im new to Python, to programming in general.
I want to remove first char from each line in a text file and write the changes back to the file. For example i have file with 36 lines, and the first char in each line contains a symbol or a number, and i want it to be removed.
I made a little code here, but it doesn't work as expected, it only duplicates whole liens. Any help would be appreciated in advance!
from sys import argv
run, filename = argv
f = open(filename, 'a+')
f.seek(0)
lines = f.readlines()
for line in lines:
f.write(line[1:])
f.close()
Your code already does remove the first character. I saved exactly your code as both dupy.py and dupy.txt, then ran python dupy.py dupy.txt, and the result is:
from sys import argv
run, filename = argv
f = open(filename, 'a+')
f.seek(0)
lines = f.readlines()
for line in lines:
f.write(line[1:])
f.close()
rom sys import argv
un, filename = argv
= open(filename, 'a+')
.seek(0)
ines = f.readlines()
or line in lines:
f.write(line[1:])
.close()
It's not copying entire lines; it's copying lines with their first character stripped.
But from the initial statement of your problem, it sounds like you want to overwrite the lines, not append new copies. To do that, don't use append mode. Read the file, then write it:
from sys import argv
run, filename = argv
f = open(filename)
lines = f.readlines()
f.close()
f = open(filename, 'w')
for line in lines:
f.write(line[1:])
f.close()
Or, alternatively, write a new file, then move it on top of the original when you're done:
import os
from sys import argv
run, filename = argv
fin = open(filename)
fout = open(filename + '.tmp', 'w')
lines = f.readlines()
for line in lines:
fout.write(line[1:])
fout.close()
fin.close()
os.rename(filename + '.tmp', filename)
(Note that this version will not work as-is on Windows, but it's simpler than the actual cross-platform version; if you need Windows, I can explain how to do this.)
You can make the code a lot simpler, more robust, and more efficient by using with statements, looping directly over the file instead of calling readlines, and using tempfile:
import tempfile
from sys import argv
run, filename = argv
with open(filename) as fin, tempfile.NamedTemporaryFile(delete=False) as fout:
for line in fin:
fout.write(line[1:])
os.rename(fout.name, filename)
On most platforms, this guarantees an "atomic write"—when your script finishes, or even if someone pulls the plug in the middle of it running, the file will end up either replaced by the new version, or untouched; there's no way it can end up half-way overwritten into unrecoverable garbage.
Again this version won't work on Windows. Without a whole lot of work, there is no way to implement this "write-temp-and-rename" algorithm on Windows. But you can come close with only a bit of extra work:
with open(filename) as fin, tempfile.NamedTemporaryFile(delete=False) as fout:
for line in fin:
fout.write(line[1:])
outname = fout.name
os.remove(filename)
os.rename(outname, filename)
This does prevent you from half-overwriting the file, but it leaves a hole where you may have deleted the original file, and left the new file in a temporary location that you'll have to search for. You can make this a little nicer by putting the file somewhere easier to find (see the NamedTemporaryFile docs to see how). Or renaming the original file to a temporary name, then writing to the original filename, then deleting the original file. Or various other possibilities. But to actually get the same behavior as on other platforms is very difficult.
You can either read all lines in memory then recreate file,
from sys import argv
run, filename = argv
with open(filename, 'r') as f:
data = [i[1:] for i in f
with open(filename, 'w') as f:
f.writelines(i+'\n' for i in data) # this is for linux. for win use \r\n
or You can create other file and move data from first file to second line by line. Then You can rename it If You'd like
from sys import argv
run, filename = argv
new_name = filename + '.tmp'
with open(filename, 'r') as f_in, open(new_name, 'w') as f_out:
for line in f_in:
f_out.write(line[1:])
os.rename(new_name, filename)
At its most basic, your problem is that you need to seek back to the beginning of the file after you read its complete contents into the array f. Since you are making the file shorter, you also need to use truncate to adjust the official length of the file after you're done. Furthermore, open mode a+ (a is for append) overrides seek and forces all writes to go to the end of the file. So your code should look something like this:
import sys
def main(argv):
filename = argv[1]
with open(filename, 'r+') as f:
lines = f.readlines()
f.seek(0)
for line in lines:
f.write(line[1:])
f.truncate()
if __name__ == '__main__': main(sys.argv)
It is better, when doing something like this, to write the changes to a new file and then rename it over the old file when you're done. This causes the update to happen "atomically" - a concurrent reader sees either the old file or the new one, not some mangled combination of the two. That looks like this:
import os
import sys
import tempfile
def main(argv):
filename = argv[1]
with open(filename, 'r') as inf:
with tempfile.NamedTemporaryFile(dir=".", delete=False) as outf:
tname = outf.name
for line in inf:
outf.write(line[1:])
os.rename(tname, filename)
if __name__ == '__main__': main(sys.argv)
(Note: Atomically replacing a file via rename does not work on Windows; you have to os.remove the old name first. This unfortunately does mean there is a brief window (no pun intended) where a concurrent reader will find that the file does not exist. As far as I know there is no way to avoid this.)
import re
with open(filename,'r+') as f:
modified = re.sub('^.','',f.read(),flags=re.MULTILINE)
f.seek(0,0)
f.write(modified)
In the regex pattern:
^ means 'start of string'
^ with flag re.MULTILINE means 'start of line'
^. means 'the only one character at the start of a line'
The start of a line is the start of the string or any position after a newline (a newline is \n)
So, we may fear that some newlines in sequences like \n\n\n\n\n\n\n could match with the regex pattern.
But the dot symbolizes any character EXCEPT a newline, then all the newlines don't match with this regex pattern.
During the reading of the file triggered by f.read(), the file's pointer goes until the end of the file.
f.seek(0,0) moves the file's pointer back to the beginning of the file
f.truncate() puts a new EOF = end of file at the point where the writing has stopped. It's necessary since the modified text is shorter than the original one.
Compare what it does with a code without this line
To be hones, i'm really not sure how good/bad is an idea of nesting with open(), but you can do something like this.
with open(filename_you_reading_lines_FROM, 'r') as f0:
with open(filename_you_appending_modified_lines_TO, 'a') as f1:
for line in f0:
f1.write(line[1:])
While there seemed to be some discussion of best practice and whether it would run on Windows or not, being new to Python, I was able to run the first example that worked and get it to run in my Win environment that has cygwin binaries in my environmental variables Path and remove the first 3 characters (which were line numbers from a sample file):
import os
from sys import argv
run, filename = argv
fin = open(filename)
fout = open(filename + '.tmp', 'w')
lines = fin.readlines()
for line in lines:
fout.write(line[3:])
fout.close()
fin.close()
I chose not to automatically overwrite since I wanted to be able to eyeball the output.
python c:\bin\remove1st3.py sampleCode.txt
Related
I posted a question yesterday in similar regards to this but didn't quite gauge the response I wanted because I wasn't specific enough. Basically the function takes a .txt file as the argument and returns a string with all \n characters replaced with an '_' on the same line. I want to do this without using WITH. I thought I did this correctly but when I run it and check the file, nothing has changed. Any pointers?
This is what I did:
def one_line(filename):
wordfile = open(filename)
text_str = wordfile.read().replace("\n", "_")
wordfile.close()
return text_str
one_line("words.txt")
but to no avail. I open the text file and it remains the same.
The contents of the textfile are:
I like to eat
pancakes every day
and the output that's supposed to be shown is:
>>> one_line("words.txt")
’I like to eat_pancakes every day_’
The fileinput module in the Python standard library allows you to do this in one fell swoop.
import fileinput
for line in fileinput.input(filename, inplace=True):
line = line.replace('\n', '_')
print(line, end='')
The requirement to avoid a with statement is trivial but rather pointless. Anything which looks like
with open(filename) as handle:
stuff
can simply be rewritten as
try:
handle = open(filename)
stuff
finally:
handle.close()
If you take out the try/finally you have a bug which leaves handle open if an error happens. The purpose of the with context manager for open() is to simplify this common use case.
You are missing some steps. After you obtain the updated string, you need to write it back to the file, example below without using with
def one_line(filename):
wordfile = open(filename)
text_str = wordfile.read().replace("\n", "_")
wordfile.close()
return text_str
def write_line(s):
# Open the file in write mode
wordfile = open("words.txt", 'w')
# Write the updated string to the file
wordfile.write(s)
# Close the file
wordfile.close()
s = one_line("words.txt")
write_line(s)
Or using with
with open("file.txt",'w') as wordfile:
#Write the updated string to the file
wordfile.write(s)
with pathlib you could achieve what you want this way:
from pathlib import Path
path = Path(filename)
contents = path.read_text()
contents = contents.replace("\n", "_")
path.write_text(contents)
I wrote the following python code snippet to append a lower p character to each line of a txt file:
f = open('helloworld.txt','r')
for line in f:
line+='p'
print(f.read())
f.close()
However, when I execute this python program, it returns nothing but an empty blank:
zhiwei#zhiwei-Lenovo-Rescuer-15ISK:~/Documents/1001/ass5$ python3 helloworld.py
Can anyone tell me what's wrong with my codes?
Currently, you are only reading each line and not writing to the file. reopen the file in write mode and write your full string to it, like so:
newf=""
with open('helloworld.txt','r') as f:
for line in f:
newf+=line.strip()+"p\n"
f.close()
with open('helloworld.txt','w') as f:
f.write(newf)
f.close()
well, type help(f) in shell, you can get "Character and line based layer over a BufferedIOBase object, buffer."
it's meaning：if you reading first buffer,you can get content, but again. it's empty。
so like this:
with open(oldfile, 'r') as f1, open(newfile, 'w') as f2:
newline = ''
for line in f1:
newline+=line.strip()+"p\n"
f2.write(newline)
open(filePath, openMode) takes two arguments, the first one is the path to your file, the second one is the mode it will be opened it. When you use 'r' as second argument, you are actually telling Python to open it as an only reading file.
If you want to write on it, you need to open it in writing mode, using 'w' as second argument. You can find more about how to read/write files in Python in its official documentation.
If you want to read and write at the same time, you have to open the file in both reading and writing modes. You can do this simply by using 'r+' mode.
It seems that your for loop has already read the file to the end, so f.read() return empty string.
If you just need to print the lines in the file, you could move the print into for loop just like print(line). And it is better to move the f.read() before for loop:
f = open("filename", "r")
lines = f.readlines()
for line in lines:
line += "p"
print(line)
f.close()
If you need to modify the file, you need to create another file obj and open it in mode of "w", and use f.write(line) to write the modified lines into the new file.
Besides, it is more better to use with clause in python instead of open(), it is more pythonic.
with open("filename", "r") as f:
lines = f.readlines()
for line in lines:
line += "p"
print(line)
When using with clause, you have no need to close file, this is more simple.
I'm fairly new to python and I'm having an issue with my python script (split_fasta.py). Here is an example of my issue:
list = ["1.fasta", "2.fasta", "3.fasta"]
for file in list:
contents = open(file, "r")
for line in contents:
if line[0] == ">":
new_file = open(file + "_chromosome.fasta", "w")
new_file.write(line)
I've left the bottom part of the program out because it's not needed. My issue is that when I run this program in the same direcoty as my fasta123 files, it works great:
python split_fasta.py *.fasta
But if I'm in a different directory and I want the program to output the new files (eg. 1.fasta_chromsome.fasta) to my current directory...it doesn't:
python /home/bin/split_fasta.py /home/data/*.fasta
This still creates the new files in the same directory as the fasta files. The issue here I'm sure is with this line:
new_file = open(file + "_chromosome.fasta", "w")
Because if I change it to this:
new_file = open("seq" + "_chromosome.fasta", "w")
It creates an output file in my current directory.
I hope this makes sense to some of you and that I can get some suggestions.
You are giving the full path of the old file, plus a new name. So basically, if file == /home/data/something.fasta, the output file will be file + "_chromosome.fasta" which is /home/data/something.fasta_chromosome.fasta
If you use os.path.basename on file, you will get the name of the file (i.e. in my example, something.fasta)
From #Adam Smith
You can use os.path.splitext to get rid of the .fasta
basename, _ = os.path.splitext(os.path.basename(file))
Getting back to the code example, I saw many things not recommended in Python. I'll go in details.
Avoid shadowing builtin names, such as list, str, int... It is not explicit and can lead to potential issues later.
When opening a file for reading or writing, you should use the with syntax. This is highly recommended since it takes care to close the file.
with open(filename, "r") as f:
data = f.read()
with open(new_filename, "w") as f:
f.write(data)
If you have an empty line in your file, line[0] == ... will result in a IndexError exception. Use line.startswith(...) instead.
Final code :
files = ["1.fasta", "2.fasta", "3.fasta"]
for file in files:
with open(file, "r") as input:
for line in input:
if line.startswith(">"):
new_name = os.path.splitext(os.path.basename(file)) + "_chromosome.fasta"
with open(new_name, "w") as output:
output.write(line)
Often, people come at me and say "that's hugly". Not really :). The levels of indentation makes clear what is which context.
I'm supposed to open a file, read it line per line and display the lines out.
Here's the code:
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import re
in_path = "../vas_output/Glyph/20140623-FLYOUT_mins_cleaned.csv"
out_path = "../vas_gender/Glyph/"
csv_read_line = open(in_path, "rb").read().split("\n")
line_number = 0
for line in csv_read_line:
line_number+=1
print str(line_number) + line
Here's the contents of the input file:
12345^67890^abcedefg
random^test^subject
this^sucks^crap
And here's the result:
this^sucks^crapjectfg
Some weird combo of all three. In addition to this, the result of line_number is missing. Printing out the result of len(csv_read_line) outputs 1, for some reason, no matter how many is in the input file. Changing the split type from \n to ^ gives the expected output, though, so I'm assuming the problem is probably with the input file.
I'm using a Mac, and did both the python code and the input file (on Sublime Text) on the Mac itself.
Am I missing something?
You seem to be splitting on "\n" which isn't necessary, and could be incorrect depending on the line terminators used in the input file. Python includes functionality to iterate over the lines of a file one at a time. The advantages are that it will worry about processing line terminators in a portable way, as well as not requiring the entire file to be held in memory at once.
Further, note that you are opening the file in binary mode (the b character in your mode string) when you actually intend to read the file as text. This can cause problems similar to the one you are experiencing.
Also, you do not close the file when you are done with it. In this case that isn't a problem, but you should get in the habit of using with blocks when possible to make sure the file gets closed at the earliest possible time.
Try this:
with open(in_path, "r") as f:
line_number = 0
for line in f:
line_number += 1
print str(line_number) + line.rstrip('\r\n')
So your example just works for me.
But then, i just copied your text into a text editor on linux, and did it that way, so any carriage returns will have been wiped out.
Try this code though:
import os
in_path = "input.txt"
with open(in_path, "rb") as inputFile:
for lineNumber, line in enumerate(inputFile):
print lineNumber, line.strip()
It's a little cleaner, and the for line in file style deals with line breaks for you in a system independent way - Python's open has universal newline support.
I'd try the following Pythonic code:
#!/usr/bin/env python
in_path = "../vas_output/Glyph/20140623-FLYOUT_mins_cleaned.csv"
out_path = "../vas_gender/Glyph/"
with open(in_path, 'rb') as f:
for i, line in enumerate(f):
print(str(i) + line)
There are several improvements that can be made here to make it more idiomatic python.
import csv
in_path = "../vas_output/Glyph/20140623-FLYOUT_mins_cleaned.csv"
out_path = "../vas_gender/Glyph/"
#Lets open the file and make sure that it closes when we unindent
with open(in_path,"rb") as input_file:
#Create a csv reader object that will parse the input for us
reader = csv.reader(input_file,delimiter="^")
#Enumerate over the rows (these will be lists of strings) and keep track of
#of the line number using python's built in enumerate function
for line_num, row in enumerate(reader):
#You can process whatever you would like here. But for now we will just
#print out what you were originally printing
print str(line_num) + "^".join(row)
I have a data file (unstructured, messy file) from which I have to scrub specific list of strings (delete strings).
Here is what I am doing but with no result:
infile = r"messy_data_file.txt"
outfile = r"cleaned_file.txt"
delete_list = ["firstname1 lastname1","firstname2 lastname2"....,"firstnamen lastnamen"]
fin=open(infile,"")
fout = open(outfile,"w+")
for line in fin:
for word in delete_list:
line = line.replace(word, "")
fout.write(line)
fin.close()
fout.close()
When I execute the file, I get the following error:
NameError: name 'word' is not defined
The readlines method returns a list of lines, not words, so your code would only work where one of your words is on a line by itself.
Since files are iterators over lines this can be done much easier:
infile = "messy_data_file.txt"
outfile = "cleaned_file.txt"
delete_list = ["word_1", "word_2", "word_n"]
with open(infile) as fin, open(outfile, "w+") as fout:
for line in fin:
for word in delete_list:
line = line.replace(word, "")
fout.write(line)
To remove the string within the same file, I used this code
f = open('./test.txt','r')
a = ['word1','word2','word3']
lst = []
for line in f:
for word in a:
if word in line:
line = line.replace(word,'')
lst.append(line)
f.close()
f = open('./test.txt','w')
for line in lst:
f.write(line)
f.close()
Based on your comment "I am double clicking the .py file. It seems to invoke the python application which disappears after a couple of seconds. I dont get any error thought" I believe your issue is the script is not finding the input file. That is also why you are not getting any output. When you double click on it... I actually can't recall where the interpreter is going to look but I think it's where the python.exe is installed.
Use a fully qualified path like so.
# Depends on your OS
infile = r"C:\tmp\messy_data_file.txt"
outfile = r"C:\tmp\cleaned_file.txt"
infile = r"/etc/tmp/messy_data_file.txt"
outfile = r"/etc/tmp/cleaned_file.txt"
Also, for your sanity, run it from the command-line instead of double clicking. It'll be much easier to catch errors/output.
To the OP,
Ross Patterson's method above works perfectly for me, i.e.
infile = "messy_data_file.txt"
outfile = "cleaned_file.txt"
delete_list = ["word_1", "word_2", "word_n"]
fin = open(infile)
fout = open(outfile, "w+")
for line in fin:
for word in delete_list:
line = line.replace(word, "")
fout.write(line)
fin.close()
fout.close()
Example:
I have a file named messy_data_file.txt that includes the following words (animals), not necessarily on the same line. Like this:
Goat
Elephant
Horse Donkey Giraffe
Lizard
Bird
Fish
When I modify the code to read (actually just adding the words to delete to the "delete_list" line):
infile = "messy_data_file.txt"
outfile = "cleaned_file.txt"
delete_list = ["Donkey", "Goat", "Fish"]
fin = open(infile)
fout = open(outfile, "w+")
for line in fin:
for word in delete_list:
line = line.replace(word, "")
fout.write(line)
fin.close()
fout.close()
The resulting "cleaned_file.txt" looks like this:
Elephant
Horse Giraffe
Lizard
Bird
There is a blank line where "Goat" used to be (where, oddly, removing "Donkey" did not) but for my purposes, this works fine.
I also add input("Press Enter to exit...") the the very end of the code to keep the command line window from opening and slamming shut on me when I'm double-clicking the remove_text.py file to run it, but take note that you'll catch no errors this way.
To do that I run it from the command line (where C:\Just_Testing is the directory where all my files are, i.e. remove_text.py and messy_text.txt)
like this:
C:\Just_Testing\>py remove_text.py
or
C:\Just_Testing>python remove_text.py
works exactly the same.
Of course, like when writing HTML, I guess it never hurts to use a fully qualified path when running py or python from somewhere other than the directory you happen to be sitting in, such as:
C:\Windows\System32\>python C:\Users\Me\Desktop\remove_text.py
Of course in the code it would be:
infile = "C:\Users\Me\Desktop\messy_data_file.txt"
outfile = "C:\Users\Me\Desktop\cleaned_file.txt"
Be careful to use the same fully qualified path to place your newly created cleaned_file.txt in or it will be created wherever you may be and that could cause confusion when looking for it.
Personally, I have the PATH in my Environment Variables set to point to all my Python installs i.e. C:\Python3.5.3, C:\Python2.7.13, etc. so I can run py or python from anywhere.
Anyway, I hope making fine-tuning adjustments to this code from Mr. Patterson can get you exactly what you need. :)
.
Maybe you can add encoding='utf-8' in your fin and fout variables.
Here is the modified one you may want to use:
fin=open(infile,"", encoding='utf-8')
fout = open(outfile,"w+", encoding='utf-8')
This(adding utf-8) mostly occurs on the OS Windows. Also for reading, writing, and appending the file, this usually isn't a problem but for advanced things to do a file like replacing text in there, etc then you should do this.
Hope this helps you.
The code below just gets the old data and checks if the string doesnt contain the string you doesnt want then continues. (this also works if you want to remove empty lines)
str = []
with open("file.txt", "r+") as f:
for i in f.readlines():
str.append(i)
with open("file.txt", "w") as f:
for i in str:
if i != "The string you want to remove":
f.write(i)