for x in file.readlines():
something()
I think this code caching all the lines when loop is started. I deleting some of the lines from the file but it still repeating deleted lines. How can I change loop while in it?
def wanted(s,d):
print("deneme = " + str(s))
count = 0
total = 0
TG_count = TC_count = TA_count = GC_count = CC_count = CG_count = GG_count = AA_count = AT_count = TT_count = CT_count = AG_count = AC_count = GT_count = 0
for x in range(d,fileCount):
print(str(x+1) + 'st file processing...')
searchFile = open(str(x) + '.txt',encoding = 'utf-8',mode = "r+")
l = searchFile.readlines()
searchFile.seek(0)
for line in l:
if s in line[:12]:
blabla()
else:
searchFile.write(line)
searchFile.truncate()
searchFile.close()
for p in range(fileCount):
searchFile = open(str(p) + '.txt',encoding = 'utf-8',mode = "r+")
for z in searchFile.readlines():
wanted(z[:12],p)
print("Progressing file " + str(p) + " complete")
I guess it's Python. Yes, readlines() reads the whole file at once. In order to avoid this you can use:
for x in file:
something()
Maybe you can find the appropriate information in the Python tutorial. It says
If you want to read all the lines of a file in a list you can also use list(f) or f.readlines().
So yes, all lines are read and stored in memory.
Also the manual says:
f.readline() reads a single line from the file;
More details can be found in the manual.
Related
points = "temp"
a = "temp"
f = "temp"
def pointincrementer():
global points
points = 0
for line in f:
for word in a:
if word in line:
scorelen = int(len(user+","))
scoreval = line[0:scorelen]
isolatedscore = line.replace(scoreval,'')
if "," in line:
scorestr = isolatedscore.replace(",","")
score = int(scorestr)
points = score + 1
print(points)
def score2():
f = open('test.txt','r')
a = [user]
lst = []
for line in f:
for word in a:
if word in line:
pointincrementer()
print(points)
point = str(points)
winning = (user+","+point+","+"\n")
line = line.replace(line,winning)
lst.append(line)
f.close()
f = open('test.txt','w')
for line in lst:
f.write(line)
f.close()
print("Points updated")
user = input("Enter username: ") #change so user = winners userid
with open('test.txt') as myfile:
if user in myfile.read():
score2()
else:
f = open('test.txt','r')
f2 = f.read()
f3 = (f2+"\n"+user)
f.close()
f = open('test.txt','w')
f.write(f3)
f.close()
score2()
This is paired with test.txt, which looks like this:
one,1,
two,5,
three,4,
four,94,
When this code is run, it it will ask the user their name (as expected) and then will print 0 (when it should instead print the user's score) and then Points updated. Anybody know how to sort this out?
There are many problems with your code. You should not be using global variables like that. Each function should be passed what it needs, do its computing, and return values for the caller to handle. You should not be reading the file multiple times. And you can't write the file while you still have it open with the with statement.
Here, I read the file at the beginning into a Python dictionary. The code just updates the dictionary, then writes it back out at the end. This makes for a simpler and more maintainable structure.
def readdata(fn):
data = {}
for row in open(fn):
info = row.strip().split(',')
data[info[0]] = int(info[1])
return data
def writedata(fn,data):
f = open(fn,'w')
for k,v in data.items():
print( f"{k},{v}", file=f )
def pointincrementer(data,user):
return data[user] + 1
def score2(data, user):
points = pointincrementer(data, user)
print(points)
data[user] = points
print("Points updated")
user = input("Enter username: ")
data = readdata( 'test.txt' )
if user not in data:
data[user] = 0
score2(data, user)
writedata( 'test.txt', data )
The f in pointincrementer() refers to the "temp" string declared on the third line. The f in score2() refers to the file handle declared immediately below the function header. To get around this, you can pass the file handle into pointincrementer():
def pointincrementer(file_handle):
global points
points = 0
for line in file_handle:
for word in a:
if word in line:
scorelen = int(len(user+","))
scoreval = line[0:scorelen]
isolatedscore = line.replace(scoreval,'')
if "," in line:
scorestr = isolatedscore.replace(",","")
score = int(scorestr)
points = score + 1
print(points)
def score2():
file_handle = open('test.txt','r')
a = [user]
lst = []
for line in f:
print(line)
for word in a:
if word in line:
pointincrementer(file_handle)
print(points)
point = str(points)
winning = (user+","+point+","+"\n")
line = line.replace(line,winning)
lst.append(line)
f.close()
f = open('test.txt','w')
for line in lst:
f.write(line)
f.close()
print("Points updated")
This leads to a parsing error. However, as you haven't described what each function is supposed to do, this is the limit to which I can help. (The code is also extremely difficult to read -- the lack of readability in this code snippet is likely what caused this issue.)
I have a .txt file of amino acids separated by ">node" like this:
Filename.txt :
>NODE_1
MSETLVLTRPDDWHVHLRDGAALQSVVPYTARQFARAIAMPNLKPPITTAEQAQAYRERI
KFFLGTDSAPHASVMKENSVCGAGCFTALSALELYAEAFEAAGALDKLEAFASFHGADFY
GLPRNTTQVTLRKTEWTLPESVPFGEAAQLKPLRGGEALRWKLD*
>NODE_2
MSTWHKVQGRPKAQARRPGRKSKDDFVTRVEHDAKNDALLQLVRAEWAMLRSDIATFRGD
MVERFGKVEGEITGIKGQIDGLKGEMQGVKGEVEGLRGSLTTTQWVVGTAMALLAVVTQV
PSIISAYRFPPAGSSAFPAPGSLPTVPGSPASAASAP*
I want to separate this file into two (or as many as there are nodes) files;
Filename1.txt :
>NODE
MSETLVLTRPDDWHVHLRDGAALQSVVPYTARQFARAIAMPNLKPPITTAEQAQAYRERI
KFFLGTDSAPHASVMKENSVCGAGCFTALSALELYAEAFEAAGALDKLEAFASFHGADFY
GLPRNTTQVTLRKTEWTLPESVPFGEAAQLKPLRGGEALRWKLD*
Filename2.txt :
>NODE
MSTWHKVQGRPKAQARRPGRKSKDDFVTRVEHDAKNDALLQLVRAEWAMLRSDIATFRGD
MVERFGKVEGEITGIKGQIDGLKGEMQGVKGEVEGLRGSLTTTQWVVGTAMALLAVVTQV
PSIISAYRFPPAGSSAFPAPGSLPTVPGSPASAASAP*
With a number after the filename
This code works, however it deletes the ">NODE" line and does not create a file for the last node (the one without a '>' afterwards).
with open('FilePathway') as fo:
op = ''
start = 0
cntr = 1
for x in fo.read().split("\n"):
if x.startswith('>'):
if start == 1:
with open (str(cntr) + '.fasta','w') as opf:
opf.write(op)
opf.close()
op = ''
cntr += 1
else:
start = 1
else:
if op == '':
op = x
else:
op = op + '\n' + x
fo.close()
I can´t seem to find the mistake. Would be thankful if you could point it out to me.
Thank you for your help!
Hi again! Thank you for all the comments. With your help, I managed to get it to work perfectly. For anyone with similar problems, this is my final code:
import os
import glob
folder_path = 'FilePathway'
for filename in glob.glob(os.path.join(folder_path, '*.fasta')):
with open(filename) as fo:
for line in fo.readlines():
if line.startswith('>'):
original = line
content = [original]
fileno = 1
filename = filename
y = filename.replace(".fasta","_")
def writefasta():
global content, fileno
if len(content) > 1:
with open(f'{y}{fileno}.fasta', 'w') as fout:
fout.write(''.join(content))
content = [line]
fileno += 1
with open('FilePathway') as fin:
for line in fin:
if line.startswith('>NODE'):
writefasta()
else:
content.append(line)
writefasta()
You could do it like this:
def writefasta(d):
if len(d['content']) > 1:
with open(f'Filename{d["fileno"]}.fasta', 'w') as fout:
fout.write(''.join(d['content']))
d['content'] = ['>NODE\n']
d['fileno'] += 1
with open('test.fasta') as fin:
D = {'content': ['>NODE\n'], 'fileno': 1}
for line in fin:
if line.startswith('>NODE'):
writefasta(D)
else:
D['content'].append(line)
writefasta(D)
This would be better way. It is going to write only on odd iterations. So that, ">NODE" will be skipped and files will be created only for the real content.
with open('filename.txt') as fo:
cntr=1
for i,content in enumerate(fo.read().split("\n")):
if i%2 == 1:
with open (str(cntr) + '.txt','w') as opf:
opf.write(content)
cntr += 1
By the way, since you are using context manager, you dont need to close the file.
Context managers allow you to allocate and release resources precisely
when you want to. It opens the file, writes some data to it and then
closes it.
Please check: https://book.pythontips.com/en/latest/context_managers.html
with open('FileName') as fo:
cntr = 1
for line in fo.readlines():
with open (f'{str(cntr)}.fasta','w') as opf:
opf.write(line)
opf.close()
op = ''
cntr += 1
fo.close()
I have INI file formatted like this:
But i need it to look like this:
What would be the easiest solution to write such converter?
I tried to do it in Python, but it don't work as expected. My code is below.
def fix_INI_file(in_INI_filepath, out_INI_filepath):
count_lines = len(open( in_INI_filepath).readlines() )
print("Line count: " + str(count_lines))
in_INI_file = open(in_INI_filepath, 'rt')
out_arr = []
temp_arr = []
line_flag = 0
for i in range(count_lines):
line = in_INI_file.readline()
print (i)
if line == '':
break
if (line.startswith("[") and "]" in line) or ("REF:" in line) or (line == "\n"):
out_arr.append(line)
else:
temp_str = ""
line2 = ""
temp_str = line.strip("\n")
wh_counter = 0
while 1:
wh_counter += 1
line = in_INI_file.readline()
if (line.startswith("[") and "]" in line) or ("REF:" in line) or (line == "\n"):
line2 += line
break
count_lines -= 1
temp_str += line.strip("\n") + " ; "
temp_str += "\n"
out_arr.append(temp_str)
out_arr.append(line2 )
out_INI_file = open(out_INI_filepath, 'wt+')
strr_blob = ""
for strr in out_arr:
strr_blob += strr
out_INI_file.write(strr_blob)
out_INI_file.close()
in_INI_file.close()
Fortunately, there's a much easier way to handle this than by parsing the text by hand. The built-in configparser module supports keys without values via the allow_no_values constructor argument.
import configparser
read_config = configparser.ConfigParser(allow_no_value=True)
read_config.read_string('''
[First section]
s1value1
s1value2
[Second section]
s2value1
s2value2
''')
write_config = configparser.ConfigParser(allow_no_value=True)
for section_name in read_config.sections():
write_config[section_name] = {';'.join(read_config[section_name]): None}
with open('/tmp/test.ini', 'w') as outfile:
write_config.write(outfile)
While I don't immediately see a way to use the same ConfigParser object for reading and writing (it maintains default values for the original keys), using the second object as a writer should yield what you're looking for.
Output from the above example:
[First section]
s1value1;s1value2
[Second section]
s2value1;s2value2
I read from a file, if it finds a ".", it should add a newline "\n" to the text and write it back to the file. I tried this code but still have the problem.
inp = open('rawCorpus.txt', 'r')
out = open("testFile.text", "w")
for line in iter(inp):
l = line.split()
if l.endswith(".")
out.write("\n")
s = '\n'.join(l)
print(s)
out.write(str(s))
inp.close()
out.close()
Try This ( Normal way ):
with open("rawCorpus.txt", 'r') as read_file:
raw_data = read_file.readlines()
my_save_data = open("testFile.text", "a")
for lines in raw_data:
if "." in lines:
re_lines = lines.replace(".", ".\r\n")
my_save_data.write(re_lines)
else:
my_save_data.write(lines + "\n")
my_save_data.close()
if your text file is not big you can try this too :
with open("rawCorpus.txt", 'r') as read_file:
raw_data = read_file.read()
re_data = raw_data.replace(".", ".\n")
with open("testFile.text", "w") as save_data:
save_data.write(re_data)
UPDATE ( output new lines depends on your text viewer too! because in some text editors "\n" is a new line but in some others "\r\n" is a new line. ) :
input sample :
This is a book. i love it.
This is a apple. i love it.
This is a laptop. i love it.
This is a pen. i love it.
This is a mobile. i love it.
Code:
last_buffer = []
read_lines = [line.rstrip('\n') for line in open('input.txt')]
my_save_data = open("output.txt", "a")
for lines in read_lines:
re_make_lines = lines.split(".")
for items in re_make_lines:
if items.replace(" ", "") == "":
pass
else:
result = items.strip() + ".\r\n"
my_save_data.write(result)
my_save_data.close()
Ouput Will Be :
This is a book.
i love it.
This is a apple.
i love it.
This is a laptop.
i love it.
This is a pen.
i love it.
This is a mobile.
i love it.
You are overwriting the string s in every loop with s = '\n'.join(l).
Allocate s = '' as empty string before the for-loop and add the new lines during every loop, e.g. with s += '\n'.join(l) (short version of s = s + '\n'.join(l)
This should work:
inp = open('rawCorpus.txt', 'r')
out = open('testFile.text', 'w')
s = '' # empty string
for line in iter(inp):
l = line.split('.')
s += '\n'.join(l) # add new lines to s
print(s)
out.write(str(s))
inp.close()
out.close()
Here is my own solution, but still I want one more newline after ".", that this solution not did this
read_lines = [line.rstrip('\n') for line in open('rawCorpus.txt')]
words = []
my_save_data = open("my_saved_data.txt", "w")
for lines in read_lines:
words.append(lines)
for word in words:
w = word.rstrip().replace('.', '\n.')
w = w.split()
my_save_data.write(str("\n".join(w)))
print("\n".join(w))
my_save_data.close()
I'm adding some new bits to one of the lines in a text file and then writing it along with the rest of the lines in the file to a new file. Referring to the 2nd if statement in the while loop, I want that to be all on the same line:
path = raw_input("Enter the name of the destination folder: ")
source_file = open("parameters")
lnum=1
for line in source_file:
nums = line.split()
if (lnum==10):
mTot = float(nums[0])
if (lnum==11):
qinit = float(nums[0])
if (lnum==12):
qfinal = float(nums[0])
if (lnum==13):
qgrowth = float(nums[0])
if (lnum==14):
K = float(nums[0])
lnum = lnum+1
q = qinit
m1 = mTot/(1+qinit)
m2 = (mTot*qinit)/(1+qinit)
taua = (1/3.7)*(mTot**(-4.0/3.0))
taue = taua/K
i = 1
infname = 'parameters'
while (q <= qfinal):
outfname = path+'/'+str(i)
oldfile = open(infname)
lnum=1
for line in oldfile:
if (lnum==17):
line = "{0:.2e}".format(m1)+' '+line
if (lnum==18):
line = "{0:.2e}".format(m2)+' '+line+' '+"{0:.2e}".format(taua)+' '+" {0:.2e}".format(taue)
newfile = open(outfname,'a')
newfile.write(line)
lnum=lnum+1
oldfile.close()
newfile.close()
i=i+1
q = q + q*(qgrowth)
m1 = mTot/(1+q)
m2 = (mTot*q)/(1+q)
but taua and taue are being written on the line below the rest of it. What am I missing here?
That is because line still contains the trailing newline, and when you concatenate it you are also including the newline.
Insert a
line = line.strip()
right after the if (lnum == 19): but before you put the longer line together to get rid of the newline.
Note that write will not add a newline automatically, so you'll want to add a trailing newline of your own.
UPDATE:
This is untested, but I think unless I messed up, you could just use this instead of your longer line:
line = line.strip()
line = "{0:.2e} {} {0:.2e} {0:.2e}\n".format(x, line, y, z)
If you use line = rstrip(line) on line before you change the line then it will trim the new line (as well as any whitespace).