Parsing a text file in python and outputting to a CSV - python

Preface - I'm pretty new to Python, having had more experience in another language.
I have a text file with single column list of strings in the generic (but slightly varying) format "./abc123a1/type/1ab2_x_data_type.file.type"
I need to extract the abc123a1 and the 1ab2 portions from all several hundred of the rows and put them under two columns (column a and b) in a csv. Sometimes there may be a "1ab2_a" and a "1ab2_b", but I only want one 1ab2. So I'd want to grab "1ab2_a" and ignore all others.
I have the regex which I THINK will work:
tmp = list()
if re.findall(re.compile(r'^([a-zA-Z0-9]{4})_'), x):
tmp = re.findall(re.compile(r'^([a-zA-Z0-9]{4})_'), x)
elif re.findall(re.compile(r'_([a-zA-Z0-9]{4})_'), x):
tmp = re.findall(re.compile(r'_([a-zA-Z0-9]{4})_'), x)
if len(tmp) == 0:
return None
elif len(tmp) > 1:
print "ERROR found multiple matches"
return "ERROR"
else:
return tmp[0].upper()
I am trying to make this script step by step and testing things to make sure it works, but it's just not.
import sys
import csv
listOfData = []
with open(sys.argv[1]) as f:
print "yes"
for line in f:
print line
for line in f:
listOfData.append([line])
print listOfData
with open('extracted.csv', 'w') as out_file:
writer = csv.writer(out_file)
writer.writerow(('column a', 'column b'))
writer.writerows(listOfData)
print listOfData
Still failing to get anything in the csv other than column headers, much less a parsed version!
Does anyone have any better ideas or formats I could do this in? A friend mentioned looking into glob.glob, but I haven't had luck getting that to work either.

IMHO, you were not far from making it work. The problem is that you read once the whole file just to print the lines, and then (once at end of file) you try to put them into a list... and get an empty list !
You should read the file only once:
import sys
import csv
listOfData = []
with open(sys.argv[1]) as f:
print "yes"
for line in f:
print line
listOfData.append([line])
print listOfData
with open('extracted.csv', 'w') as out_file:
writer = csv.writer(out_file)
writer.writerow(('column a', 'column b'))
writer.writerows(listOfData)
print listOfData
once it works, you still have to use the regex to get relevant data to put into the csv file

I am not sure about your regex (it will most probably not work) , but the reason why your current (non-regex , simple) code does not work is because -
with open(sys.argv[1]) as f:
print "yes"
for line in f:
print line
for line in f:
listOfData.append([line])
As you can see you are first iterating over each line in file and printing it, it should be fine, but after the loop ends, the file pointer is at the end of file, so trying to iterate over it again , would not produce any result. You should only iterate over it once, and do both printing and appending to list in it. Example -
with open(sys.argv[1]) as f:
print "yes"
for line in f:
print line
listOfData.append([line])

I think at least part of the problem is the two for loops in the following:
with open(sys.argv[1]) as f:
print "yes"
for line in f:
print line
for line in f:
listOfData.append([line])
The first one prints all the lines of f, so there's nothing left for the second one to iterate over unless you first f.seek(0) and rewind the file.
An alternative way would to simply to this:
with open(sys.argv[1]) as f:
print "yes"
for line in f:
print line
listOfData.append([line])
It's hard to tell if your regexes are OK without more than one line of sample input data.

Are you sure you need all of the regular expressions? You seem to be parsing a list of paths and filenames. The path could be split up using a split command, for example:
print "./abc123a1/type/1ab2_a_data_type.file.type".split("/")
Would give:
['.', 'abc123a1', 'type', '1ab2_a_data_type.file.type']
You could then create a set consisting of the second entry and up to the '_' in forth entry, e.g.
('abc123a1', '1ab2')
This could then be used to print only the first entry from each:
pairs = set()
with open(sys.argv[1], 'r') as in_file, open('extracted.csv', 'wb') as out_file:
writer = csv.writer(out_file)
for row in in_file:
folders = row.split("/")
col_a = folders[1]
col_b = folders[3].split("_")[0]
if (col_a, col_b) not in pairs:
pairs.add((col_a, col_b))
writer.writerow([col_a, col_b])
So for an input looking like this:
./abc123a1/type/1ab2_a_data_type.file.type
./abc123a1/type/1ab2_b_data_type.file.type
./abc123a2/type/1ab2_a_data_type.file.type
./abc123a3/type/1ab2_a_data_type.file.type
You would get a CSV file looking like:
abc123a1,1ab2
abc123a2,1ab2
abc123a3,1ab2

Related

Python: How to delete line from text file [duplicate]

Let's say I have a text file full of nicknames. How can I delete a specific nickname from this file, using Python?
First, open the file and get all your lines from the file. Then reopen the file in write mode and write your lines back, except for the line you want to delete:
with open("yourfile.txt", "r") as f:
lines = f.readlines()
with open("yourfile.txt", "w") as f:
for line in lines:
if line.strip("\n") != "nickname_to_delete":
f.write(line)
You need to strip("\n") the newline character in the comparison because if your file doesn't end with a newline character the very last line won't either.
Solution to this problem with only a single open:
with open("target.txt", "r+") as f:
d = f.readlines()
f.seek(0)
for i in d:
if i != "line you want to remove...":
f.write(i)
f.truncate()
This solution opens the file in r/w mode ("r+") and makes use of seek to reset the f-pointer then truncate to remove everything after the last write.
The best and fastest option, rather than storing everything in a list and re-opening the file to write it, is in my opinion to re-write the file elsewhere.
with open("yourfile.txt", "r") as file_input:
with open("newfile.txt", "w") as output:
for line in file_input:
if line.strip("\n") != "nickname_to_delete":
output.write(line)
That's it! In one loop and one only you can do the same thing. It will be much faster.
This is a "fork" from #Lother's answer (which I believe that should be considered the right answer).
For a file like this:
$ cat file.txt
1: october rust
2: november rain
3: december snow
This fork from Lother's solution works fine:
#!/usr/bin/python3.4
with open("file.txt","r+") as f:
new_f = f.readlines()
f.seek(0)
for line in new_f:
if "snow" not in line:
f.write(line)
f.truncate()
Improvements:
with open, which discard the usage of f.close()
more clearer if/else for evaluating if string is not present in the current line
The issue with reading lines in first pass and making changes (deleting specific lines) in the second pass is that if you file sizes are huge, you will run out of RAM. Instead, a better approach is to read lines, one by one, and write them into a separate file, eliminating the ones you don't need. I have run this approach with files as big as 12-50 GB, and the RAM usage remains almost constant. Only CPU cycles show processing in progress.
I liked the fileinput approach as explained in this answer:
Deleting a line from a text file (python)
Say for example I have a file which has empty lines in it and I want to remove empty lines, here's how I solved it:
import fileinput
import sys
for line_number, line in enumerate(fileinput.input('file1.txt', inplace=1)):
if len(line) > 1:
sys.stdout.write(line)
Note: The empty lines in my case had length 1
If you use Linux, you can try the following approach.
Suppose you have a text file named animal.txt:
$ cat animal.txt
dog
pig
cat
monkey
elephant
Delete the first line:
>>> import subprocess
>>> subprocess.call(['sed','-i','/.*dog.*/d','animal.txt'])
then
$ cat animal.txt
pig
cat
monkey
elephant
Probably, you already got a correct answer, but here is mine.
Instead of using a list to collect unfiltered data (what readlines() method does), I use two files. One is for hold a main data, and the second is for filtering the data when you delete a specific string. Here is a code:
main_file = open('data_base.txt').read() # your main dataBase file
filter_file = open('filter_base.txt', 'w')
filter_file.write(main_file)
filter_file.close()
main_file = open('data_base.txt', 'w')
for line in open('filter_base'):
if 'your data to delete' not in line: # remove a specific string
main_file.write(line) # put all strings back to your db except deleted
else: pass
main_file.close()
Hope you will find this useful! :)
I think if you read the file into a list, then do the you can iterate over the list to look for the nickname you want to get rid of. You can do it much efficiently without creating additional files, but you'll have to write the result back to the source file.
Here's how I might do this:
import, os, csv # and other imports you need
nicknames_to_delete = ['Nick', 'Stephen', 'Mark']
I'm assuming nicknames.csv contains data like:
Nick
Maria
James
Chris
Mario
Stephen
Isabella
Ahmed
Julia
Mark
...
Then load the file into the list:
nicknames = None
with open("nicknames.csv") as sourceFile:
nicknames = sourceFile.read().splitlines()
Next, iterate over to list to match your inputs to delete:
for nick in nicknames_to_delete:
try:
if nick in nicknames:
nicknames.pop(nicknames.index(nick))
else:
print(nick + " is not found in the file")
except ValueError:
pass
Lastly, write the result back to file:
with open("nicknames.csv", "a") as nicknamesFile:
nicknamesFile.seek(0)
nicknamesFile.truncate()
nicknamesWriter = csv.writer(nicknamesFile)
for name in nicknames:
nicknamesWriter.writeRow([str(name)])
nicknamesFile.close()
In general, you can't; you have to write the whole file again (at least from the point of change to the end).
In some specific cases you can do better than this -
if all your data elements are the same length and in no specific order, and you know the offset of the one you want to get rid of, you could copy the last item over the one to be deleted and truncate the file before the last item;
or you could just overwrite the data chunk with a 'this is bad data, skip it' value or keep a 'this item has been deleted' flag in your saved data elements such that you can mark it deleted without otherwise modifying the file.
This is probably overkill for short documents (anything under 100 KB?).
I like this method using fileinput and the 'inplace' method:
import fileinput
for line in fileinput.input(fname, inplace =1):
line = line.strip()
if not 'UnwantedWord' in line:
print(line)
It's a little less wordy than the other answers and is fast enough for
Save the file lines in a list, then remove of the list the line you want to delete and write the remain lines to a new file
with open("file_name.txt", "r") as f:
lines = f.readlines()
lines.remove("Line you want to delete\n")
with open("new_file.txt", "w") as new_f:
for line in lines:
new_f.write(line)
here's some other method to remove a/some line(s) from a file:
src_file = zzzz.txt
f = open(src_file, "r")
contents = f.readlines()
f.close()
contents.pop(idx) # remove the line item from list, by line number, starts from 0
f = open(src_file, "w")
contents = "".join(contents)
f.write(contents)
f.close()
You can use the re library
Assuming that you are able to load your full txt-file. You then define a list of unwanted nicknames and then substitute them with an empty string "".
# Delete unwanted characters
import re
# Read, then decode for py2 compat.
path_to_file = 'data/nicknames.txt'
text = open(path_to_file, 'rb').read().decode(encoding='utf-8')
# Define unwanted nicknames and substitute them
unwanted_nickname_list = ['SourDough']
text = re.sub("|".join(unwanted_nickname_list), "", text)
Do you want to remove a specific line from file so use this snippet short and simple code you can easily remove any line with sentence or prefix(Symbol).
with open("file_name.txt", "r") as f:
lines = f.readlines()
with open("new_file.txt", "w") as new_f:
for line in lines:
if not line.startswith("write any sentence or symbol to remove line"):
new_f.write(line)
To delete a specific line of a file by its line number:
Replace variables filename and line_to_delete with the name of your file and the line number you want to delete.
filename = 'foo.txt'
line_to_delete = 3
initial_line = 1
file_lines = {}
with open(filename) as f:
content = f.readlines()
for line in content:
file_lines[initial_line] = line.strip()
initial_line += 1
f = open(filename, "w")
for line_number, line_content in file_lines.items():
if line_number != line_to_delete:
f.write('{}\n'.format(line_content))
f.close()
print('Deleted line: {}'.format(line_to_delete))
Example output:
Deleted line: 3
Take the contents of the file, split it by newline into a tuple. Then, access your tuple's line number, join your result tuple, and overwrite to the file.

Open and Read a CSV File without libraries

I have the following problem. I am supposed to open a CSV file (its an excel table) and read it without using any library.
I tried already a lot and have now the first row in a tuple and this in a list. But only the first line. The header. But no other row.
This is what I have so far.
with open(path, 'r+') as file:
results=[]
text = file.readline()
while text != '':
for line in text.split('\n'):
a=line.split(',')
b=tuple(a)
results.append(b)
return results
The output should: be every line in a tuple and all the tuples in a list.
My question is now, how can I read the other lines in python?
I am really sorry, I am new to programming all together and so I have a real hard time finding my mistake.
Thank you very much in advance for helping me out!
This problem was many times on Stackoverflow so you should find working code.
But much better is to use module csv for this.
You have wrong indentation and you use return results after reading first line so it exits function and it never try read other lines.
But after changing this there are still other problems so it still will not read next lines.
You use readline() so you read only first line and your loop will works all time with the same line - and maybe it will never ends because you never set text = ''
You should use read() to get all text which later you split to lines using split("\n") or you could use readlines() to get all lines as list and then you don't need split(). OR you can use for line in file: In all situations you don't need while
def read_csv(path):
with open(path, 'r+') as file:
results = []
text = file.read()
for line in text.split('\n'):
items = line.split(',')
results.append(tuple(items))
# after for-loop
return results
def read_csv(path):
with open(path, 'r+') as file:
results = []
lines = file.readlines()
for line in lines:
line = line.rstrip('\n') # remove `\n` at the end of line
items = line.split(',')
results.append(tuple(items))
# after for-loop
return results
def read_csv(path):
with open(path, 'r+') as file:
results = []
for line in file:
line = line.rstrip('\n') # remove `\n` at the end of line
items = line.split(',')
results.append(tuple(items))
# after for-loop
return results
All this version will not work correctly if you will '\n' or , inside item which shouldn't be treated as end of row or as separtor between items. These items will be in " " which also can make problem to remove them. All these problem you can resolve using standard module csv.
Your code is pretty well and you are near goal:
with open(path, 'r+') as file:
results=[]
text = file.read()
#while text != '':
for line in text.split('\n'):
a=line.split(',')
b=tuple(a)
results.append(b)
return results
Your Code:
with open(path, 'r+') as file:
results=[]
text = file.readline()
while text != '':
for line in text.split('\n'):
a=line.split(',')
b=tuple(a)
results.append(b)
return results
So enjoy learning :)
One caveat is that the csv may not end with a blank line as this would result in an ugly tuple at the end of the list like ('',) (Which looks like a smiley)
To prevent this you have to check for empty lines: if line != '': after the for will do the trick.

Find unique entries in files

guess you have a solution concerning the following issue:
I want to compare two lists for common entries (on the basis of column 10) and write common entries to one file and unique entries for the first list into another file. The code I wrote is:
INFILE1 = open ("c:\\python\\test\\58962.filtered.csv", "r")
INFILE2 = open ("c:\\python\\test\\83887.filtered.csv", "r")
OUTFILE1 = open ("c:\\python\\test\\58962_vs_83887.common.csv", "w")
OUTFILE2 = open ("c:\\python\\test\\58962_vs_83887.unique.csv", "w")
for line in INFILE1:
line = line.rstrip().split(",")
if line[11] in INFILE2:
OUTFILE1.write(line)
else:
OUTFILE2.write(line)
INFILE1.close()
INFILE2.close()
OUTFILE1.close()
OUTFILE2.close()
The following error appears:
8 OUTFILE1.write(line)
9 else:
---> 10 OUTFILE2.write(line)
11 INFILE1.close()
TypeError: write() argument must be str, not list
Does somebody know about help for this?
Best
This line
line = line.rstrip().split(",")
replaces the line you read from a file by it's splitted list. You then try to write the splitted list to your file - thats not how the write method works and it tells you exactly that.
Change it to :
for line in INFILE1:
lineList = line.rstrip().split(",") # dont overwrite line, use lineList
if lineList[11] in INFILE2: # used lineList
OUTFILE1.write(line) # corrected indentation
else:
OUTFILE2.write(line)
You could have easily found your error yourself, just printing out the line before and after splitting or just befrore writing.
Please read How to debug small programs (#1) and follow it - its easier to find and fix bugs yourself then posting questions here.
You have some other problem at hand, though:
Files are stream based, they start with a position of 0 in the file. The position is advanced if you access parts of the file. When at the end, you wont get anything by using INFILE2.read() or other methods.
So if you want to repeatadly check if some lines column of file1 is somewhere in file2 you need to read file2 into a list (or other datastructure) so your repeated checks work. In other words, this:
if lineList[11] in INFILE2:
might work once, then the file is consumed and it will return false all the time.
You also might want to change from:
f = open(...., ...)
# do something with f
f.close()
to
with open(name,"r") as f:
# do something with f, no close needed, closed when leaving block
as it is safer, will close the file even if exceptions happen.
To solve that try this (untested) code:
with open ("c:\\python\\test\\83887.filtered.csv", "r") as file2:
infile2 = file2.readlines() # read in all lines as list
with open ("c:\\python\\test\\58962.filtered.csv", "r") as INFILE1:
# next 2 lines are 1 line, \ at end signifies line continues
with open ("c:\\python\\test\\58962_vs_83887.common.csv", "w") as OUTFILE1, \
with open ("c:\\python\\test\\58962_vs_83887.unique.csv", "w") as OUTFILE2:
for line in INFILE1:
lineList = line.rstrip().split(",")
if any(lineList[11] in x for x in infile2): # check the list of lines if
# any contains line[11]
OUTFILE1.write(line)
else:
OUTFILE2.write(line)
# all files are autoclosed here
Links to read:
the-with-statement
any() and other built-ins

python: Open file, edit one line, save it as the same file

I want to open a file, search for a specific word, change the word and save the file again. Sounds really easy - but I just can't get it working... I know that I have to overwrite the whole file but only change this one word!
My Code:
f = open('./myfile', 'r')
linelist = f.readlines()
f.close
for line in linelist:
i =0;
if 'word' in line:
for number in arange(0,1,0.1)):
myNumber = 2 - number
myNumberasString = str(myNumber)
myChangedLine = line.replace('word', myNumberasString)
f2 = open('./myfile', 'w')
f2.write(line)
f2.close
#here I have to do some stuff with these files so there is a reason
#why everything is in this for loop. And I know that it will
#overwrite the file every loop and that is good so. I want that :)
If I make it like this, the 'new' myfile file contains only the changed line. But I want the whole file with the changed line... Can anyone help me?
****EDIT*****
I fixed it! I just turned the loops around and now it works perfectly like this:
f=open('myfile','r')
text = f.readlines()
f.close()
i =0;
for number in arange(0,1,0.1):
fw=open('mynewfile', 'w')
myNumber = 2 - number
myNumberasString = str(myNumber)
for line in text:
if 'word' in line:
line = line.replace('word', myNumberasString)
fw.write(line)
fw.close()
#do my stuff here where I need all these input files
You just need to write out all the other lines as you go. As I said in my comment, I don't know what you are really trying to do with your replace, but here's a slightly simplified version in which we're just replacing all occurrences of 'word' with 'new':
f = open('./myfile', 'r')
linelist = f.readlines()
f.close
# Re-open file here
f2 = open('./myfile', 'w')
for line in linelist:
line = line.replace('word', 'new')
f2.write(line)
f2.close()
Or using contexts:
with open('./myfile', 'r') as f:
lines = f.readlines()
with open('./myfile', 'w') as f:
for line in lines:
line = line.replace('word', 'new')
f.write(line)
Use fileinput passing in whatever you want to replace:
import fileinput
for line in fileinput.input("in.txt",inplace=True):
print(line.replace("whatever","foo"),end="")
You don't seem to be doing anything special in your loop that cannot be calculated first outside the loop, so create the string you want to replace the word with and pass it to replace.
inplace=True will mean the original file is changed. If you want to verify everything looks ok then remove the inplace=True for the first run and you will actually see the replaced output instead of the lines being written to the file.
If you want to write to a temporary file, you can use a NamedTemporaryFile with shutil.move:
from tempfile import NamedTemporaryFile
from shutil import move
with open("in.txt") as f, NamedTemporaryFile(dir=".",delete=False) as out:
for line in f:
out.write(line.replace("whatever","foo"))
move("in.txt",out.name)
One problem you may encounter is matching substrings with replace so if you know the word is always followed in the middle of a sentence surrounded by whitespace you could add that but if not you will need to split and check every word.
from tempfile import NamedTemporaryFile
from shutil import move
from string import punctuation
with open("in.txt") as f, NamedTemporaryFile(dir=".",delete=False) as out:
for line in f:
out.write(" ".join(word if word.strip(punctuation) != "whatever" else "foo"
for word in line.split()))
The are three issues with your current code. First, create the f2 file handle before starting the loop, otherwise you'll overwrite the file in each iteration. Third, you are writing an unmodified line in f2.write(line). I guess you meant f2.write(myChangedLine)? Third, you should add an else statement that writes unmodified lines to the file. So:
f = open('./myfile', 'r')
linelist = f.readlines()
f.close
f2 = open('./myfile', 'w')
for line in linelist:
i =0;
if 'word' in line:
for number in arange(0,1,0.1)):
myNumber = 2 - number
myNumberasString = str(myNumber)
myChangedLine = line.replace('word', myNumberasString)
f2.write(myChangedLine)
else:
f2.write(line)
f2.close()

Python- How to Remove Columns from a File

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')])

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