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How do I read every line of a file in Python and store each line as an element in a list?
I want to read the file line by line and append each line to the end of the list.
This code will read the entire file into memory and remove all whitespace characters (newlines and spaces) from the end of each line:
with open(filename) as file:
lines = [line.rstrip() for line in file]
If you're working with a large file, then you should instead read and process it line-by-line:
with open(filename) as file:
for line in file:
print(line.rstrip())
In Python 3.8 and up you can use a while loop with the walrus operator like so:
with open(filename) as file:
while (line := file.readline().rstrip()):
print(line)
Depending on what you plan to do with your file and how it was encoded, you may also want to manually set the access mode and character encoding:
with open(filename, 'r', encoding='UTF-8') as file:
while (line := file.readline().rstrip()):
print(line)
See Input and Ouput:
with open('filename') as f:
lines = f.readlines()
or with stripping the newline character:
with open('filename') as f:
lines = [line.rstrip('\n') for line in f]
This is more explicit than necessary, but does what you want.
with open("file.txt") as file_in:
lines = []
for line in file_in:
lines.append(line)
This will yield an "array" of lines from the file.
lines = tuple(open(filename, 'r'))
open returns a file which can be iterated over. When you iterate over a file, you get the lines from that file. tuple can take an iterator and instantiate a tuple instance for you from the iterator that you give it. lines is a tuple created from the lines of the file.
According to Python's Methods of File Objects, the simplest way to convert a text file into a list is:
with open('file.txt') as f:
my_list = list(f)
# my_list = [x.rstrip() for x in f] # remove line breaks
Demo
If you just need to iterate over the text file lines, you can use:
with open('file.txt') as f:
for line in f:
...
Old answer:
Using with and readlines() :
with open('file.txt') as f:
lines = f.readlines()
If you don't care about closing the file, this one-liner will work:
lines = open('file.txt').readlines()
The traditional way:
f = open('file.txt') # Open file on read mode
lines = f.read().splitlines() # List with stripped line-breaks
f.close() # Close file
If you want the \n included:
with open(fname) as f:
content = f.readlines()
If you do not want \n included:
with open(fname) as f:
content = f.read().splitlines()
You could simply do the following, as has been suggested:
with open('/your/path/file') as f:
my_lines = f.readlines()
Note that this approach has 2 downsides:
1) You store all the lines in memory. In the general case, this is a very bad idea. The file could be very large, and you could run out of memory. Even if it's not large, it is simply a waste of memory.
2) This does not allow processing of each line as you read them. So if you process your lines after this, it is not efficient (requires two passes rather than one).
A better approach for the general case would be the following:
with open('/your/path/file') as f:
for line in f:
process(line)
Where you define your process function any way you want. For example:
def process(line):
if 'save the world' in line.lower():
superman.save_the_world()
(The implementation of the Superman class is left as an exercise for you).
This will work nicely for any file size and you go through your file in just 1 pass. This is typically how generic parsers will work.
Having a Text file content:
line 1
line 2
line 3
We can use this Python script in the same directory of the txt above
>>> with open("myfile.txt", encoding="utf-8") as file:
... x = [l.rstrip("\n") for l in file]
>>> x
['line 1','line 2','line 3']
Using append:
x = []
with open("myfile.txt") as file:
for l in file:
x.append(l.strip())
Or:
>>> x = open("myfile.txt").read().splitlines()
>>> x
['line 1', 'line 2', 'line 3']
Or:
>>> x = open("myfile.txt").readlines()
>>> x
['linea 1\n', 'line 2\n', 'line 3\n']
Or:
def print_output(lines_in_textfile):
print("lines_in_textfile =", lines_in_textfile)
y = [x.rstrip() for x in open("001.txt")]
print_output(y)
with open('001.txt', 'r', encoding='utf-8') as file:
file = file.read().splitlines()
print_output(file)
with open('001.txt', 'r', encoding='utf-8') as file:
file = [x.rstrip("\n") for x in file]
print_output(file)
output:
lines_in_textfile = ['line 1', 'line 2', 'line 3']
lines_in_textfile = ['line 1', 'line 2', 'line 3']
lines_in_textfile = ['line 1', 'line 2', 'line 3']
Introduced in Python 3.4, pathlib has a really convenient method for reading in text from files, as follows:
from pathlib import Path
p = Path('my_text_file')
lines = p.read_text().splitlines()
(The splitlines call is what turns it from a string containing the whole contents of the file to a list of lines in the file.)
pathlib has a lot of handy conveniences in it. read_text is nice and concise, and you don't have to worry about opening and closing the file. If all you need to do with the file is read it all in in one go, it's a good choice.
To read a file into a list you need to do three things:
Open the file
Read the file
Store the contents as list
Fortunately Python makes it very easy to do these things so the shortest way to read a file into a list is:
lst = list(open(filename))
However I'll add some more explanation.
Opening the file
I assume that you want to open a specific file and you don't deal directly with a file-handle (or a file-like-handle). The most commonly used function to open a file in Python is open, it takes one mandatory argument and two optional ones in Python 2.7:
Filename
Mode
Buffering (I'll ignore this argument in this answer)
The filename should be a string that represents the path to the file. For example:
open('afile') # opens the file named afile in the current working directory
open('adir/afile') # relative path (relative to the current working directory)
open('C:/users/aname/afile') # absolute path (windows)
open('/usr/local/afile') # absolute path (linux)
Note that the file extension needs to be specified. This is especially important for Windows users because file extensions like .txt or .doc, etc. are hidden by default when viewed in the explorer.
The second argument is the mode, it's r by default which means "read-only". That's exactly what you need in your case.
But in case you actually want to create a file and/or write to a file you'll need a different argument here. There is an excellent answer if you want an overview.
For reading a file you can omit the mode or pass it in explicitly:
open(filename)
open(filename, 'r')
Both will open the file in read-only mode. In case you want to read in a binary file on Windows you need to use the mode rb:
open(filename, 'rb')
On other platforms the 'b' (binary mode) is simply ignored.
Now that I've shown how to open the file, let's talk about the fact that you always need to close it again. Otherwise it will keep an open file-handle to the file until the process exits (or Python garbages the file-handle).
While you could use:
f = open(filename)
# ... do stuff with f
f.close()
That will fail to close the file when something between open and close throws an exception. You could avoid that by using a try and finally:
f = open(filename)
# nothing in between!
try:
# do stuff with f
finally:
f.close()
However Python provides context managers that have a prettier syntax (but for open it's almost identical to the try and finally above):
with open(filename) as f:
# do stuff with f
# The file is always closed after the with-scope ends.
The last approach is the recommended approach to open a file in Python!
Reading the file
Okay, you've opened the file, now how to read it?
The open function returns a file object and it supports Pythons iteration protocol. Each iteration will give you a line:
with open(filename) as f:
for line in f:
print(line)
This will print each line of the file. Note however that each line will contain a newline character \n at the end (you might want to check if your Python is built with universal newlines support - otherwise you could also have \r\n on Windows or \r on Mac as newlines). If you don't want that you can could simply remove the last character (or the last two characters on Windows):
with open(filename) as f:
for line in f:
print(line[:-1])
But the last line doesn't necessarily has a trailing newline, so one shouldn't use that. One could check if it ends with a trailing newline and if so remove it:
with open(filename) as f:
for line in f:
if line.endswith('\n'):
line = line[:-1]
print(line)
But you could simply remove all whitespaces (including the \n character) from the end of the string, this will also remove all other trailing whitespaces so you have to be careful if these are important:
with open(filename) as f:
for line in f:
print(f.rstrip())
However if the lines end with \r\n (Windows "newlines") that .rstrip() will also take care of the \r!
Store the contents as list
Now that you know how to open the file and read it, it's time to store the contents in a list. The simplest option would be to use the list function:
with open(filename) as f:
lst = list(f)
In case you want to strip the trailing newlines you could use a list comprehension instead:
with open(filename) as f:
lst = [line.rstrip() for line in f]
Or even simpler: The .readlines() method of the file object by default returns a list of the lines:
with open(filename) as f:
lst = f.readlines()
This will also include the trailing newline characters, if you don't want them I would recommend the [line.rstrip() for line in f] approach because it avoids keeping two lists containing all the lines in memory.
There's an additional option to get the desired output, however it's rather "suboptimal": read the complete file in a string and then split on newlines:
with open(filename) as f:
lst = f.read().split('\n')
or:
with open(filename) as f:
lst = f.read().splitlines()
These take care of the trailing newlines automatically because the split character isn't included. However they are not ideal because you keep the file as string and as a list of lines in memory!
Summary
Use with open(...) as f when opening files because you don't need to take care of closing the file yourself and it closes the file even if some exception happens.
file objects support the iteration protocol so reading a file line-by-line is as simple as for line in the_file_object:.
Always browse the documentation for the available functions/classes. Most of the time there's a perfect match for the task or at least one or two good ones. The obvious choice in this case would be readlines() but if you want to process the lines before storing them in the list I would recommend a simple list-comprehension.
Clean and Pythonic Way of Reading the Lines of a File Into a List
First and foremost, you should focus on opening your file and reading its contents in an efficient and pythonic way. Here is an example of the way I personally DO NOT prefer:
infile = open('my_file.txt', 'r') # Open the file for reading.
data = infile.read() # Read the contents of the file.
infile.close() # Close the file since we're done using it.
Instead, I prefer the below method of opening files for both reading and writing as it
is very clean, and does not require an extra step of closing the file
once you are done using it. In the statement below, we're opening the file
for reading, and assigning it to the variable 'infile.' Once the code within
this statement has finished running, the file will be automatically closed.
# Open the file for reading.
with open('my_file.txt', 'r') as infile:
data = infile.read() # Read the contents of the file into memory.
Now we need to focus on bringing this data into a Python List because they are iterable, efficient, and flexible. In your case, the desired goal is to bring each line of the text file into a separate element. To accomplish this, we will use the splitlines() method as follows:
# Return a list of the lines, breaking at line boundaries.
my_list = data.splitlines()
The Final Product:
# Open the file for reading.
with open('my_file.txt', 'r') as infile:
data = infile.read() # Read the contents of the file into memory.
# Return a list of the lines, breaking at line boundaries.
my_list = data.splitlines()
Testing Our Code:
Contents of the text file:
A fost odatã ca-n povesti,
A fost ca niciodatã,
Din rude mãri împãrãtesti,
O prea frumoasã fatã.
Print statements for testing purposes:
print my_list # Print the list.
# Print each line in the list.
for line in my_list:
print line
# Print the fourth element in this list.
print my_list[3]
Output (different-looking because of unicode characters):
['A fost odat\xc3\xa3 ca-n povesti,', 'A fost ca niciodat\xc3\xa3,',
'Din rude m\xc3\xa3ri \xc3\xaemp\xc3\xa3r\xc3\xa3testi,', 'O prea
frumoas\xc3\xa3 fat\xc3\xa3.']
A fost odatã ca-n povesti, A fost ca niciodatã, Din rude mãri
împãrãtesti, O prea frumoasã fatã.
O prea frumoasã fatã.
Here's one more option by using list comprehensions on files;
lines = [line.rstrip() for line in open('file.txt')]
This should be more efficient way as the most of the work is done inside the Python interpreter.
f = open("your_file.txt",'r')
out = f.readlines() # will append in the list out
Now variable out is a list (array) of what you want. You could either do:
for line in out:
print (line)
Or:
for line in f:
print (line)
You'll get the same results.
Another option is numpy.genfromtxt, for example:
import numpy as np
data = np.genfromtxt("yourfile.dat",delimiter="\n")
This will make data a NumPy array with as many rows as are in your file.
Read and write text files with Python 2 and Python 3; it works with Unicode
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Define data
lines = [' A first string ',
'A Unicode sample: €',
'German: äöüß']
# Write text file
with open('file.txt', 'w') as fp:
fp.write('\n'.join(lines))
# Read text file
with open('file.txt', 'r') as fp:
read_lines = fp.readlines()
read_lines = [line.rstrip('\n') for line in read_lines]
print(lines == read_lines)
Things to notice:
with is a so-called context manager. It makes sure that the opened file is closed again.
All solutions here which simply make .strip() or .rstrip() will fail to reproduce the lines as they also strip the white space.
Common file endings
.txt
More advanced file writing/reading
CSV: Super simple format (read & write)
JSON: Nice for writing human-readable data; VERY commonly used (read & write)
YAML: YAML is a superset of JSON, but easier to read (read & write, comparison of JSON and YAML)
pickle: A Python serialization format (read & write)
MessagePack (Python package): More compact representation (read & write)
HDF5 (Python package): Nice for matrices (read & write)
XML: exists too *sigh* (read & write)
For your application, the following might be important:
Support by other programming languages
Reading/writing performance
Compactness (file size)
See also: Comparison of data serialization formats
In case you are rather looking for a way to make configuration files, you might want to read my short article Configuration files in Python.
If you'd like to read a file from the command line or from stdin, you can also use the fileinput module:
# reader.py
import fileinput
content = []
for line in fileinput.input():
content.append(line.strip())
fileinput.close()
Pass files to it like so:
$ python reader.py textfile.txt
Read more here: http://docs.python.org/2/library/fileinput.html
The simplest way to do it
A simple way is to:
Read the whole file as a string
Split the string line by line
In one line, that would give:
lines = open('C:/path/file.txt').read().splitlines()
However, this is quite inefficient way as this will store 2 versions of the content in memory (probably not a big issue for small files, but still). [Thanks Mark Amery].
There are 2 easier ways:
Using the file as an iterator
lines = list(open('C:/path/file.txt'))
# ... or if you want to have a list without EOL characters
lines = [l.rstrip() for l in open('C:/path/file.txt')]
If you are using Python 3.4 or above, better use pathlib to create a path for your file that you could use for other operations in your program:
from pathlib import Path
file_path = Path("C:/path/file.txt")
lines = file_path.read_text().split_lines()
# ... or ...
lines = [l.rstrip() for l in file_path.open()]
Just use the splitlines() functions. Here is an example.
inp = "file.txt"
data = open(inp)
dat = data.read()
lst = dat.splitlines()
print lst
# print(lst) # for python 3
In the output you will have the list of lines.
If you are faced with a very large / huge file and want to read faster (imagine you are in a TopCoder or HackerRank coding competition), you might read a considerably bigger chunk of lines into a memory buffer at one time, rather than just iterate line by line at file level.
buffersize = 2**16
with open(path) as f:
while True:
lines_buffer = f.readlines(buffersize)
if not lines_buffer:
break
for line in lines_buffer:
process(line)
The easiest ways to do that with some additional benefits are:
lines = list(open('filename'))
or
lines = tuple(open('filename'))
or
lines = set(open('filename'))
In the case with set, we must be remembered that we don't have the line order preserved and get rid of the duplicated lines.
Below I added an important supplement from #MarkAmery:
Since you're not calling .close on the file object nor using a with statement, in some Python implementations the file may not get closed after reading and your process will leak an open file handle.
In CPython (the normal Python implementation that most people use), this isn't a problem since the file object will get immediately garbage-collected and this will close the file, but it's nonetheless generally considered best practice to do something like:
with open('filename') as f: lines = list(f)
to ensure that the file gets closed regardless of what Python implementation you're using.
Use this:
import pandas as pd
data = pd.read_csv(filename) # You can also add parameters such as header, sep, etc.
array = data.values
data is a dataframe type, and uses values to get ndarray. You can also get a list by using array.tolist().
In case that there are also empty lines in the document I like to read in the content and pass it through filter to prevent empty string elements
with open(myFile, "r") as f:
excludeFileContent = list(filter(None, f.read().splitlines()))
Outline and Summary
With a filename, handling the file from a Path(filename) object, or directly with open(filename) as f, do one of the following:
list(fileinput.input(filename))
using with path.open() as f, call f.readlines()
list(f)
path.read_text().splitlines()
path.read_text().splitlines(keepends=True)
iterate over fileinput.input or f and list.append each line one at a time
pass f to a bound list.extend method
use f in a list comprehension
I explain the use-case for each below.
In Python, how do I read a file line-by-line?
This is an excellent question. First, let's create some sample data:
from pathlib import Path
Path('filename').write_text('foo\nbar\nbaz')
File objects are lazy iterators, so just iterate over it.
filename = 'filename'
with open(filename) as f:
for line in f:
line # do something with the line
Alternatively, if you have multiple files, use fileinput.input, another lazy iterator. With just one file:
import fileinput
for line in fileinput.input(filename):
line # process the line
or for multiple files, pass it a list of filenames:
for line in fileinput.input([filename]*2):
line # process the line
Again, f and fileinput.input above both are/return lazy iterators.
You can only use an iterator one time, so to provide functional code while avoiding verbosity I'll use the slightly more terse fileinput.input(filename) where apropos from here.
In Python, how do I read a file line-by-line into a list?
Ah but you want it in a list for some reason? I'd avoid that if possible. But if you insist... just pass the result of fileinput.input(filename) to list:
list(fileinput.input(filename))
Another direct answer is to call f.readlines, which returns the contents of the file (up to an optional hint number of characters, so you could break this up into multiple lists that way).
You can get to this file object two ways. One way is to pass the filename to the open builtin:
filename = 'filename'
with open(filename) as f:
f.readlines()
or using the new Path object from the pathlib module (which I have become quite fond of, and will use from here on):
from pathlib import Path
path = Path(filename)
with path.open() as f:
f.readlines()
list will also consume the file iterator and return a list - a quite direct method as well:
with path.open() as f:
list(f)
If you don't mind reading the entire text into memory as a single string before splitting it, you can do this as a one-liner with the Path object and the splitlines() string method. By default, splitlines removes the newlines:
path.read_text().splitlines()
If you want to keep the newlines, pass keepends=True:
path.read_text().splitlines(keepends=True)
I want to read the file line by line and append each line to the end of the list.
Now this is a bit silly to ask for, given that we've demonstrated the end result easily with several methods. But you might need to filter or operate on the lines as you make your list, so let's humor this request.
Using list.append would allow you to filter or operate on each line before you append it:
line_list = []
for line in fileinput.input(filename):
line_list.append(line)
line_list
Using list.extend would be a bit more direct, and perhaps useful if you have a preexisting list:
line_list = []
line_list.extend(fileinput.input(filename))
line_list
Or more idiomatically, we could instead use a list comprehension, and map and filter inside it if desirable:
[line for line in fileinput.input(filename)]
Or even more directly, to close the circle, just pass it to list to create a new list directly without operating on the lines:
list(fileinput.input(filename))
Conclusion
You've seen many ways to get lines from a file into a list, but I'd recommend you avoid materializing large quantities of data into a list and instead use Python's lazy iteration to process the data if possible.
That is, prefer fileinput.input or with path.open() as f.
I would try one of the below mentioned methods. The example file that I use has the name dummy.txt. You can find the file here. I presume that the file is in the same directory as the code (you can change fpath to include the proper file name and folder path).
In both the below mentioned examples, the list that you want is given by lst.
1. First method
fpath = 'dummy.txt'
with open(fpath, "r") as f: lst = [line.rstrip('\n \t') for line in f]
print lst
>>>['THIS IS LINE1.', 'THIS IS LINE2.', 'THIS IS LINE3.', 'THIS IS LINE4.']
2. In the second method, one can use csv.reader module from Python Standard Library:
import csv
fpath = 'dummy.txt'
with open(fpath) as csv_file:
csv_reader = csv.reader(csv_file, delimiter=' ')
lst = [row[0] for row in csv_reader]
print lst
>>>['THIS IS LINE1.', 'THIS IS LINE2.', 'THIS IS LINE3.', 'THIS IS LINE4.']
You can use either of the two methods. The time taken for the creation of lst is almost equal for the two methods.
I like to use the following. Reading the lines immediately.
contents = []
for line in open(filepath, 'r').readlines():
contents.append(line.strip())
Or using list comprehension:
contents = [line.strip() for line in open(filepath, 'r').readlines()]
You could also use the loadtxt command in NumPy. This checks for fewer conditions than genfromtxt, so it may be faster.
import numpy
data = numpy.loadtxt(filename, delimiter="\n")
Here is a Python(3) helper library class that I use to simplify file I/O:
import os
# handle files using a callback method, prevents repetition
def _FileIO__file_handler(file_path, mode, callback = lambda f: None):
f = open(file_path, mode)
try:
return callback(f)
except Exception as e:
raise IOError("Failed to %s file" % ["write to", "read from"][mode.lower() in "r rb r+".split(" ")])
finally:
f.close()
class FileIO:
# return the contents of a file
def read(file_path, mode = "r"):
return __file_handler(file_path, mode, lambda rf: rf.read())
# get the lines of a file
def lines(file_path, mode = "r", filter_fn = lambda line: len(line) > 0):
return [line for line in FileIO.read(file_path, mode).strip().split("\n") if filter_fn(line)]
# create or update a file (NOTE: can also be used to replace a file's original content)
def write(file_path, new_content, mode = "w"):
return __file_handler(file_path, mode, lambda wf: wf.write(new_content))
# delete a file (if it exists)
def delete(file_path):
return os.remove() if os.path.isfile(file_path) else None
You would then use the FileIO.lines function, like this:
file_ext_lines = FileIO.lines("./path/to/file.ext"):
for i, line in enumerate(file_ext_lines):
print("Line {}: {}".format(i + 1, line))
Remember that the mode ("r" by default) and filter_fn (checks for empty lines by default) parameters are optional.
You could even remove the read, write and delete methods and just leave the FileIO.lines, or even turn it into a separate method called read_lines.
Command line version
#!/bin/python3
import os
import sys
abspath = os.path.abspath(__file__)
dname = os.path.dirname(abspath)
filename = dname + sys.argv[1]
arr = open(filename).read().split("\n")
print(arr)
Run with:
python3 somefile.py input_file_name.txt
I'm looking for some help with my code which is rigth below :
for file in file_name :
if os.path.isfile(file):
for line_number, line in enumerate(fileinput.input(file, inplace=1)):
print file
os.system("pause")
if line_number ==1:
line = line.replace('Object','#Object')
sys.stdout.write(line)
I wanted to modify some previous extracted files in order to plot them with matplotlib. To do so, I remove some lines, comment some others.
My problem is the following :
Using for line_number, line in enumerate(fileinput.input(file, inplace=1)): gives me only 4 out of 5 previous extracted files (when looking file_name list contains 5 references !)
Using for line_number, line in enumerate(file): gives me the 5 previous extracted file, BUT I don't know how to make modifications using the same file without creating another one...
Did you have an idea on this issue? Is this a normal issue?
There a number of things that might help you.
Firstly file_name appears to be a list of file names. It might be better named file_names and then you could use file_name for each one. You have verified that this does hold 5 entries.
The enumerate() function is used to help when enumerating a list of items to provide both an index and the item for each loop. This saves you having to use a separate counter variable, e.g.
for index, item in enumerate(["item1", "item2", "item3"]):
print index, item
would print:
0 item1
1 item2
2 item3
This is not really required, as you have chosen to use the fileinput library. This is designed to take a list of files and iterate over all of the lines in all of the files in one single loop. As such you need to tweak your approach a bit, assuming your list of files is called file_names then you write something as follows:
# Keep only files in the file list
file_names = [file_name for file_name in file_names if os.path.isfile(file_name)]
# Iterate all lines in all files
for line in fileinput.input(file_names, inplace=1):
if fileinput.filelineno() == 1:
line = line.replace('Object','#Object')
sys.stdout.write(line)
The main point here being that it is better to pre filter any non-filenames before passing the list to fileinput. I will leave it up to you to fix the output.
fileinput provides a number of functions to help you figure out which file or line number is currently being processed.
Assuming you're still having trouble, my typical approach is to open a file read-only, read its contents into a variable, close the file, make an edited variable, open the file to write (wiping out original file), and finally write the edited contents.
I like this approach since I can simply change the file_name that gets written out if I want to test my edits without wiping out the original file.
Also, I recommend naming containers using plural nouns, like #Martin Evans suggests.
import os
file_names = ['file_1.txt', 'file_2.txt', 'file_3.txt', 'file_4.txt', 'file_5.txt']
file_names = [x for x in file_names if os.path.isfile(x)] # see #Martin's answer again
for file_name in file_names:
# Open read-only and put contents into a list of line strings
with open(file_name, 'r') as f_in:
lines = f_in.read().splitlines()
# Put the lines you want to write out in out_lines
out_lines = []
for index_no, line in enumerate(lines):
if index_no == 1:
out_lines.append(line.replace('Object', '#Object'))
elif ...
else:
out_lines.append(line)
# Uncomment to write to different file name for edits testing
# with open(file_name + '.out', 'w') as f_out:
# f_out.write('\n'.join(out_lines))
# Write out the file, clobbering the original
with open(file_name, 'w') as f_out:
f_out.write('\n'.join(out_lines))
Downside with this approach is that each file needs to be small enough to fit into memory twice (lines + out_lines).
Best of luck!
I am trying to compare columns in two files to see if the values match, and if there is a match I want to merge/concatenate the data for that row together. My issue is that when reading line by line from the two files separately, I can't get python to iterate through the files together and look for a match. Instead it will iterate properly through one file and iterate over the same line in the second file multiple times...
I have had this issue in the past and still not really found a way around it. I know that indentation is one problem since I mess with the loop by using "for line in a, for line in b" so I thought that what I tried below would work but it hasn't. I have looked around for solutions but nobody seems to be using the same method so I wonder if I am completely off track as to how to do this? Can anyone explain what is a better way to do this, and whether my method would work at all and if not, why not? Thanks, it is much appreciated!
These are the formats of my two files, basically I want to compare the columns filename in both files and if they match I want to merge the rows together.
file1:
cluster_id hypothesis_id filename M1_name_offset Orientation
1 71133076 unique_name_1.png esc_sox2_Sox1_80_4 forward
1 50099120 unique_name_4.png hb_cebpb_ETS1_139_7 forward
1 91895576 unique_name_11.png he_tal1_at_AC_acptr_258_11 forward
file2:
Name Cluster_No Pattern filename
esc_sox2_Sox1_80 Cluster1 AP1(1N)ETS unique_name_4.png
hb_cebpb_ETS1_139 Cluster1 CREB(1N)ETS unique_name_11.png
he_tal1_at_AC_acptr_258 Cluster2 ETS(-1N)ZIC unique_name_3.png
What I have tried:
for aline in file1:
motif1 = aline.split()[2]
for bline in file2:
motif2 = bline.split()[-1]
if motif1 = motif2:
print "match", aline, bline
I have also tried:
for aline in file1:
motif1 = aline.split()[2]
for bline in file2:
motif2 = bline.split()[-1]
if motif1 = motif2:
print "match", aline, bline
I have also tried using string formatting but that didn't make a difference. The first way iterates through file2 incorrectly and the second way doesn't give me any output. I have played around with it a lot and tried various indentations and extra bits but I am stumped as to how to even try and fix it! Please help me :(
Use the zip builtin function.
with open(file1) as f1, open(file2) as f2:
for line1, line2 in zip(f1, f2):
motif1 = line1.split()[0]
motif2 = line2.split()[0]
...
Note that zip behaves differently in python2 and python3. In python2, it would be more efficient to use itertools.izip instead.
I'm assuming you're using Python 3. Here's a nice abstraction, iterlines. It hides the complexity of opening, reading, pairing, and closing n files. Note the use of zip_longest, this prevents the ends of longer files being silently discarded.
def iterlines(*paths, fillvalue=None, **open_kwargs):
files = []
try:
for path in paths:
files.append(open(path, **open_kwargs))
for lines in zip_longest(*files, fillvalue=fillvalue):
yield lines
finally:
for file_ in files:
with suppress():
file_.close()
Usage
for line_a, line_b in iterlines('a.txt', 'b.txt'):
print(line_a, line_b)
Complete code
from contextlib import suppress
from itertools import zip_longest
def iterlines(*paths, fillvalue=None, **open_kwargs):
files = []
try:
for path in paths:
files.append(open(path, **open_kwargs))
for lines in zip_longest(*files, fillvalue=fillvalue):
yield lines
finally:
for file_ in files:
with suppress():
file_.close()
for lines in iterlines('a.txt', 'b.txt', 'd.txt'):
print(lines)
I am trying to remove duplicates of 3-column tab-delimited txt file, but as long as the first two columns are duplicates, then it should be removed even if the two has different 3rd column.
from operator import itemgetter
import sys
input = sys.argv[1]
output = sys.argv[2]
#Pass any column number you want, note that indexing starts at 0
ig = itemgetter(0,1)
seen = set()
data = []
for line in input.splitlines():
key = ig(line.split())
if key not in seen:
data.append(line)
seen.add(key)
file = open(output, "w")
file.write(data)
file.close()
First, I get error
key = ig(line.split())
IndexError: list index out of range
Also, I can't see how to save the result to output.txt
People say saving to output.txt is a really basic matter. But no tutorial helped.
I tried methods that use codec, those that use with, those that use file.write(data) and all didn't help.
I could learn MatLab quite easily. The online tutorial was fantastic and a series of Googling always helped a lot.
But I can't find a helpful tutorial of Python yet. This is obviously because I am a complete novice. For complete novices like me, what would be the best tutorial with 1) comprehensiveness AND 2) lots of examples 3) line by line explanation that dosen't leave any line without explanation?
And why is the above code causing error and not saving result?
I'm assuming since you assign input to the first command line argument with input = sys.argv[1] and output to the second, you intend those to be your input and output file names. But you're never opening any file for the input data, so you're callling .splitlines() on a file name, not on file contents.
Next, splitlines() is the wrong approach here anyway. To iterate over a file line-by-line, simply use for line in f, where f is an open file. Those lines will include the newline at the end of the line, so it needs to be stripped if it's not supposed to be part of the third columns data.
Then you're opening and closing the file inside your loop, which means you'll try to write the entire contents of data to the file every iteration, effectively overwriting any data written to the file before. Therefore I moved that block out of the loop.
It's good practice to use the with statement for opening files. with open(out_fn, "w") as outfile will open the file named out_fn and assign the open file to outfile, and close it for you as soon as you exit that indented block.
input is a builtin function in Python. I therefore renamed your variables so no builtin names get shadowed.
You're trying to directly write data to the output file. This won't work since data is a list of lines. You need to join those lines first in order to turn them in a single string again before writing it to a file.
So here's your code with all those issues addressed:
from operator import itemgetter
import sys
in_fn = sys.argv[1]
out_fn = sys.argv[2]
getkey = itemgetter(0, 1)
seen = set()
data = []
with open(in_fn, 'r') as infile:
for line in infile:
line = line.strip()
key = getkey(line.split())
if key not in seen:
data.append(line)
seen.add(key)
with open(out_fn, "w") as outfile:
outfile.write('\n'.join(data))
Why is the above code causing error?
Because you haven't opened the file, you are trying to work with the string input.txtrather than with the file. Then when you try to access your item, you get a list index out of range because line.split() returns ['input.txt'].
How to fix that: open the file and then work with it, not with its name.
For example, you can do (I tried to stay as close to your code as possible)
input = sys.argv[1]
infile = open(input, 'r')
(...)
lines = infile.readlines()
infile.close()
for line in lines:
(...)
Why is this not saving result?
Because you are opening/closing the file inside the loop. What you need to do is write the data once you're out of the loop. Also, you cannot write directly a list to a file. Hence, you need to do something like (outside of your loop):
outfile = open(output, "w")
for item in data:
outfile.write(item)
outfile.close()
All together
There are other ways of reading/writing files, and it is pretty well documented on the internet but I tried to stay close to your code so that you would understand better what was wrong with it
from operator import itemgetter
import sys
input = sys.argv[1]
infile = open(input, 'r')
output = sys.argv[2]
#Pass any column number you want, note that indexing starts at 0
ig = itemgetter(0,1)
seen = set()
data = []
lines = infile.readlines()
infile.close()
for line in lines:
print line
key = ig(line.split())
if key not in seen:
data.append(line)
seen.add(key)
print data
outfile = open(output, "w")
for item in data:
outfile.write(item)
outfile.close()
PS: it seems to produce the result that you needed there Python to remove duplicates using only some, not all, columns
I have a file named a.txt which looks like this:
I'm the first line
I'm the second line.
There may be more lines here.
I'm below an empty line.
I'm a line.
More lines here.
Now, I want to remove the contents above the empty line(including the empty line itself).
How could I do this in a Pythonic way?
Basically you can't delete stuff from the beginning of a file, so you will have to write to a new file.
I think the pythonic way looks like this:
# get a iterator over the lines in the file:
with open("input.txt", 'rt') as lines:
# while the line is not empty drop it
for line in lines:
if not line.strip():
break
# now lines is at the point after the first paragraph
# so write out everything from here
with open("output.txt", 'wt') as out:
out.writelines(lines)
Here are some simpler versions of this, without with for older Python versions:
lines = open("input.txt", 'rt')
for line in lines:
if not line.strip():
break
open("output.txt", 'wt').writelines(lines)
and a very straight forward version that simply splits the file at the empty line:
# first, read everything from the old file
text = open("input.txt", 'rt').read()
# split it at the first empty line ("\n\n")
first, rest = text.split('\n\n',1)
# make a new file and write the rest
open("output.txt", 'wt').write(rest)
Note that this can be pretty fragile, for example windows often uses \r\n as a single linebreak, so a empty line would be \r\n\r\n instead. But often you know the format of the file uses one kind of linebreaks only, so this could be fine.
Naive approach by iterating over the lines in the file one by one top to bottom:
#!/usr/bin/env python
with open("4692065.txt", 'r') as src, open("4692065.cut.txt", "w") as dest:
keep = False
for line in src:
if keep: dest.write(line)
if line.strip() == '': keep = True
The fileinput module (from the standard library) is convenient for this kind of thing. It sets things up so you can act as though your are editing the file "in-place":
import fileinput
import sys
fileobj=iter(fileinput.input(['a.txt'], inplace=True))
# iterate through the file until you find an empty line.
for line in fileobj:
if not line.strip():
break
# Iterators (like `fileobj`) pick up where they left off.
# Starting a new for-loop saves you one `if` statement and boolean variable.
for line in fileobj:
sys.stdout.write(line)
Any idea how big the file is going to be?
You could read the file into memory:
f = open('your_file', 'r')
lines = f.readlines()
which will read the file line by line and store those lines in a list (lines).
Then, close the file and reopen with 'w':
f.close()
f = open('your_file', 'w')
for line in lines:
if your_if_here:
f.write(line)
This will overwrite the current file. Then you can pick and choose which lines from the list you want to write back in. Probably not a very good idea if the file gets to large though, since the entire file has to reside in memory. But, it doesn't require that you create a second file to dump your output.
from itertools import dropwhile, islice
def content_after_emptyline(file_object):
return islice(dropwhile(lambda line: line.strip(), file_object), 1, None)
with open("filename") as f:
for line in content_after_emptyline(f):
print line,
You could do a little something like this:
with open('a.txt', 'r') as file:
lines = file.readlines()
blank_line = lines.index('\n')
lines = lines[blank_line+1:] #\n is the index of the blank line
with open('a.txt', 'w') as file:
file.write('\n'.join(lines))
and that makes the job much simpler.