I have to write substrings to a new file by reading from another file. The problem I am facing is that it only writes the last found substring.
Here is what I've tried.
def get_fasta(site):
with open('file1.txt', 'r') as myfile:
data=myfile.read()
site = site-1
str1 = data[site:site+1+20]
temp = data[site-20:site]
final_sequence = temp+str1
with open('positive_results_sequences.txt', 'w') as my_new_file:
my_new_file.write(final_sequence + '\n')
def main():
# iterate over the list of IDS
for k,v in zip(site_id_list):
get_fasta(v)
if __name__ == '__main__':
main()
That's because you've opened the inner file in w mode which recreates the file each time. So the end result is that only last write persists. You want to use a mode (which stands for "append").
Also there are some other issues with your code. For example you open and close both files in each loop iteration. You should move file opening code outside and pass them as parameters:
def main():
with open('file1.txt', 'r') as myfile:
with open('positive_results_sequences.txt', 'a') as my_new_file:
for k,v in zip(site_id_list):
get_fasta(v, myfile, my_new_file)
Related
I need to define a fucntion that will, in short:
Open and grab the content from an existing file
Transform that content
Create a new file
Write that new content in this new file
Print the content of the new file
I'm a complete begginer, but I got this until now. How can I improve this?
def text():
#open the existing file
text_file = open('music.txt', 'r')
#reads the file
reading = text_file.read ()
#this turns everything to lower case, counts the words and displays the list vertically
from collections import Counter
new_text = reading.lower()
list_words = Counter(new_text.split())
ordered_list = sorted(list_words.items())
#creates a new file and writes the content there
with open('finheiro_saida.txt', 'x') as final_file:
for i in ordem:
finheiro_saida.write(str(i) + '\n')
#not sure how to open this new file and print its content, when I tried it says the new file doesn't exist in the directory - tried everything.
final = open('C:/Users/maria/OneDrive/Documents/SD_DTM/ficheiro_saida.txt', 'r')
read_file = final.read ()
print(read_file)
You can open the new file and print its content the same way you read and wrote to it!
# ...After all your previous code...
with open('finheiro_saida.txt', 'r') as final_file:
final_file_content = final_file.read()
print(final_file_content)
Fixed some syntax error in your code.
you can display the the same way you read.
Also provide all imports to the start of the file.
you can also read all lines from the file as a list using file.readlines()
from collections import Counter
def text():
# open the existing file
text_file = open("music.txt", "r")
# reads the file
reading = text_file.read()
# this turns everything to lower case, counts the words and displays the list vertically
new_text = reading.lower()
list_words = Counter(new_text.split())
ordered_list = sorted(list_words.items())
# creates a new file and writes the content there
file_name = "finheiro_saida.txt"
with open("finheiro_saida.txt", "x") as final_file:
for i in ordered_list:
final_file.write(str(i) + "\n")
return file_name
def display(final_file_name):
with open(final_file_name) as file:
print(file.read())
final_file_name = text()
display(final_file_name)
Here below is my code about how to edit text file.
Since python can't just edit a line and save it at the same time,
I save the previous text file's content into a list first then write it out.
For example,if there are two text files called sample1.txt and sample2.txt in the same folder.
Sample1.txt
A for apple.
Second line.
Third line.
Sample2.txt
First line.
An apple a day.
Third line.
Execute python
import glob
import os
#search all text files which are in the same folder with python script
path = os.path.dirname(os.path.abspath(__file__))
txtlist = glob.glob(path + '\*.txt')
for file in txtlist:
fp1 = open(file, 'r+')
strings = [] #create a list to store the content
for line in fp1:
if 'apple' in line:
strings.append('banana\n') #change the content and store into list
else:
strings.append(line) #store the contents did not be changed
fp2 = open (file, 'w+') # rewrite the original text files
for line in strings:
fp2.write(line)
fp1.close()
fp2.close()
Sample1.txt
banana
Second line.
Third line.
Sample2.txt
First line.
banana
Third line.
That's how I edit specific line for text file.
My question is : Is there any method can do the same thing?
Like using the other functions or using the other data type rather than list.
Thank you everyone.
Simplify it to this:
with open(fname) as f:
content = f.readlines()
content = ['banana' if line.find('apple') != -1 else line for line in content]
and then write value of content to file back.
Instead of putting all the lines in a list and writing it, you can read it into memory, replace, and write it using same file.
def replace_word(filename):
with open(filename, 'r') as file:
data = file.read()
data = data.replace('word1', 'word2')
with open(filename, 'w') as file:
file.write(data)
Then you can loop through all of your files and apply this function
The built-in fileinput module makes this quite simple:
import fileinput
import glob
with fileinput.input(files=glob.glob('*.txt'), inplace=True) as files:
for line in files:
if 'apple' in line:
print('banana')
else:
print(line, end='')
fileinput redirects print into the active file.
import glob
import os
def replace_line(file_path, replace_table: dict) -> None:
list_lines = []
need_rewrite = False
with open(file_path, 'r') as f:
for line in f:
flag_rewrite = False
for key, new_val in replace_table.items():
if key in line:
list_lines.append(new_val+'\n')
flag_rewrite = True
need_rewrite = True
break # only replace first find the words.
if not flag_rewrite:
list_lines.append(line)
if not need_rewrite:
return
with open(file_path, 'w') as f:
[f.write(line) for line in list_lines]
if __name__ == '__main__':
work_dir = os.path.dirname(os.path.abspath(__file__))
txt_list = glob.glob(work_dir + '/*.txt')
replace_dict = dict(apple='banana', orange='grape')
for txt_path in txt_list:
replace_line(txt_path, replace_dict)
I am unable to write the result of the following code to a file
import boto3
ACCESS_KEY= "XXX"
SECRET_KEY= "XXX"
regions = ['us-east-1','us-west-1','us-west-2','eu-west-1','sa-east-1','ap-southeast-1','ap-southeast-2','ap-northeast-1']
for region in regions:
client = boto3.client('ec2',aws_access_key_id=ACCESS_KEY,aws_secret_access_key=SECRET_KEY,region_name=region,)
addresses_dict = client.describe_addresses()
#f = open('/root/temps','w')
for eip_dict in addresses_dict['Addresses']:
with open('/root/temps', 'w') as f:
if 'PrivateIpAddress' in eip_dict:
print eip_dict['PublicIp']
f.write(eip_dict['PublicIp'])
This results in printing the IP's but nothing gets written in file, the result of print is :
22.1.14.1
22.1.15.1
112.121.41.41
....
I just need to write the content in this format only
for eip_dict in addresses_dict['Addresses']:
with open('/root/temps', 'w') as f:
if 'PrivateIpAddress' in eip_dict:
print eip_dict['PublicIp']
f.write(eip_dict['PublicIp'])
You are re-opening the file for writing at each iteration of the loop. Perhaps the last iteration has no members with 'PrivateIpAddress' in its dict, so the file gets opened, truncated, and left empty. Write it this way instead:
with open('/root/temps', 'w') as f:
for eip_dict in addresses_dict['Addresses']:
if 'PrivateIpAddress' in eip_dict:
print eip_dict['PublicIp']
f.write(eip_dict['PublicIp'])
open file in append mode
with open('/root/temps', 'a') as f:
or
declare the file outside the loop
I'm trying to make a code to rewrite a specific line from a .txt file.
I can get to write in the line i want, but i can't erase the previous text on the line.
Here is my code:
(i'm trying a couple of things)
def writeline(file,n_line, text):
f=open(file,'r+')
count=0
for line in f:
count=count+1
if count==n_line :
f.write(line.replace(str(line),text))
#f.write('\r'+text)
You can use this code to make a test file for testing:
with open('writetest.txt','w') as f:
f.write('1 \n2 \n3 \n4 \n5')
writeline('writetest.txt',4,'This is the fourth line')
Edit: For Some reason, if i use 'if count==5:' the code compiles ok (even if it doen't erase the previous text), but if i do 'if count==n_line: ', the file ends up with a lot of garbage.
The Answers work, but i would like to know what are the problems with my code, and why i can't read and write. Thanks!
You are reading from the file and also writing to it. Don't do that. Instead, you should write to a NamedTemporaryFile and then rename it over the original file after you finish writing and close it.
Or if the size of the file is guaranteed to be small, you can use readlines() to read all of it, then close the file, modify the line you want, and write it back out:
def editline(file,n_line,text):
with open(file) as infile:
lines = infile.readlines()
lines[n_line] = text+' \n'
with open(file, 'w') as outfile:
outfile.writelines(lines)
Use temporary file:
import os
import shutil
def writeline(filename, n_line, text):
tmp_filename = filename + ".tmp"
count = 0
with open(tmp_filename, 'wt') as tmp:
with open(filename, 'rt') as src:
for line in src:
count += 1
if count == n_line:
line = line.replace(str(line), text + '\n')
tmp.write(line)
shutil.copy(tmp_filename, filename)
os.remove(tmp_filename)
def create_test(fname):
with open(fname,'w') as f:
f.write('1 \n2 \n3 \n4 \n5')
if __name__ == "__main__":
create_test('writetest.txt')
writeline('writetest.txt', 4, 'This is the fourth line')
I've seen really complex answers on this website as how to edit a specific line on a file but I was wondering if there was a simple way to do it?
I want to search for a name in a file, and on the line that I find that name on, I want to add an integer to the end of the line (as it is a score for a quiz). Or could you tell me how I can replace the entirety of the line with new data?
I have tried a lot of coding but either no change is made, or all of the data in the file gets deleted.
I tried this....
with open ('File.py', 'r') as class_file:
for number, line in enumerate(class_file):
if name in line:
s=open('File.py', 'r').readlines()
s[number]=str(data)
class_file=open('File.py', 'w')
class_file.writelines(new_score)
class_file.close()
As well as this function....
def replace (file, line_number, add_score):
s=open(file, 'w')
new_data=line[line_number].replace(line, add_score)
s.write(str(new_data))
s.close()
As well as this...
def replace_score(file_name, line_num, text):
new = open(file_name, 'r').readlines()
new[line_num] = text
adding_score= open(file_name, 'w')
adding_score.writelines(new)
adding_score.close()
But I still can't get it to work.
The last code works if I'm trying to replace the first line, but not the others.
You need to get the content of the file. Close the file. Modify the content and rewrite the file with the modified content. Try the following:
def replace_score(file_name, line_num, text):
f = open(file_name, 'r')
contents = f.readlines()
f.close()
contents[line_num] = text+"\n"
f = open(file_name, "w")
contents = "".join(contents)
f.write(contents)
f.close()
replace_score("file_path", 10, "replacing_text")
This is Tim Osadchiy's code:
def replace_score(file_name, line_num, text):
f = open(file_name, 'r')
contents = f.readlines()
f.close()
contents[line_num] = text+"\n"
f = open(file_name, "w")
contents = "".join(contents)
f.write(contents)
f.close()
replace_score("file_path", 10, "replacing_text")
This code does work but just remember that the line_num will always be one above the actual line number (as it is an index). So if you wanted line 9 then enter 8, not 9. Also, do not forget to put .txt at the end of the file path (I would've commented but do not have a high enough reputation)