt
hw2.txt
Would it be wise to put the compare logic under the for fname in fileList? How do i make sure it compares the two text files inside the specific folder and not with other fnames in the fileList?
This is the full code that i am trying to add this functionality into. I appologize for the Frankenstein nature of it but i am still working on a refined version but it does not work yet.
from collections import defaultdict
from operator import itemgetter
from itertools import groupby
from collections import deque
import os
class avs_auto:
def load_and_compare(self, input_file1, input_file2, output_file1, output_file2, result_file):
self.load(input_file1, input_file2, output_file1, output_file2)
self.compare(output_file1, output_file2)
self.final(result_file)
def load(self, fileIn1, fileIn2, fileOut1, fileOut2):
with open(fileIn1+'.txt') as fin1, open(fileIn2+'.txt') as fin2:
frame_rects = defaultdict(list)
for row in (map(str, line.split()) for line in fin1):
id, frame, rect = row[0], row[2], [row[3],row[4],row[5],row[6]]
frame_rects[frame].append(id)
frame_rects[frame].append(rect)
frame_rects2 = defaultdict(list)
for row in (map(str, line.split()) for line in fin2):
id, frame, rect = row[0], row[2], [row[3],row[4],row[5],row[6]]
frame_rects2[frame].append(id)
frame_rects2[frame].append(rect)
with open(fileOut1+'.txt', 'w') as fout1, open(fileOut2+'.txt', 'w') as fout2:
for frame, rects in sorted(frame_rects.iteritems()):
fout1.write('{{{}:{}}}\n'.format(frame, rects))
for frame, rects in sorted(frame_rects2.iteritems()):
fout2.write('{{{}:{}}}\n'.format(frame, rects))
def compare(self, fileOut1, fileOut2):
with open(fileOut1+'.txt', 'r') as fin1:
with open(fileOut2+'.txt', 'r') as fin2:
lines1 = fin1.readlines()
lines2 = fin2.readlines()
diff_lines = [l.strip() for l in lines1 if l not in lines2]
diffs = defaultdict(list)
with open(fileOut1+'x'+fileOut2+'.txt', 'w') as result_file:
for line in diff_lines:
d = eval(line)
for k in d:
list_ids = d[k]
for i in range(0, len(d[k]), 2):
diffs[d[k][i]].append(k)
for id_ in diffs:
diffs[id_].sort()
for k, g in groupby(enumerate(diffs[id_]), lambda (i, x): i - x):
group = map(itemgetter(1), g)
result_file.write('{0} {1} {2}\n'.format(id_, group[0], group[-1]))
def final(self, result_file):
with open(result_file+'.txt', 'r') as fin:
lines = (line.split() for line in fin)
for k, g in groupby(lines, itemgetter(0)):
fst = next(g)
lst = next(iter(deque(g, 1)), fst)
with open('final/{}.avs'.format(k), 'w') as fout:
fout.write('video0=ImageSource("old\%06d.jpeg", {}-3, {}+3, 15)\n'.format(fst[1], lst[2]))
fout.write('video1=ImageSource("new\%06d.jpeg", {}-3, {}+3, 15)\n'.format(fst[1], lst[2]))
fout.write('video0=BilinearResize(video0,640,480)\n')
fout.write('video1=BilinearResize(video1,640,480)\n')
fout.write('StackHorizontal(video0,video1)\n')
fout.write('Subtitle("ID: {}", font="arial", size=30, align=8)'.format(k))
using the load_and_compare() function, i define two input text files, two output text files, a file for the comparison results and a final phase that writes many files for all of the differences.
What i am trying to do is have this whole class run on the current working directory and go through every sub folder, compare the two text files, and write everything into the same folder, specifically the final() results.
You can indeed use os.walk(), since that already separates the directories from the files. You only need the directories it returns, because that's where you're looking for your 2 specific files.
You could also use os.listdir() but that returns directories as well files in the same list, so you would have to check for directories yourself.
Either way, once you have the directories, you iterate over them (for subdir in dirnames) and join the various path components you have: The dirpath, the subdir name that you got from iterating over the list and your filename.
Assuming there are also some directories that don't have the specific 2 files, it's a good idea to wrap the open() calls in a try..except block and thus ignore the directories where one of the files (or both of them) doesn't exist.
Finally, if you used os.walk(), you can easily choose if you only want to go into directories one level deep or walk the whole depth of the tree. In the former case, you just clear the dirnames list by dirnames[:] = []. Note that dirnames = [] wouldn't work, since that would just create a new empty list and put that reference into the variable instead of clearing the old list.
Replace the print("do something ...") with your program logic.
#!/usr/bin/env python
import errno
import os
f1 = "test1"
f2 = "test2"
path = "."
for dirpath, dirnames, _ in os.walk(path):
for subdir in dirnames:
filepath1, filepath2 = [os.path.join(dirpath, subdir, f + ".txt") for f in f1, f2]
try:
with open(filepath1, 'r') as fin1, open(filepath2, 'r') as fin2:
print("do something with " + str(fin1) + " and " + str(fin2))
except IOError as e:
# ignore directiories that don't contain the 2 files
if e.errno != errno.ENOENT:
# reraise exception if different from "file or directory doesn't exist"
raise
# comment the next line out if you want to traverse all subsubdirectories
dirnames[:] = []
Edit:
Based on your comments, I hope I understand your question better now.
Try the following code snippet instead. The overall structure stays the same, only now I'm using the returned filenames of os.walk(). Unfortunately, that would also make it harder to do something like "go only into the subdirectories 1 level deep", so I hope walking the tree recursively is fine with you. If not, I'll have to add a little code to later.
#!/usr/bin/env python
import fnmatch
import os
filter_pattern = "*.txt"
path = "."
for dirpath, dirnames, filenames in os.walk(path):
# comment this out if you don't want to filter
filenames = [fn for fn in filenames if fnmatch.fnmatch(fn, filter_pattern)]
if len(filenames) == 2:
# comment this out if you don't want the 2 filenames to be sorted
filenames.sort(key=str.lower)
filepath1, filepath2 = [os.path.join(dirpath, fn) for fn in filenames]
with open(filepath1, 'r') as fin1, open(filepath2, 'r') as fin2:
print("do something with " + str(fin1) + " and " + str(fin2))
I'm still not really sure what your program logic does, so you will have to interface the two yourself.
However, I noticed that you're adding the ".txt" extension to the file name explicitly all over your code, so depending on how you are going to use the snippet, you might or might not need to remove the ".txt" extension first before handing the filenames over. That would be achieved by inserting the following line after or before the sort:
filenames = [os.path.splitext(fn)[0] for fn in filenames]
Also, I still don't understand why you're using eval(). Do the text files contain python code? In any case, eval() should be avoided and be replaced by code that's more specific to the task at hand.
If it's a list of comma separated strings, use line.split(",") instead.
If there might be whitespace before or after the comma, use [word.strip() for word in line.split(",")] instead.
If it's a list of comma separated integers, use [int(num) for num in line.split(",")] instead - for floats it works analogously.
etc.
Related
My goal is to concatenate files in a folder based on a string in the middle of the filename, ideally using python or bash. To simplify the question, here is an example:
P16C-X128-22MB-LL_merged_trimmed.fastq
P16C-X128-27MB-LR_merged_trimmed.fastq
P16C-X1324-14DL-UL_merged_trimmed.fastq
P16C-X1324-21DL-LL_merged_trimmed.fastq
I would like to concatenate based on the value after the first dash but before the second (e.g. X128 or X1324), so that I am left with (in this example), two additional files that contain the concatenated contents of the individual files:
P16C-X128-Concat.fastq (concat of 2 files with X128)
P16C-X1324-Concat.fastq (concat of 2 files with X1324)
Any help would be appreciated.
For simple string manipulations, I prefer to avoid the use of regular expressions. I think that str.split() is enough in this case. Besides, for simple file name matching, the library fnmatch provides enough functionality.
import fnmatch
import os
from itertools import groupby
path = '/full/path/to/files/'
ext = ".fastq"
files = fnmatch.filter(os.listdir(path), '*' + ext)
def by(fname): return fname.split('-')[1] # Ej. X128
# You said:
# I would like to concatenate based on the value after the first dash
# but before the second (e.g. X128 or X1324)
# If you want to keep both parts together, uncomment the following:
# def by(fname): return '-'.join(fname.split('-')[:2]) # Ej. P16C-X128
for k, g in groupby(sorted(files, key=by), key=by):
dst = str(k) + '-Concat' + ext
with open(os.path.join(path, dst), 'w') as dstf:
for fname in g:
with open(os.path.join(path, fname), 'r') as srcf:
dstf.write(srcf.read())
Instead of the read, write in Python, you could also delegate the concatenation to the OS. You would normally use a bash command like this:
cat *-X128-*.fastq > X128.fastq
Using the subprocess library:
import subprocess
for k, g in groupby(sorted(files, key=by), key=by):
dst = str(k) + '-Concat' + ext
with open(os.path.join(path, dst), 'w') as dstf:
command = ['cat'] # +++
for fname in g:
command.append(os.path.join(path, fname)) # +++
subprocess.run(command, stdout=dstf) # +++
Also, for a batch job like this one, you should consider placing the concatenated files in a separate directory, but that is easily done by changing the dst filename.
You can use open to read and write (create) files, os.listdir to get all files (and directories) in a certain directory and re to match file name as needed.
Use a dictionary to store contents by filename prefix (the file's name up until 3rd hyphen -) and concatenate the contents together.
import os
import re
contents = {}
file_extension = "fastq"
# Get all files and directories that are in current working directory
for file_name in os.listdir('./'):
# Use '.' so it doesn't match directories
if file_name.endswith('.' + file_extension):
# Match the first 2 hyphen-separated values from file name
prefix_match = re.match("^([^-]+\-[^-]+)", file_name)
file_prefix = prefix_match.group(1)
# Read the file and concatenate contents with previous contents
contents[file_prefix] = contents.get(file_prefix, '')
with open(file_name, 'r') as the_file:
contents[file_prefix] += the_file.read() + '\n'
# Create new file for each file id and write contents to it
for file_prefix in contents:
file_contents = contents[file_prefix]
with open(file_prefix + '-Concat.' + file_extension, 'w') as the_file:
the_file.write(file_contents)
I have different csv files in different directories. so i want to find specific cells in different columns that correspond to a specific date in my input.txt file.
here is what i have until now:
import glob, os, csv, numpy
import re, csv
if __name__ == '__main__':
Input=open('Input.txt','r');
output = []
for i, line in enumerate(Input):
if i==0:
header_Input = Input.readline().replace('\n','').split(',');
else:
date_input = Input.readline().replace('\n','').split(',');
a=os.walk("path to the directory")
[x[0] for x in os.walk("path to the directory")]
print(a)
b=next(os.walk('.'))[1] # immediate child directories.
for dirname, dirnames, filenames in os.walk('.'):
# print path to all subdirectories first.
for subdirname in dirnames:
print(os.path.join(dirname, subdirname))
# print path to all filenames.
for filename in filenames:
#print(os.path.join(dirname, filename))
csvfile = 'csv_file'
if csvfile in filename:
print(os.path.join(dirname, filename))
Now I have the csv files, so i need to find the date_input in every file, and print the line that contains all the information. Or if possible, to get only the cells that are in the columns with header == header_input.
This is not intended to be a full answer to your question. But you may want to consider replacing
for i, line in enumerate(Input):
if i==0:
header_Input = Input.readline().replace('\n','').split(',');
else:
date_input = Input.readline().replace('\n','').split(',');
with
header_Input = Input.readline().strip().split(',')
date_input = Input.readline().strip().split(',')
The enumerate(Input) expression reads lines from the file, and so do calls to readline() in the loop body. This will most likely result in some unfortunate results like reading alternating lines from the file.
The strip() method removes whitespace from the start and end of the line. Alternatively you may want to know that s[:-1] strips off the last character of s.
How to find out if two file exists with same pattern inside a file.If all filenames have two-set of filenames ( csv.new and csv) then go ahead to next step otherwise exit with error message.
The prefix "abc_package" will have two files one with extension "csv.new" and second file with extension "csv". There could be many filenames inside the "list_of_files.txt".
Ex: List_of_files.txt
abc_package.1406728501.csv.new
abc_package.1406728501.csv
abc_package.1406724901.csv.new
abc_package.1406724901.csv
For matching the file name name in python you can use fnmatch module..I will provide you a sample code from the documentation.
import fnmatch
import os
for file in os.listdir('.'):
if fnmatch.fnmatch(file, '*.txt'):
print file
The syntax would be fnmatch.fnmatchcase(filename, pattern)
Please have a look here for more examples
with open("in.txt","r") as fo:
f = fo.readlines()
cs_new = set()
cs = set()
for ele in f:
ele = ele.rstrip()
if not ele.endswith(".new"):
cs.add(ele)
else:
cs_new.add(ele.split(".new")[0])
diff = cs ^ cs_new
for fi in diff:
print fi
As you need either filename you will need to check for the existence against both lists:
with open("in.txt","r") as f:
f = [x.rstrip() for x in f]
cs, cs_new, diff = [],[],[]
for ind, ele in enumerate(f):
if ele.endswith(".csv"):
cs.append(ele)
else:
cs_new.append([ele.split(".new")[0],ind]) # keep track of original element in with the ind/index
for ele in cs:
if not any(ele in x for x in cs_new):
diff.append(ele)
for ele in cs_new:
if not any(ele[0] in x for x in cs):
diff.append(f[ele[1]]) # append original element with full extension
Assuming the file isn't so ridiculously huge that you can't fit it into memory, just create a set of all .csv.new files and a set of all .csv files and verify that they're identical. For example:
csvfiles = set()
newfiles = set()
with open('List_of_files.txt') as f:
for line in f:
line = line.rstrip()
if line.endswith('.csv.new'):
newfiles.add(line[:-4])
elif line.endswith('.csv'):
csvfiles.add(line)
if csvfiles != newfiles:
raise ValueError('Mismatched files!')
If you want to know which files were mismatched, csvfiles - newfiles gives you the .csv files without corresponding .csv.new, and newfiles - csvfiles gives you the opposite.
(There are ways to make this cleaner and more readable, from using os.path.splitext to using a general partition-an-iterable-by-filter function, but I think this should be the easiest for a novice to immediately understand.)
I am trying to get filtered list of all Text and Python file, like below
from walkdir import filtered_walk, dir_paths, all_paths, file_paths
vdir=raw_input ("enter director :")
files = file_paths(filtered_walk(vdir, depth=0,included_files=['*.py', '*.txt']))
I want to:
know the total number of files found in given directory
I have tried options like : Number_of_files= len (files) or for n in files n=n+1 but all are failing as "files" is something called "generator" Object which I searched on python docs but couldn't make use of it
I also want to find a string e.g. "import sys" in the list of files found in above and store the file names having my search string in new file called "found.txt"
I believe this does what you want, if I misunderstood your specification, please let me know after you give this a test. I've hardcoded the directory searchdir, so you'll have to prompt for it.
import os
searchdir = r'C:\blabla'
searchstring = 'import sys'
def found_in_file(fname, searchstring):
with open(fname) as infp:
for line in infp:
if searchstring in line:
return True
return False
with open('found.txt', 'w') as outfp:
count = 0
search_count = 0
for root, dirs, files in os.walk(searchdir):
for name in files:
(base, ext) = os.path.splitext(name)
if ext in ('.txt', '.py'):
count += 1
full_name = os.path.join(root, name)
if found_in_file(full_name, searchstring):
outfp.write(full_name + '\n')
search_count += 1
print 'total number of files found %d' % count
print 'number of files with search string %d' % search_count
Using with to open the file will also close the file automatically for you later.
A python generator is a special kind of iterator. It yields one item after the other, without knowing in advance how much items there are. You only can know it at the end.
It should be ok, though, to do
n = 0
for item in files:
n += 1
do_something_with(items)
print "I had", n, "items."
You can think of a generator (or generally, an iterator) as a list that gives you one item at a time. (NO, it is not a list). So, you cannot count how much items it will give you unless you go through them all, because you have to take them one by one. (This is just a basic idea, now you should be able to understand the docs, and I'm sure there are lots of questions here about them too).
Now, for your case, you used a not-so-wrong approach:
count = 0
for filename in files:
count += 1
What you were doing wrong was taking f and incrementing, but f here is the filename! Incrementing makes no sense, and an Exception too.
Once you have these filenames, you have to open each individual file, read it, search for your string and return the filename.
def contains(filename, match):
with open(filename, 'r') as f:
for line in f:
if f.find(match) != -1:
return True
return False
match_files = []
for filename in files:
if contains(filename, "import sys"):
match_file.append(filename)
# or a one-liner:
match_files = [f for f in files if contains(f, "import sys")]
Now, as an example of a generator (don't read this before you read the docs):
def matching(filenames):
for filename in files:
if contains(filename, "import sys"):
# feed the names one by one, you are not storing them in a list
yield filename
# usage:
for f in matching(files):
do_something_with_the_files_that_match_without_storing_them_all_in_a_list()
You should try os.walk
import os
dir = raw_input("Enter Dir:")
files = [file for path, dirname, filenames in os.walk(dir) for file in filenames if file[-3:] in [".py", ".txt"]]
nfiles = len(files)
print nfiles
For searching for a string in a file look at Search for string in txt file Python
Combining both these your code would be something like
import os
import mmap
dir = raw_input("Enter Dir:")
print "Directory %s" %(dir)
search_str = "import sys"
count = 0
search_count = 0
write_file = open("found.txt", "w")
for dirpath, dirnames, filenames in os.walk(dir):
for file in filenames:
if file.split(".")[-1] in ["py", "txt"]:
count += 1
print dirpath, file
f = open(dirpath+"/"+file)
# print f.read()
if search_str in f.read():
search_count += 1
write_file.write(dirpath+"/"+file)
write_file.close()
print "Number of files: %s" %(count)
print "Number of files containing string: %s" %(search_count)
I need to iterate through a folder and find every instance where the filenames are identical (except for extension) and then zip (preferably using tarfile) each of these into one file.
So I have 5 files named: "example1" each with different file extensions. I need to zip them up together and output them as "example1.tar" or something similar.
This would be easy enough with a simple for loop such as:
tar = tarfile.open('example1.tar',"w")
for output in glob ('example1*'):
tar.add(output)
tar.close()
however, there are 300 "example" files and I need to iterate through each one and their associated 5 files in order to make this work. This is way over my head. Any advice greatly appreciated.
The pattern you're describing generalizes to MapReduce. I found a simple implementation of MapReduce online, from which an even-simpler version is:
def map_reduce(data, mapper, reducer):
d = {}
for elem in data:
key, value = mapper(elem)
d.setdefault(key, []).append(value)
for key, grp in d.items():
d[key] = reducer(key, grp)
return d
You want to group all files by their name without the extension, which you can get from os.path.splitext(fname)[0]. Then, you want to make a tarball out of each group by using the tarfile module. In code, that is:
import os
import tarfile
def make_tar(basename, files):
tar = tarfile.open(basename + '.tar', 'w')
for f in files:
tar.add(f)
tar.close()
map_reduce(os.listdir('.'),
lambda x: (os.path.splitext(x)[0], x),
make_tar)
Edit: If you want to group files in different ways, you just need to modify the second argument to map_reduce. The code above groups files that have the same value for the expression os.path.splitext(x)[0]. So to group by the base file name with all the extensions stripped off, you could replace that expression with strip_all_ext(x) and add:
def strip_all_ext(path):
head, tail = os.path.split(path)
basename = tail.split(os.extsep)[0]
return os.path.join(head, basename)
You could do this:
list all files in the directory
create a dictionary where the basename is the key and all the extensions are values
then tar all the files by dictionary key
Something like this:
import os
import tarfile
from collections import defaultdict
myfiles = os.listdir(".") # List of all files
totar = defaultdict(list)
# now fill the defaultdict with entries; basename as keys, extensions as values
for name in myfiles:
base, ext = os.path.splitext(name)
totar[base].append(ext)
# iterate through all the basenames
for base in totar:
files = [base+ext for ext in totar[base]]
# now tar all the files in the list "files"
tar = tarfile.open(base+".tar", "w")
for item in files:
tar.add(item)
tar.close()
You have to problems. Solve the separately.
Finding matching names. Use a collections.defaultict
Creating tar files after you find the matching names. You've got that pretty well covered.
So. Solve problem 1 first.
Use glob to get all the names. Use os.path.basename to split the path and basename. Use os.path.splitext to split the name and extension.
A dictionary of lists can be used to save all files that have the same name.
Is that what you're doing in part 1?
Part 2 is putting the files into tar archives. For that, you've got most of the code you need.
Try using the glob module: http://docs.python.org/library/glob.html
#! /usr/bin/env python
import os
import tarfile
tarfiles = {}
for f in os.listdir ('files'):
prefix = f [:f.rfind ('.') ]
if prefix in tarfiles: tarfiles [prefix] += [f]
else: tarfiles [prefix] = [f]
for k, v in tarfiles.items ():
tf = tarfile.open ('%s.tar.gz' % k, 'w:gz')
for f in v: tf.addfile (tarfile.TarInfo (f), file ('files/%s' % f) )
tf.close ()
import os
import tarfile
allfiles = {}
for filename in os.listdir("."):
basename = '.'.join (filename.split(".")[:-1] )
if not basename in all_files:
allfiles[basename] = [filename]
else:
allfiles[basename].append(filename)
for basename, filenames in allfiles.items():
if len(filenames) < 2:
continue
tardata = tarfile.open(basename+".tar", "w")
for filename in filenames:
tardata.add(filename)
tardata.close()