I'm new to Python, and I need to do a parsing exercise. I got a file, and I need to parse it (just the headers), but after the process, i need to keep the file the same format, the same extension, and at the same place in disk, but only with the differences of new headers..
I tried this code...
for line in open ('/home/name/db/str/dir/numbers/str.phy'):
if line.startswith('ENS'):
linepars = re.sub ('ENS([A-Z]+)0+([0-9]{6})','\\1\\2',line)
print linepars
..and it does the job, but I don't know how to "overwrite" the file with the new parsing.
The easiest way, but not the most efficient (by far, and especially for long files) would be to rewrite the complete file.
You could do this by opening a second file handle and rewriting each line, except in the case of the header, you'd write the parsed header. For example,
fr = open('/home/name/db/str/dir/numbers/str.phy')
fw = open('/home/name/db/str/dir/numbers/str.phy.parsed', 'w') # Name this whatever makes sense
for line in fr:
if line.startswith('ENS'):
linepars = re.sub ('ENS([A-Z]+)0+([0-9]{6})','\\1\\2',line)
fw.write(linepars)
else:
fw.write(line)
fw.close()
fr.close()
EDIT: Note that this does not use readlines(), so its more memory efficient. It also does not store every output line, but only one at a time, writing it to file immediately.
Just as a cool trick, you could use the with statement on the input file to avoid having to close it (Python 2.5+):
fw = open('/home/name/db/str/dir/numbers/str.phy.parsed', 'w') # Name this whatever makes sense
with open('/home/name/db/str/dir/numbers/str.phy') as fr:
for line in fr:
if line.startswith('ENS'):
linepars = re.sub ('ENS([A-Z]+)0+([0-9]{6})','\\1\\2',line)
fw.write(linepars)
else:
fw.write(line)
fw.close()
P.S. Welcome :-)
As others are saying here, you want to open a file and use that file object's .write() method.
The best approach would be to open an additional file for writing:
import os
current_cfg = open(...)
parsed_cfg = open(..., 'w')
for line in current_cfg:
new_line = parse(line)
print new_line
parsed.cfg.write(new_line + '\n')
current_cfg.close()
parsed_cfg.close()
os.rename(....) # Rename old file to backup name
os.rename(....) # Rename new file into place
Additionally I'd suggest looking at the tempfile module and use one of its methods for either naming your new file or opening/creating it. Personally I'd favor putting the new file in the same directory as the existing file to ensure that os.rename will work atomically (the configuration file named will be guaranteed to either point at the old file or the new file; in no case would it point at a partially written/copied file).
The following code DOES the job.
I mean it DOES overwrite the file ON ONESELF; that's what the OP asked for. That's possible because the transformations are only removing characters, so the file's pointer fo that writes is always BEHIND the file's pointer fi that reads.
import re
regx = re.compile('\AENS([A-Z]+)0+([0-9]{6})')
with open('bomo.phy','rb+') as fi, open('bomo.phy','rb+') as fo:
fo.writelines(regx.sub('\\1\\2',line) for line in fi)
I think that the writing isn't performed by the operating system one line at a time but through a buffer. So several lines are read before a pool of transformed lines are written. That's what I think.
newlines = []
for line in open ('/home/name/db/str/dir/numbers/str.phy').readlines():
if line.startswith('ENS'):
linepars = re.sub ('ENS([A-Z]+)0+([0-9]{6})','\\1\\2',line)
newlines.append( linepars )
open ('/home/name/db/str/dir/numbers/str.phy', 'w').write('\n'.join(newlines))
(sidenote: Of course if you are working with large files, you should be aware that the level of optimization required may depend on your situation. Python by nature is very non-lazily-evaluated. The following solution is not a good choice if you are parsing large files, such as database dumps or logs, but a few tweaks such as nesting the with clauses and using lazy generators or a line-by-line algorithm can allow O(1)-memory behavior.)
targetFile = '/home/name/db/str/dir/numbers/str.phy'
def replaceIfHeader(line):
if line.startswith('ENS'):
return re.sub('ENS([A-Z]+)0+([0-9]{6})','\\1\\2',line)
else:
return line
with open(targetFile, 'r') as f:
newText = '\n'.join(replaceIfHeader(line) for line in f)
try:
# make backup of targetFile
with open(targetFile, 'w') as f:
f.write(newText)
except:
# error encountered, do something to inform user where backup of targetFile is
edit: thanks to Jeff for suggestion
Related
Started Python a week ago and I have some questions to ask about reading and writing to the same files. I've gone through some tutorials online but I am still confused about it. I can understand simple read and write files.
openFile = open("filepath", "r")
readFile = openFile.read()
print readFile
openFile = open("filepath", "a")
appendFile = openFile.write("\nTest 123")
openFile.close()
But, if I try the following I get a bunch of unknown text in the text file I am writing to. Can anyone explain why I am getting such errors and why I cannot use the same openFile object the way shown below.
# I get an error when I use the codes below:
openFile = open("filepath", "r+")
writeFile = openFile.write("Test abc")
readFile = openFile.read()
print readFile
openFile.close()
I will try to clarify my problems. In the example above, openFile is the object used to open file. I have no problems if I want write to it the first time. If I want to use the same openFile to read files or append something to it. It doesn't happen or an error is given. I have to declare the same/different open file object before I can perform another read/write action to the same file.
#I have no problems if I do this:
openFile = open("filepath", "r+")
writeFile = openFile.write("Test abc")
openFile2 = open("filepath", "r+")
readFile = openFile2.read()
print readFile
openFile.close()
I will be grateful if anyone can tell me what I did wrong here or is it just a Pythong thing. I am using Python 2.7. Thanks!
Updated Response:
This seems like a bug specific to Windows - http://bugs.python.org/issue1521491.
Quoting from the workaround explained at http://mail.python.org/pipermail/python-bugs-list/2005-August/029886.html
the effect of mixing reads with writes on a file open for update is
entirely undefined unless a file-positioning operation occurs between
them (for example, a seek()). I can't guess what
you expect to happen, but seems most likely that what you
intend could be obtained reliably by inserting
fp.seek(fp.tell())
between read() and your write().
My original response demonstrates how reading/writing on the same file opened for appending works. It is apparently not true if you are using Windows.
Original Response:
In 'r+' mode, using write method will write the string object to the file based on where the pointer is. In your case, it will append the string "Test abc" to the start of the file. See an example below:
>>> f=open("a","r+")
>>> f.read()
'Test abc\nfasdfafasdfa\nsdfgsd\n'
>>> f.write("foooooooooooooo")
>>> f.close()
>>> f=open("a","r+")
>>> f.read()
'Test abc\nfasdfafasdfa\nsdfgsd\nfoooooooooooooo'
The string "foooooooooooooo" got appended at the end of the file since the pointer was already at the end of the file.
Are you on a system that differentiates between binary and text files? You might want to use 'rb+' as a mode in that case.
Append 'b' to the mode to open the file in binary mode, on systems
that differentiate between binary and text files; on systems that
don’t have this distinction, adding the 'b' has no effect.
http://docs.python.org/2/library/functions.html#open
Every open file has an implicit pointer which indicates where data will be read and written. Normally this defaults to the start of the file, but if you use a mode of a (append) then it defaults to the end of the file. It's also worth noting that the w mode will truncate your file (i.e. delete all the contents) even if you add + to the mode.
Whenever you read or write N characters, the read/write pointer will move forward that amount within the file. I find it helps to think of this like an old cassette tape, if you remember those. So, if you executed the following code:
fd = open("testfile.txt", "w+")
fd.write("This is a test file.\n")
fd.close()
fd = open("testfile.txt", "r+")
print fd.read(4)
fd.write(" IS")
fd.close()
... It should end up printing This and then leaving the file content as This IS a test file.. This is because the initial read(4) returns the first 4 characters of the file, because the pointer is at the start of the file. It leaves the pointer at the space character just after This, so the following write(" IS") overwrites the next three characters with a space (the same as is already there) followed by IS, replacing the existing is.
You can use the seek() method of the file to jump to a specific point. After the example above, if you executed the following:
fd = open("testfile.txt", "r+")
fd.seek(10)
fd.write("TEST")
fd.close()
... Then you'll find that the file now contains This IS a TEST file..
All this applies on Unix systems, and you can test those examples to make sure. However, I've had problems mixing read() and write() on Windows systems. For example, when I execute that first example on my Windows machine then it correctly prints This, but when I check the file afterwards the write() has been completely ignored. However, the second example (using seek()) seems to work fine on Windows.
In summary, if you want to read/write from the middle of a file in Windows I'd suggest always using an explicit seek() instead of relying on the position of the read/write pointer. If you're doing only reads or only writes then it's pretty safe.
One final point - if you're specifying paths on Windows as literal strings, remember to escape your backslashes:
fd = open("C:\\Users\\johndoe\\Desktop\\testfile.txt", "r+")
Or you can use raw strings by putting an r at the start:
fd = open(r"C:\Users\johndoe\Desktop\testfile.txt", "r+")
Or the most portable option is to use os.path.join():
fd = open(os.path.join("C:\\", "Users", "johndoe", "Desktop", "testfile.txt"), "r+")
You can find more information about file IO in the official Python docs.
Reading and Writing happens where the current file pointer is and it advances with each read/write.
In your particular case, writing to the openFile, causes the file-pointer to point to the end of file. Trying to read from the end would result EOF.
You need to reset the file pointer, to point to the beginning of the file before through seek(0) before reading from it
You can read, modify and save to the same file in python but you have actually to replace the whole content in file, and to call before updating file content:
# set the pointer to the beginning of the file in order to rewrite the content
edit_file.seek(0)
I needed a function to go through all subdirectories of folder and edit content of the files based on some criteria, if it helps:
new_file_content = ""
for directories, subdirectories, files in os.walk(folder_path):
for file_name in files:
file_path = os.path.join(directories, file_name)
# open file for reading and writing
with io.open(file_path, "r+", encoding="utf-8") as edit_file:
for current_line in edit_file:
if condition in current_line:
# update current line
current_line = current_line.replace('john', 'jack')
new_file_content += current_line
# set the pointer to the beginning of the file in order to rewrite the content
edit_file.seek(0)
# delete actual file content
edit_file.truncate()
# rewrite updated file content
edit_file.write(new_file_content)
# empties new content in order to set for next iteration
new_file_content = ""
edit_file.close()
I am a newbie to python. I have a code in which I must write the contents again to my same file,but when I do it it clears my content.Please help to fix it.
How should I modify my code such that the contents will be written back on the same file?
My code:
import re
numbers = {}
with open('1.txt') as f,open('11.txt', 'w') as f1:
for line in f:
row = re.split(r'(\d+)', line.strip())
words = tuple(row[::2])
if words not in numbers:
numbers[words] = [int(n) for n in row[1::2]]
numbers[words] = [n+1 for n in numbers[words]]
row[1::2] = map(str, numbers[words])
indentation = (re.match(r"\s*", line).group())
print (indentation + ''.join(row))
f1.write(indentation + ''.join(row) + '\n')
In general, it's a bad idea to write over a file you're still processing (or change a data structure over which you are iterating). It can be done...but it requires much care, and there is little safety or restart-ability should something go wrong in the middle (an error, a power failure, etc.)
A better approach is to write a clean new file, then rename it to the old name. For example:
import re
import os
filename = '1.txt'
tempname = "temp{0}_{1}".format(os.getpid(), filename)
numbers = {}
with open(filename) as f, open(tempname, 'w') as f1:
# ... file processing as before
os.rename(tempname, filename)
Here I've dropped filenames (both original and temporary) into variables, so they can be easily referred to multiple times or changed. This also prepares for the moment when you hoist this code into a function (as part of a larger program), as opposed to making it the main line of your program.
You don't strictly need the temporary name to embed the process id, but it's a standard way of making sure the temp file is uniquely named (temp32939_1.txt vs temp_1.txt or tempfile.txt, say).
It may also be helpful to create backups of the files as they were before processing. In which case, before the os.rename(tempname, filename) you can drop in code to move the original data to a safer location or a backup name. E.g.:
backupname = filename + ".bak"
os.rename(filename, backupname)
os.rename(tempname, filename)
While beyond the scope of this question, if you used a read-process-overwrite strategy frequently, it would be possible to create a separate module that abstracted these file-handling details away from your processing code. Here is an example.
Use
open('11.txt', 'a')
To append to the file instead of w for writing (a new or overwriting a file).
If you want to read and modify file in one time use "r+' mode.
f=file('/path/to/file.txt', 'r+')
content=f.read()
content=content.replace('oldstring', 'newstring') #for example change some substring in whole file
f.seek(0) #move to beginning of file
f.write(content)
f.truncate() #clear file conent "tail" on disk if new content shorter then old
f.close()
Started Python a week ago and I have some questions to ask about reading and writing to the same files. I've gone through some tutorials online but I am still confused about it. I can understand simple read and write files.
openFile = open("filepath", "r")
readFile = openFile.read()
print readFile
openFile = open("filepath", "a")
appendFile = openFile.write("\nTest 123")
openFile.close()
But, if I try the following I get a bunch of unknown text in the text file I am writing to. Can anyone explain why I am getting such errors and why I cannot use the same openFile object the way shown below.
# I get an error when I use the codes below:
openFile = open("filepath", "r+")
writeFile = openFile.write("Test abc")
readFile = openFile.read()
print readFile
openFile.close()
I will try to clarify my problems. In the example above, openFile is the object used to open file. I have no problems if I want write to it the first time. If I want to use the same openFile to read files or append something to it. It doesn't happen or an error is given. I have to declare the same/different open file object before I can perform another read/write action to the same file.
#I have no problems if I do this:
openFile = open("filepath", "r+")
writeFile = openFile.write("Test abc")
openFile2 = open("filepath", "r+")
readFile = openFile2.read()
print readFile
openFile.close()
I will be grateful if anyone can tell me what I did wrong here or is it just a Pythong thing. I am using Python 2.7. Thanks!
Updated Response:
This seems like a bug specific to Windows - http://bugs.python.org/issue1521491.
Quoting from the workaround explained at http://mail.python.org/pipermail/python-bugs-list/2005-August/029886.html
the effect of mixing reads with writes on a file open for update is
entirely undefined unless a file-positioning operation occurs between
them (for example, a seek()). I can't guess what
you expect to happen, but seems most likely that what you
intend could be obtained reliably by inserting
fp.seek(fp.tell())
between read() and your write().
My original response demonstrates how reading/writing on the same file opened for appending works. It is apparently not true if you are using Windows.
Original Response:
In 'r+' mode, using write method will write the string object to the file based on where the pointer is. In your case, it will append the string "Test abc" to the start of the file. See an example below:
>>> f=open("a","r+")
>>> f.read()
'Test abc\nfasdfafasdfa\nsdfgsd\n'
>>> f.write("foooooooooooooo")
>>> f.close()
>>> f=open("a","r+")
>>> f.read()
'Test abc\nfasdfafasdfa\nsdfgsd\nfoooooooooooooo'
The string "foooooooooooooo" got appended at the end of the file since the pointer was already at the end of the file.
Are you on a system that differentiates between binary and text files? You might want to use 'rb+' as a mode in that case.
Append 'b' to the mode to open the file in binary mode, on systems
that differentiate between binary and text files; on systems that
don’t have this distinction, adding the 'b' has no effect.
http://docs.python.org/2/library/functions.html#open
Every open file has an implicit pointer which indicates where data will be read and written. Normally this defaults to the start of the file, but if you use a mode of a (append) then it defaults to the end of the file. It's also worth noting that the w mode will truncate your file (i.e. delete all the contents) even if you add + to the mode.
Whenever you read or write N characters, the read/write pointer will move forward that amount within the file. I find it helps to think of this like an old cassette tape, if you remember those. So, if you executed the following code:
fd = open("testfile.txt", "w+")
fd.write("This is a test file.\n")
fd.close()
fd = open("testfile.txt", "r+")
print fd.read(4)
fd.write(" IS")
fd.close()
... It should end up printing This and then leaving the file content as This IS a test file.. This is because the initial read(4) returns the first 4 characters of the file, because the pointer is at the start of the file. It leaves the pointer at the space character just after This, so the following write(" IS") overwrites the next three characters with a space (the same as is already there) followed by IS, replacing the existing is.
You can use the seek() method of the file to jump to a specific point. After the example above, if you executed the following:
fd = open("testfile.txt", "r+")
fd.seek(10)
fd.write("TEST")
fd.close()
... Then you'll find that the file now contains This IS a TEST file..
All this applies on Unix systems, and you can test those examples to make sure. However, I've had problems mixing read() and write() on Windows systems. For example, when I execute that first example on my Windows machine then it correctly prints This, but when I check the file afterwards the write() has been completely ignored. However, the second example (using seek()) seems to work fine on Windows.
In summary, if you want to read/write from the middle of a file in Windows I'd suggest always using an explicit seek() instead of relying on the position of the read/write pointer. If you're doing only reads or only writes then it's pretty safe.
One final point - if you're specifying paths on Windows as literal strings, remember to escape your backslashes:
fd = open("C:\\Users\\johndoe\\Desktop\\testfile.txt", "r+")
Or you can use raw strings by putting an r at the start:
fd = open(r"C:\Users\johndoe\Desktop\testfile.txt", "r+")
Or the most portable option is to use os.path.join():
fd = open(os.path.join("C:\\", "Users", "johndoe", "Desktop", "testfile.txt"), "r+")
You can find more information about file IO in the official Python docs.
Reading and Writing happens where the current file pointer is and it advances with each read/write.
In your particular case, writing to the openFile, causes the file-pointer to point to the end of file. Trying to read from the end would result EOF.
You need to reset the file pointer, to point to the beginning of the file before through seek(0) before reading from it
You can read, modify and save to the same file in python but you have actually to replace the whole content in file, and to call before updating file content:
# set the pointer to the beginning of the file in order to rewrite the content
edit_file.seek(0)
I needed a function to go through all subdirectories of folder and edit content of the files based on some criteria, if it helps:
new_file_content = ""
for directories, subdirectories, files in os.walk(folder_path):
for file_name in files:
file_path = os.path.join(directories, file_name)
# open file for reading and writing
with io.open(file_path, "r+", encoding="utf-8") as edit_file:
for current_line in edit_file:
if condition in current_line:
# update current line
current_line = current_line.replace('john', 'jack')
new_file_content += current_line
# set the pointer to the beginning of the file in order to rewrite the content
edit_file.seek(0)
# delete actual file content
edit_file.truncate()
# rewrite updated file content
edit_file.write(new_file_content)
# empties new content in order to set for next iteration
new_file_content = ""
edit_file.close()
in a py module, I write:
outFile = open(fileName, mode='w')
if A:
outFile.write(...)
if B:
outFile.write(...)
and in these lines, I didn't use flush or close method.
Then after these lines, I want to check whether this "outFile" object is empty or not. How can I do with it?
There are a few problems with your code.
You can't .write to a file that you opened with 'r'. You need to open(fileName, 'w').
If A or B then you've certainly written to the file, so it's not empty!
Barring those. you can get the length of a file with
os.stat(outFile.fileno())
EDIT: I'll explain what flush does. Python is often used to do quite large amounts of file reads and writes, which can be slow. It is thus tweaked to make them as fast as possible. One way that is does so is to "buffer" such writes and then do them all in one big block: when you write a small string, Python will remember it but won't actually write it to the file until it thinks it should.
This means that if you want to tell whether you have written data to the file by inspecting the file, you have to tell Python to write all the data it's remembering first, or else you might not see it. flush is the command to write all the buffered data.
Of course, if you ask Python whether it's written anything to the file, say by inspecting the position in the file (.tell()), then it will know about the buffering.
If you've already written to the file, you can use .tell() to check if the current file position is nonzero:
>>> handle = open('/tmp/file.txt', 'w')
>>> handle.write('foo')
>>> handle.tell()
3
This won't work if you .seek() back to the beginning of the file.
You can use os.stat to get file info:
import os
fileSize = os.stat(fileName).st_size
with open("filename.txt", "r+") as f:
if f.read():
# file isn't empty
f.write("something")
# uncomment this line if you want to delete everything else in the file
# f.truncate()
else:
# file is empty
f.write("somethingelse")
"r+" mode always you to read & write.
"with" will automatically close file
Hey I need to split a large file in python into smaller files that contain only specific lines. How do I do this?
You're probably going to want to do something like this:
big_file = open('big_file', 'r')
small_file1 = open('small_file1', 'w')
small_file2 = open('small_file2', 'w')
for line in big_file:
if 'Charlie' in line: small_file1.write(line)
if 'Mark' in line: small_file2.write(line)
big_file.close()
small_file1.close()
small_file2.close()
Opening a file for reading returns an object that allows you to iterate over the lines. You can then check each line (which is just a string of whatever that line contains) for whatever condition you want, then write it to the appropriate file that you opened for writing. It is worth noting that when you open a file with 'w' it will overwrite anything already written to that file. If you want to simply add to the end, you should open it with 'a', to append.
Additionally, if you expect there to be some possibility of error in your reading/writing code, and want to make sure the files are closed, you can use:
with open('big_file', 'r') as big_file:
<do stuff prone to error>
Do you mean breaking it down into subsections? Like if I had a file with chapter 1, chapter 2, and chapter 3, you want it to be broken down into separate files for each chapter?
The way I've done this is similar to Wilduck's response, but closes the input file as soon as it reads in the data and keeps all the lines read in.
data_file = open('large_file_name', 'r')
lines = data_file.readlines()
data_file.close()
outputFile = open('output_file_one', 'w')
for line in lines:
if 'SomeName' in line:
outputFile.write(line)
outputFile.close()
If you wanted to have more than one output file you could either add more loops or open more than one outputFile at a time.
I'd recommend using Wilducks response, however, as it uses less space and will take less time with larger files since the file is read only once.
How big and does it need to be done in python? If this is on unix, would split/csplit/grep suffice?
First, open the big file for reading.
Second, open all the smaller file names for writing.
Third, iterate through every line. Every iteration, check to see what kind of line it is, then write it to that file.
More info on File I/O: http://docs.python.org/tutorial/inputoutput.html