I have multiple text files containing different text.
They all contain a single appearance of the same 2 lines I am interested in:
================================================================
Result: XX/100
I am trying to write a script to collect all those XX values (numerical values between 0 and 100), and paste them in a CSV file with the text file name in column A and the numerical value in column B.
I have considered using Python or PowerShell for this purpose.
How can I identify the line where "Result" appears under the string of "===..", collect its content until '\n', and then strip it from "Result: " and "/100"?
"Result" and other numerical values could appear in the files, but never in the quoted format, and below "=====", like the line im interested in.
Thank you!
Edit: I have written this poor naive attempt to collect the numerical values.
import os
dir_path = os.path.dirname(os.path.realpath(__file__))
for filename in os.listdir(dir_path):
if filename.endswith(".txt"):
with open(filename,"r") as f:
lineFound=False
for index, line in enumerate(f):
if lineFound:
line=line.replace("Result: ", "")
line=line.replace("/100","")
line.strip()
grade=line
lineFound=False
print(grade, end='')
continue
if index>3:
if "================================================================" in line:
lineFound=True
I'd still be happy to learn if there's a simple way to do this with PowerShell tbh
For the output, I used csv writer to append the results to a file one by one.
So there's two steps involved here, first is to get a list of files. There's a ton of answers for that one on stackoverflow, but this one is stupidly complete.
Once you have the list of files, you can simply just load the files themselves one by one, and then do some simple string.split() to get the value you want.
Finally, write the results into a CSV file. Since the CSV file is a simple one, you don't need to use the CSV library for this.
See the code example below. Note that I copied/pasted the function for generating the list of files from my personal github repo. I reuse that one a lot.
import os
def get_files_from_path(path: str = ".", ext:str or list=None) -> list:
"""Find files in path and return them as a list.
Gets all files in folders and subfolders
See the answer on the link below for a ridiculously
complete answer for this.
https://stackoverflow.com/a/41447012/9267296
Args:
path (str, optional): Which path to start on.
Defaults to '.'.
ext (str/list, optional): Optional file extention.
Defaults to None.
Returns:
list: list of file paths
"""
result = []
for subdir, dirs, files in os.walk(path):
for fname in files:
filepath = f"{subdir}{os.sep}{fname}"
if ext == None:
result.append(filepath)
elif type(ext) == str and fname.lower().endswith(ext.lower()):
result.append(filepath)
elif type(ext) == list:
for item in ext:
if fname.lower().endswith(item.lower()):
result.append(filepath)
return result
filelist = get_files_from_path("path/to/files/", ext=".txt")
split1 = "================================================================\nResult: "
split2 = "/100"
with open("output.csv", "w") as outfile:
outfile.write('filename, value\n')
for filename in filelist:
with open(filename) as infile:
value = infile.read().split(split1)[1].split(split2)[0]
print(value)
outfile.write(f'"{filename}", {value}\n')
You could try this.
In this example the filename written to the CSV will be its full (absolute) path. You may just want the base filename.
Uses the same, albeit seemingly unnecessary, mechanism for deriving the source directory. It would be unusual to have your Python script in the same directory as your data.
import os
import glob
equals = '=' * 64
dir_path = os.path.dirname(os.path.realpath(__file__))
outfile = os.path.join(dir_path, 'foo.csv')
with open(outfile, 'w') as csv:
print('A,B', file=csv)
for file in glob.glob(os.path.join(dir_path, '*.txt')):
prev = None
with open(file) as indata:
for line in indata:
t = line.split()
if len(t) == 2 and t[0] == 'Result:' and prev.startswith(equals):
v = t[1].split('/')
if len(v) == 2 and v[1] == '100':
print(f'{file},{v[0]}', file=csv)
break
prev = line
Related
I have been trying to merge several .csv files form different subfolders (all with the same name) into one. I tried with R but I got the result of not enough memory for carry the process (it should merge more than 20 million of rows). I am now working with a python script to try to get it (see below) it has many columns too so I don't need all of them but also I dont know if can choose which columns to add to the new csv:
import glob
import csv
import os
path= 'C:\\path\\to\\folder\\where\\all\\files\\are-allowated-in-subfolders'
result = glob.glob('*/certificates.csv')
#for i in result:
#full_path = "C:\\path\\to\\folder\\where\\all\\files\\are-allowated-in-subfolders\\" + result
#print(full_path)
os.chdir(path)
i=0
for root, directories, files in os.walk(path, topdown=False):
for name in files:
print(name)
try:
i += 1
if i % 10000 == 0:
#just to see the progress
print(i)
if name == 'certificates.csv':
creader = csv.reader(open(name))
cwriter = csv.writer(open('processed_' + name, 'w'))
for cline in creader:
new_line = [val for col, val in enumerate(cline)]
cwriter.writerow(new_line)
except:
print('problem with file: ' + name)
pass
but it doesn't work, and neither return any error so at the moment I am completely stuck.
Your indentation is wrong, and you are overwriting the output file for each new input file. Also, you are not using the glob result for anything. If the files you want to read are all immediately in subdirectories of path, you can do away with the os.walk() call and do the glob after you os.chdir().
import glob
import csv
import os
# No real need to have a variable for this really
path = 'C:\\path\\to\\folder\\where\\all\\files\\are-allowated-in-subfolders'
os.chdir(path)
# Obviously, can't use input file name in output file name
# because there is only one output file for many input files
with open('processed.csv', 'w') as dest:
cwriter = csv.writer(dest)
for i, name in enumerate(glob.glob('*/certificates.csv'), 1):
if i % 10000 == 0:
#just to see the progress
print(i)
try:
with open(name) as csvin:
creader = csv.reader(csvin)
for cline in creader:
# no need to enumerate fields
cwriter.writerow(cline)
except:
print('problem with file: ' + name)
You probably just need to keep a merged.csv file open whilst reading in each of the certificates.csv files. glob.glob() can be used to recursively find all suitable files:
import glob
import csv
import os
path = r'C:\path\to\folder\where\all\files\are-allowated-in-subfolders'
os.chdir(path)
with open('merged.csv', 'w', newline='') as f_merged:
csv_merged = csv.writer(f_merged)
for filename in glob.glob(os.path.join(path, '*/certificates.csv'), recursive=True):
print(filename)
try:
with open(filename) as f_csv:
csv_merged.writerows(csv.reader(f_csv))
except:
print('problem with file: ', filename)
An r prefix can be added to your path to avoid needing to escape each backslash. Also newline='' should be added to the open() when using a csv.writer() to stop extra blank lines being written to your output file.
I have more than 30 text files. I need to do some processing on each text file and save them again in text files with different names.
Example-1: precise_case_words.txt ---- processing ---- precise_case_sentences.txt
Example-2: random_case_words.txt ---- processing ---- random_case_sentences.txt
Like this i need to do for all text files.
present code:
new_list = []
with open('precise_case_words.txt') as inputfile:
for line in inputfile:
new_list.append(line)
final = open('precise_case_sentences.txt', 'w+')
for item in new_list:
final.write("%s\n" % item)
Am manually copy+paste this code all the times and manually changing the names everytime. Please suggest me a solution to avoid manual job using python.
Suppose you have all your *_case_words.txt in the present dir
import glob
in_file = glob.glob('*_case_words.txt')
prefix = [i.split('_')[0] for i in in_file]
for i, ifile in enumerate(in_file):
data = []
with open(ifile, 'r') as f:
for line in f:
data.append(line)
with open(prefix[i] + '_case_sentence.txt' , 'w') as f:
f.write(data)
This should give you an idea about how to handle it:
def rename(name,suffix):
"""renames a file with one . in it by splitting and inserting suffix before the ."""
a,b = name.split('.')
return ''.join([a,suffix,'.',b]) # recombine parts including suffix in it
def processFn(name):
"""Open file 'name', process it, save it under other name"""
# scramble data by sorting and writing anew to renamed file
with open(name,"r") as r, open(rename(name,"_mang"),"w") as w:
for line in r:
scrambled = ''.join(sorted(line.strip("\n")))+"\n"
w.write(scrambled)
# list of filenames, see link below for how to get them with os.listdir()
names = ['fn1.txt','fn2.txt','fn3.txt']
# create demo data
for name in names:
with open(name,"w") as w:
for i in range(12):
w.write("someword"+str(i)+"\n")
# process files
for name in names:
processFn(name)
For file listings: see How do I list all files of a directory?
I choose to read/write line by line, you can read in one file fully, process it and output it again on block to your liking.
fn1.txt:
someword0
someword1
someword2
someword3
someword4
someword5
someword6
someword7
someword8
someword9
someword10
someword11
into fn1_mang.txt:
0demoorsw
1demoorsw
2demoorsw
3demoorsw
4demoorsw
5demoorsw
6demoorsw
7demoorsw
8demoorsw
9demoorsw
01demoorsw
11demoorsw
I happened just today to be writing some code that does this.
I would run the following code for multiple fastq files in a folder. In a folder I have different fastq files; first I have to read one file and perform the required operations, then store results in a separate file. fastq and then read second file, perform the same operations and save results in new 2nd file.fastq. Repeat the same procedure for all the files in the folder.
How can I do? Can someone suggest me a way to this this?
from Bio.SeqIO.QualityIO import FastqGeneralIterator
fout=open("prova_FiltraN_CE_filt.fastq","w")
fin=open("prova_FiltraN_CE.fastq","rU")
maxN=0
countall=0
countincl=0
with open("prova_FiltraN_CE.fastq", "rU") as handle:
for (title, sequence, quality) in FastqGeneralIterator(handle):
countN = sequence.count("N", 0, len(sequence))
countall+=1
if countN==maxN:
fout.write("#%s\n%s\n+\n%s\n" % (title, sequence, quality))
countincl+=1
fin.close
fout.close
print countall, countincl
I think the following will do what you want. What I did was make your code into a function (and modified it to be what I think is more correct) and then called that function for every .fastq file found in the designated folder. The output file names are generated from the input files found.
from Bio.SeqIO.QualityIO import FastqGeneralIterator
import glob
import os
def process(in_filepath, out_filepath):
maxN = 0
countall = 0
countincl = 0
with open(in_filepath, "rU") as fin:
with open(out_filepath, "w") as fout:
for (title, sequence, quality) in FastqGeneralIterator(fin):
countN = sequence.count("N", 0, len(sequence))
countall += 1
if countN == maxN:
fout.write("#%s\n%s\n+\n%s\n" % (title, sequence, quality))
countincl += 1
print os.path.split(in_filepath)[1], countall, countincl
folder = "/path/to/folder" # folder to process
for in_filepath in glob.glob(os.path.join(folder, "*.fastq")):
root, ext = os.path.splitext(in_filepath)
if not root.endswith("_filt"): # avoid processing existing output files
out_filepath = root + "_filt" + ext
process(in_filepath, out_filepath)
I have a folder with many text files (EPA10.txt, EPA55.txt, EPA120.txt..., EPA150.txt). I have 2 strings that are to be searched in each file and the result of the search is written in a text file result.txt. So far I have it working for a single file. Here is the working code:
if 'LZY_201_335_R10A01' and 'LZY_201_186_R5U01' in open('C:\\Temp\\lamip\\EPA150.txt').read():
with open("C:\\Temp\\lamip\\result.txt", "w") as f:
f.write('Current MW in node is EPA150')
else:
with open("C:\\Temp\\lamip\\result.txt", "w") as f:
f.write('NOT EPA150')
Now I want this to be repeated for all the text files in the folder. Please help.
Given that you have some amount of files named from EPA1.txt to EPA150.txt, but you don't know all the names, you can put them all together inside a folder, then read all the files in that folder using the os.listdir() method to get a list of filenames. You can read the file names using listdir("C:/Temp/lamip").
Also, your if statement is wrong, you should do this instead:
text = file.read()
if "string1" in text and "string2" in text
Here's the code:
from os import listdir
with open("C:/Temp/lamip/result.txt", "w") as f:
for filename in listdir("C:/Temp/lamip"):
with open('C:/Temp/lamip/' + filename) as currentFile:
text = currentFile.read()
if ('LZY_201_335_R10A01' in text) and ('LZY_201_186_R5U01' in text):
f.write('Current MW in node is ' + filename[:-4] + '\n')
else:
f.write('NOT ' + filename[:-4] + '\n')
PS: You can use / instead of \\ in your paths, Python automatically converts them for you.
Modularise! Modularise!
Well, not in the terms of having to write distinct Python modules, but isolate the different tasks at hand.
Find the files you wish to search.
Read the file and locate the text.
Write the result into a separate file.
Each of these tasks can be solved independently. I.e. to list the files, you have os.listdir which you might want to filter.
For step 2, it does not matter whether you have 1 or 1,000 files to search. The routine is the same. You merely have to iterate over each file found in step 1. This indicates that step 2 could be implemented as a function that takes the filename (and possible search-string) as argument, and returns True or False.
Step 3 is the combination of each element from step 1 and the result of step 2.
The result:
files = [fn for fn in os.listdir('C:/Temp/lamip') if fn.endswith('.txt')]
# perhaps filter `files`
def does_fn_contain_string(filename):
with open('C:/Temp/lamip/' + filename) as blargh:
content = blargh.read()
return 'string1' in content and/or 'string2' in content
with open('results.txt', 'w') as output:
for fn in files:
if does_fn_contain_string(fn):
output.write('Current MW in node is {1}\n'.format(fn[:-4]))
else:
output.write('NOT {1}\n'.format(fn[:-4]))
You can do this by creating a for loop that runs through all your .txt files in the current working directory.
import os
with open("result.txt", "w") as resultfile:
for result in [txt for txt in os.listdir(os.getcwd()) if txt.endswith(".txt")]:
if 'LZY_201_335_R10A01' and 'LZY_201_186_R5U01' in open(result).read():
resultfile.write('Current MW in node is {1}'.format(result[:-4]))
else:
resultfile.write('NOT {0}'.format(result[:-4]))
I am writing a Python code and would like some more insight on how to approach this issue.
I am trying to read in multiple files in order that end with .log. With this, I hope to write specific values to a .csv file.
Within the text file, there are X/Y values that are extracted below:
Textfile.log:
X/Y = 5
X/Y = 6
Textfile.log.2:
X/Y = 7
X/Y = 8
DesiredOutput in the CSV file:
5
6
7
8
Here is the code I've come up with so far:
def readfile():
import os
i = 0
for file in os.listdir("\mydir"):
if file.endswith(".log"):
return file
def main ():
import re
list = []
list = readfile()
for line in readfile():
x = re.search(r'(?<=X/Y = )\d+', line)
if x:
list.append(x.group())
else:
break
f = csv.write(open(output, "wb"))
while 1:
if (i>len(list-1)):
break
else:
f.writerow(list(i))
i += 1
if __name__ == '__main__':
main()
I'm confused on how to make it read the .log file, then the .log.2 file.
Is it possible to just have it automatically read all the files in 1 directory without typing them in individually?
Update: I'm using Windows 7 and Python V2.7
The simplest way to read files sequentially is to build a list and then loop over it. Something like:
for fname in list_of_files:
with open(fname, 'r') as f:
#Do all the stuff you do to each file
This way whatever you do to read each file will be repeated and applied to every file in list_of_files. Since lists are ordered, it will occur in the same order as the list is sorted to.
Borrowing from #The2ndSon's answer, you can pick up the files with os.listdir(dir). This will simply list all files and directories within dir in an arbitrary order. From this you can pull out and order all of your files like this:
allFiles = os.listdir(some_dir)
logFiles = [fname for fname in allFiles if "log" in fname.split('.')]
logFiles.sort(key = lambda x: x.split('.')[-1])
logFiles[0], logFiles[-1] = logFiles[-1], logFiles[0]
The above code will work with files name like "somename.log", "somename.log.2" and so on. You can then take logFiles and plug it in as list_of_files. Note that the last line is only necessary if the first file is "somename.log" instead of "somename.log.1". If the first file has a number on the end, just exclude the last step
Line By Line Explanation:
allFiles = os.listdir(some_dir)
This line takes all files and directories within some_dir and returns them as a list
logFiles = [fname for fname in allFiles if "log" in fname.split('.')]
Perform a list comprehension to gather all of the files with log in the name as part of the extension. "something.log.somethingelse" will be included, "log_something.somethingelse" will not.
logFiles.sort(key = lambda x: x.split('.')[-1])
Sort the list of log files in place by the last extension. x.split('.')[-1] splits the file name into a list of period delimited values and takes the last entry. If the name is "name.log.5", it will be sorted as "5". If the name is "name.log", it will be sorted as "log".
logFiles[0], logFiles[-1] = logFiles[-1], logFiles[0]
Swap the first and last entries of the list of log files. This is necessary because the sorting operation will put "name.log" as the last entry and "nane.log.1" as the first.
If you change the naming scheme for your log files you can easily return of list of files that have the ".log" extension. For example if you change the file names to Textfile1.log and Textfile2.log you can update readfile() to be:
import os
def readfile():
my_list = []
for file in os.listdir("."):
if file.endswith(".log"):
my_list.append(file)
print my_list will return ['Textfile1.log', 'Textfile2.log']. Using the word 'list' as a variable is generally avoided, as it is also used to for an object in python.