Related
I have a problem reading characters from a file. I have a file called fst.fasta and I want to know the number of occurrences of the letters A and T.
This is the first code sample :
f = open("fst.fasta","r")
a = f.read().count("A")
t = f.read().count("T")
print "nbr de A : ", a
print "nbr de T : ", t
The result:
nbr of A : 255
nbr of T : 0
Even if there are Ts i get always 0
But after that, I tried this :
f = open("fst.fasta","r")
a = f.read().count("A")
f = open("fst.fasta","r")
t = f.read().count("T")
print "nbr de A : ", a
print "nbr de T : ", t
This worked! Is there any other way to avoid repeating f = open("fst.fasta","r") ?
You're dealing with the fact that read() has a side effect (to use the term really loosely): it reads through the file and as it does so sets a pointer to where it is in that file. When it returns you can expect that pointer to be set to the last position. Therefore, executing read() again starts from that position and doesn't give you anything back. This is what you want:
f = open("fst.fasta","r")
contents = f.read()
a = contents.count("A")
t = contents.count("T")
The documentation also indicates other ways you can use read:
next_value = f.read(1)
if next_value == "":
# We have reached the end of the file
What has happened in the code above is that, instead of getting all the characters in the file, the file handler has only returned 1 character. You could replace 1 with any number, or even a variable to get a certain chunk of the file. The file handler remembers where the above-mentioned pointer is, and you can pick up where you left off. (Note that this is a really good idea for very large files, where reading it all into memory is prohibitive.)
Only once you call f.close() does the file handler 'forget' where it is - but it also forgets the file, and you'd have to open() it again to start from the beginning.
There are other functions provided (such as seek() and readline()) that will let you move around a file using different semantics. f.tell() will tell you where the pointer is in the file currently.
Each time you call f.read(), it consumes the entire remaining contents of the file and returns it. You then use that data only to count the as, and then attempt to read the data thats already been used. There are two solutions"
Option 1: Use f.seek(0)
a = f.read().count("A")
f.seek(0)
t = f.read().count("T")
The f.seek call sets the psoition of the file back to the beginning.
Option 2. Store the result of f.read():
data = f.read()
a = data.count("A")
t = data.count("T")
f.seek(0) before the second f.read() will reset the file pointer to the beginning of the file. Or more sanely, save the result of f.read() to a variable, and you can then call .count on that variable to your heart's content without rereading the file pointlessly.
Try the with construct:
with open("fst.fasta","r") as f:
file_as_string = f.read()
a = file_as_string.count("A")
t = file_as_string.count("T")
This keeps the file open until you exit the block.
Read it into a string:
f = open ("fst.fasta")
allLines = f.readlines()
f.close()
# At this point, you are no longer using the file handler.
for line in allLines:
print (line.count("A"), " ", line.count("T"))
Is there a way to do this? Say I have a file that's a list of names that goes like this:
Alfred
Bill
Donald
How could I insert the third name, "Charlie", at line x (in this case 3), and automatically send all others down one line? I've seen other questions like this, but they didn't get helpful answers. Can it be done, preferably with either a method or a loop?
This is a way of doing the trick.
with open("path_to_file", "r") as f:
contents = f.readlines()
contents.insert(index, value)
with open("path_to_file", "w") as f:
contents = "".join(contents)
f.write(contents)
index and value are the line and value of your choice, lines starting from 0.
If you want to search a file for a substring and add a new text to the next line, one of the elegant ways to do it is the following:
import os, fileinput
old = "A"
new = "B"
for line in fileinput.FileInput(file_path, inplace=True):
if old in line :
line += new + os.linesep
print(line, end="")
There is a combination of techniques which I found useful in solving this issue:
with open(file, 'r+') as fd:
contents = fd.readlines()
contents.insert(index, new_string) # new_string should end in a newline
fd.seek(0) # readlines consumes the iterator, so we need to start over
fd.writelines(contents) # No need to truncate as we are increasing filesize
In our particular application, we wanted to add it after a certain string:
with open(file, 'r+') as fd:
contents = fd.readlines()
if match_string in contents[-1]: # Handle last line to prevent IndexError
contents.append(insert_string)
else:
for index, line in enumerate(contents):
if match_string in line and insert_string not in contents[index + 1]:
contents.insert(index + 1, insert_string)
break
fd.seek(0)
fd.writelines(contents)
If you want it to insert the string after every instance of the match, instead of just the first, remove the else: (and properly unindent) and the break.
Note also that the and insert_string not in contents[index + 1]: prevents it from adding more than one copy after the match_string, so it's safe to run repeatedly.
You can just read the data into a list and insert the new record where you want.
names = []
with open('names.txt', 'r+') as fd:
for line in fd:
names.append(line.split(' ')[-1].strip())
names.insert(2, "Charlie") # element 2 will be 3. in your list
fd.seek(0)
fd.truncate()
for i in xrange(len(names)):
fd.write("%d. %s\n" %(i + 1, names[i]))
The accepted answer has to load the whole file into memory, which doesn't work nicely for large files. The following solution writes the file contents with the new data inserted into the right line to a temporary file in the same directory (so on the same file system), only reading small chunks from the source file at a time. It then overwrites the source file with the contents of the temporary file in an efficient way (Python 3.8+).
from pathlib import Path
from shutil import copyfile
from tempfile import NamedTemporaryFile
sourcefile = Path("/path/to/source").resolve()
insert_lineno = 152 # The line to insert the new data into.
insert_data = "..." # Some string to insert.
with sourcefile.open(mode="r") as source:
destination = NamedTemporaryFile(mode="w", dir=str(sourcefile.parent))
lineno = 1
while lineno < insert_lineno:
destination.file.write(source.readline())
lineno += 1
# Insert the new data.
destination.file.write(insert_data)
# Write the rest in chunks.
while True:
data = source.read(1024)
if not data:
break
destination.file.write(data)
# Finish writing data.
destination.flush()
# Overwrite the original file's contents with that of the temporary file.
# This uses a memory-optimised copy operation starting from Python 3.8.
copyfile(destination.name, str(sourcefile))
# Delete the temporary file.
destination.close()
EDIT 2020-09-08: I just found an answer on Code Review that does something similar to above with more explanation - it might be useful to some.
You don't show us what the output should look like, so one possible interpretation is that you want this as the output:
Alfred
Bill
Charlie
Donald
(Insert Charlie, then add 1 to all subsequent lines.) Here's one possible solution:
def insert_line(input_stream, pos, new_name, output_stream):
inserted = False
for line in input_stream:
number, name = parse_line(line)
if number == pos:
print >> output_stream, format_line(number, new_name)
inserted = True
print >> output_stream, format_line(number if not inserted else (number + 1), name)
def parse_line(line):
number_str, name = line.strip().split()
return (get_number(number_str), name)
def get_number(number_str):
return int(number_str.split('.')[0])
def format_line(number, name):
return add_dot(number) + ' ' + name
def add_dot(number):
return str(number) + '.'
input_stream = open('input.txt', 'r')
output_stream = open('output.txt', 'w')
insert_line(input_stream, 3, 'Charlie', output_stream)
input_stream.close()
output_stream.close()
Parse the file into a python list using file.readlines() or file.read().split('\n')
Identify the position where you have to insert a new line, according to your criteria.
Insert a new list element there using list.insert().
Write the result to the file.
location_of_line = 0
with open(filename, 'r') as file_you_want_to_read:
#readlines in file and put in a list
contents = file_you_want_to_read.readlines()
#find location of what line you want to insert after
for index, line in enumerate(contents):
if line.startswith('whatever you are looking for')
location_of_line = index
#now you have a list of every line in that file
context.insert(location_of_line, "whatever you want to append to middle of file")
with open(filename, 'w') as file_to_write_to:
file_to_write_to.writelines(contents)
That is how I ended up getting whatever data I want to insert to the middle of the file.
this is just pseudo code, as I was having a hard time finding clear understanding of what is going on.
essentially you read in the file to its entirety and add it into a list, then you insert your lines that you want to that list, and then re-write to the same file.
i am sure there are better ways to do this, may not be efficient, but it makes more sense to me at least, I hope it makes sense to someone else.
A simple but not efficient way is to read the whole content, change it and then rewrite it:
line_index = 3
lines = None
with open('file.txt', 'r') as file_handler:
lines = file_handler.readlines()
lines.insert(line_index, 'Charlie')
with open('file.txt', 'w') as file_handler:
file_handler.writelines(lines)
I write this in order to reutilize/correct martincho's answer (accepted one)
! IMPORTANT: This code loads all the file into ram and rewrites content to the file
Variables index, value may be what you desire, but pay attention to making value string and end with '\n' if you don't want it to mess with existing data.
with open("path_to_file", "r+") as f:
# Read the content into a variable
contents = f.readlines()
contents.insert(index, value)
# Reset the reader's location (in bytes)
f.seek(0)
# Rewrite the content to the file
f.writelines(contents)
See the python docs about file.seek method: Python docs
Below is a slightly awkward solution for the special case in which you are creating the original file yourself and happen to know the insertion location (e.g. you know ahead of time that you will need to insert a line with an additional name before the third line, but won't know the name until after you've fetched and written the rest of the names). Reading, storing and then re-writing the entire contents of the file as described in other answers is, I think, more elegant than this option, but may be undesirable for large files.
You can leave a buffer of invisible null characters ('\0') at the insertion location to be overwritten later:
num_names = 1_000_000 # Enough data to make storing in a list unideal
max_len = 20 # The maximum allowed length of the inserted line
line_to_insert = 2 # The third line is at index 2 (0-based indexing)
with open(filename, 'w+') as file:
for i in range(line_to_insert):
name = get_name(i) # Returns 'Alfred' for i = 0, etc.
file.write(F'{i + 1}. {name}\n')
insert_position = file.tell() # Position to jump back to for insertion
file.write('\0' * max_len + '\n') # Buffer will show up as a blank line
for i in range(line_to_insert, num_names):
name = get_name(i)
file.write(F'{i + 2}. {name}\n') # Line numbering now bumped up by 1.
# Later, once you have the name to insert...
with open(filename, 'r+') as file: # Must use 'r+' to write to middle of file
file.seek(insert_position) # Move stream to the insertion line
name = get_bonus_name() # This lucky winner jumps up to 3rd place
new_line = F'{line_to_insert + 1}. {name}'
file.write(new_line[:max_len]) # Slice so you don't overwrite next line
Unfortunately there is no way to delete-without-replacement any excess null characters that did not get overwritten (or in general any characters anywhere in the middle of a file), unless you then re-write everything that follows. But the null characters will not affect how your file looks to a human (they have zero width).
i = 1 # keep track of file number
directory = '/some/directory/'
for i in range(1, 5170): #number of files in directory
filename = directory + 'D' + str(i) + '.txt'
input = open(filename)
output = open('output.txt', 'w')
input.readline() #ignore first line
for g in range(0, 7): #write next seven lines to output.txt
output.write(input.readline())
output.write('\n') #add newline to avoid mess
output.close()
input.close()
i = i + 1
I have this code, and i am trying to get one file and rewrite it to output.txt, but when i want to attach next file, my code overwrite older file that has been attached. In result when code is complete i have something like this:
dataA[5169]=26
dataB[5169]=0
dataC[5169]=y
dataD[5169]='something'
dataE[5169]=x
data_date[5169]=2012.06.02
Instead of datas ranging from files 0 to 5169. Any tips how to fix it?
You probably want to open output.txt before your for loop (and close it after). As it is written, you overwrite the file output.txt everytime you open it. (an alternative would be to open for appending: output = open('output.txt','a'), but that's definitely not the best way to do it here ...
Of course, these days it's better to use a context manager (with statement):
i = 1 # keep track of file number <-- This line is useless in the code you posted
directory = '/some/directory/' #<-- os.path.join is better for this stuff.
with open('output.txt','w') as output:
for i in range(1, 5170): #number of files in directory
filename = directory + 'D' + str(i) + '.txt'
with open(filename) as input:
input.readline() #ignore first line
for g in range(0, 7): #write next seven lines to output.txt
output.write(input.readline())
output.write('\n') #add newline to avoid mess
i = i + 1 #<---also useless line in the code you posted
Your issue is that you open in write mode. To append to file you want to use append. See here.
Is there a way to do this? Say I have a file that's a list of names that goes like this:
Alfred
Bill
Donald
How could I insert the third name, "Charlie", at line x (in this case 3), and automatically send all others down one line? I've seen other questions like this, but they didn't get helpful answers. Can it be done, preferably with either a method or a loop?
This is a way of doing the trick.
with open("path_to_file", "r") as f:
contents = f.readlines()
contents.insert(index, value)
with open("path_to_file", "w") as f:
contents = "".join(contents)
f.write(contents)
index and value are the line and value of your choice, lines starting from 0.
If you want to search a file for a substring and add a new text to the next line, one of the elegant ways to do it is the following:
import os, fileinput
old = "A"
new = "B"
for line in fileinput.FileInput(file_path, inplace=True):
if old in line :
line += new + os.linesep
print(line, end="")
There is a combination of techniques which I found useful in solving this issue:
with open(file, 'r+') as fd:
contents = fd.readlines()
contents.insert(index, new_string) # new_string should end in a newline
fd.seek(0) # readlines consumes the iterator, so we need to start over
fd.writelines(contents) # No need to truncate as we are increasing filesize
In our particular application, we wanted to add it after a certain string:
with open(file, 'r+') as fd:
contents = fd.readlines()
if match_string in contents[-1]: # Handle last line to prevent IndexError
contents.append(insert_string)
else:
for index, line in enumerate(contents):
if match_string in line and insert_string not in contents[index + 1]:
contents.insert(index + 1, insert_string)
break
fd.seek(0)
fd.writelines(contents)
If you want it to insert the string after every instance of the match, instead of just the first, remove the else: (and properly unindent) and the break.
Note also that the and insert_string not in contents[index + 1]: prevents it from adding more than one copy after the match_string, so it's safe to run repeatedly.
You can just read the data into a list and insert the new record where you want.
names = []
with open('names.txt', 'r+') as fd:
for line in fd:
names.append(line.split(' ')[-1].strip())
names.insert(2, "Charlie") # element 2 will be 3. in your list
fd.seek(0)
fd.truncate()
for i in xrange(len(names)):
fd.write("%d. %s\n" %(i + 1, names[i]))
The accepted answer has to load the whole file into memory, which doesn't work nicely for large files. The following solution writes the file contents with the new data inserted into the right line to a temporary file in the same directory (so on the same file system), only reading small chunks from the source file at a time. It then overwrites the source file with the contents of the temporary file in an efficient way (Python 3.8+).
from pathlib import Path
from shutil import copyfile
from tempfile import NamedTemporaryFile
sourcefile = Path("/path/to/source").resolve()
insert_lineno = 152 # The line to insert the new data into.
insert_data = "..." # Some string to insert.
with sourcefile.open(mode="r") as source:
destination = NamedTemporaryFile(mode="w", dir=str(sourcefile.parent))
lineno = 1
while lineno < insert_lineno:
destination.file.write(source.readline())
lineno += 1
# Insert the new data.
destination.file.write(insert_data)
# Write the rest in chunks.
while True:
data = source.read(1024)
if not data:
break
destination.file.write(data)
# Finish writing data.
destination.flush()
# Overwrite the original file's contents with that of the temporary file.
# This uses a memory-optimised copy operation starting from Python 3.8.
copyfile(destination.name, str(sourcefile))
# Delete the temporary file.
destination.close()
EDIT 2020-09-08: I just found an answer on Code Review that does something similar to above with more explanation - it might be useful to some.
You don't show us what the output should look like, so one possible interpretation is that you want this as the output:
Alfred
Bill
Charlie
Donald
(Insert Charlie, then add 1 to all subsequent lines.) Here's one possible solution:
def insert_line(input_stream, pos, new_name, output_stream):
inserted = False
for line in input_stream:
number, name = parse_line(line)
if number == pos:
print >> output_stream, format_line(number, new_name)
inserted = True
print >> output_stream, format_line(number if not inserted else (number + 1), name)
def parse_line(line):
number_str, name = line.strip().split()
return (get_number(number_str), name)
def get_number(number_str):
return int(number_str.split('.')[0])
def format_line(number, name):
return add_dot(number) + ' ' + name
def add_dot(number):
return str(number) + '.'
input_stream = open('input.txt', 'r')
output_stream = open('output.txt', 'w')
insert_line(input_stream, 3, 'Charlie', output_stream)
input_stream.close()
output_stream.close()
Parse the file into a python list using file.readlines() or file.read().split('\n')
Identify the position where you have to insert a new line, according to your criteria.
Insert a new list element there using list.insert().
Write the result to the file.
location_of_line = 0
with open(filename, 'r') as file_you_want_to_read:
#readlines in file and put in a list
contents = file_you_want_to_read.readlines()
#find location of what line you want to insert after
for index, line in enumerate(contents):
if line.startswith('whatever you are looking for')
location_of_line = index
#now you have a list of every line in that file
context.insert(location_of_line, "whatever you want to append to middle of file")
with open(filename, 'w') as file_to_write_to:
file_to_write_to.writelines(contents)
That is how I ended up getting whatever data I want to insert to the middle of the file.
this is just pseudo code, as I was having a hard time finding clear understanding of what is going on.
essentially you read in the file to its entirety and add it into a list, then you insert your lines that you want to that list, and then re-write to the same file.
i am sure there are better ways to do this, may not be efficient, but it makes more sense to me at least, I hope it makes sense to someone else.
A simple but not efficient way is to read the whole content, change it and then rewrite it:
line_index = 3
lines = None
with open('file.txt', 'r') as file_handler:
lines = file_handler.readlines()
lines.insert(line_index, 'Charlie')
with open('file.txt', 'w') as file_handler:
file_handler.writelines(lines)
I write this in order to reutilize/correct martincho's answer (accepted one)
! IMPORTANT: This code loads all the file into ram and rewrites content to the file
Variables index, value may be what you desire, but pay attention to making value string and end with '\n' if you don't want it to mess with existing data.
with open("path_to_file", "r+") as f:
# Read the content into a variable
contents = f.readlines()
contents.insert(index, value)
# Reset the reader's location (in bytes)
f.seek(0)
# Rewrite the content to the file
f.writelines(contents)
See the python docs about file.seek method: Python docs
Below is a slightly awkward solution for the special case in which you are creating the original file yourself and happen to know the insertion location (e.g. you know ahead of time that you will need to insert a line with an additional name before the third line, but won't know the name until after you've fetched and written the rest of the names). Reading, storing and then re-writing the entire contents of the file as described in other answers is, I think, more elegant than this option, but may be undesirable for large files.
You can leave a buffer of invisible null characters ('\0') at the insertion location to be overwritten later:
num_names = 1_000_000 # Enough data to make storing in a list unideal
max_len = 20 # The maximum allowed length of the inserted line
line_to_insert = 2 # The third line is at index 2 (0-based indexing)
with open(filename, 'w+') as file:
for i in range(line_to_insert):
name = get_name(i) # Returns 'Alfred' for i = 0, etc.
file.write(F'{i + 1}. {name}\n')
insert_position = file.tell() # Position to jump back to for insertion
file.write('\0' * max_len + '\n') # Buffer will show up as a blank line
for i in range(line_to_insert, num_names):
name = get_name(i)
file.write(F'{i + 2}. {name}\n') # Line numbering now bumped up by 1.
# Later, once you have the name to insert...
with open(filename, 'r+') as file: # Must use 'r+' to write to middle of file
file.seek(insert_position) # Move stream to the insertion line
name = get_bonus_name() # This lucky winner jumps up to 3rd place
new_line = F'{line_to_insert + 1}. {name}'
file.write(new_line[:max_len]) # Slice so you don't overwrite next line
Unfortunately there is no way to delete-without-replacement any excess null characters that did not get overwritten (or in general any characters anywhere in the middle of a file), unless you then re-write everything that follows. But the null characters will not affect how your file looks to a human (they have zero width).
I'd like to remove the first column from a file. The file contains 3 columns separated by space and the columns has the following titles:
X', 'Displacement' and 'Force' (Please see the image).
I have came up with the following code, but to my disappointment it doesn't work!
f = open("datafile.txt", 'w')
for line in f:
line = line.split()
del x[0]
f.close()
Any help is much appreciated !
Esan
First of all, you're attempting to read from a file (by iterating through the file contents) that is open for writing. This will give you an IOError.
Second, there is no variable named x in existence (you have not declared/set one in the script). This will generate a NameError.
Thirdly and finally, once you have finished (correctly) reading and editing the columns in your file, you will need to write the data back into the file.
To avoid loading a (potentially large) file into memory all at once, it is probably a good idea to read from one file (line by line) and write to a new file simultaneously.
Something like this might work:
f = open("datafile.txt", "r")
g = open("datafile_fixed.txt", "w")
for line in f:
if line.strip():
g.write("\t".join(line.split()[1:]) + "\n")
f.close()
g.close()
Some reading about python i/o might be helpful, but something like the following should get you on your feet:
with open("datafile.txt", "r") as fin:
with open("outputfile.txt", "w") as fout:
for line in fin:
line = line.split(' ')
if len(line) == 3:
del line[0]
fout.write(line[0] + ' ' + line[1])
else:
fout.write('\n')
EDIT: fixed to work with blank lines
print ''.join([' '.join(l.split()[1:]) for l in file('datafile.txt')])
or, if you want to preserve spaces and you know that the second column always starts at the, say, 10th character:
print ''.join([l[11:] for l in file('datafile.txt')])