I have approximately 200 files (plus more in the future) that I need to transpose data from columns into rows. I'm a microbiologist, so coding isn't my forte (have worked with Linux and R in the past). One of my computer science friends was trying to help me write code in Python, but I have never used it before today.
The files are in .lvm format, and I'm working on a Mac. Items with 2 stars on either side are paths that I've hidden to protect my privacy.
The for loop is where I've been getting the error, but I'm not sure if that's where my problem lies or if it's something else.
This is the Python code I've been working on:
import os
lvm_directory = "/Users/**path**"
output_file = "/Users/**path**/Transposed.lvm"
newFile = True
output_delim = "\t"
for filename in os.listdir(lvm_directory):
header = []
data = []
f = open(lvm_directory + "/" + filename)
for l in f:
sl = l.split()
if (newFile):
header += [sl[1]]
f. close()
This is the error message I've been getting and I can't figure out how to work through it:
File "<pyshell#97>", line 5, in <module>
for l in f:
File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd6 in position 345: invalid continuation byte
The rest of the code after this error is as follows, but I haven't worked through it yet due to the above error:
f = open(output_file, 'w')
f.write(output_delim.join(header))
newFile = False
else:
f = open(output_file, 'a')
f.write("\n"+output_delim.join(data))
f.close()
Looks like your files have a different encoding than the default utf-8 format. Probably ASCII. You'd use something like:
with open(lvm_directory + "/" + filename, encoding="ascii") as f:
for l in f:
# rest of your code here
^ It's generally more "pythonic" to use a with statement to handle resource management (i.e. opening and closing a file), hence the with approach demonstrated above. If your files aren't ASCII, see if any other encoding work. There are command-line tools like chardet that can help you identify the file's encoding.
Related
I am using this code to find a string in Python:
buildSucceeded = "Build succeeded."
datafile = r'C:\PowerBuild\logs\Release\BuildAllPart2.log'
with open(datafile, 'r') as f:
for line in f:
if buildSucceeded in line:
print(line)
I am quite sure there is the string in the file although it does not return anything.
If I just print one line by line it returns a lot of 'NUL' characters between each "valid" character.
EDIT 1:
The problem was the encoding of Windows. I changed the encoding following this post and it worked: Why doesn't Python recognize my utf-8 encoded source file?
Anyway the file looks like this:
Line 1.
Line 2.
...
Build succeeded.
0 Warning(s)
0 Error(s)
...
I am currently testing with Sublime for Windows editor - which outputs a 'NUL' character between each "real" character which is very odd.
Using python command line I have this output:
C:\Dev>python readFile.py
Traceback (most recent call last):
File "readFile.py", line 7, in <module>
print(line)
File "C:\Program Files\Python35\lib\encodings\cp437.py", line 19, in encode
return codecs.charmap_encode(input,self.errors,encoding_map)[0]
UnicodeEncodeError: 'charmap' codec can't encode character '\xfe' in position 1: character maps to <undefined>
Thanks for your help anyway...
If your file is not that big you can do a simple find. Otherwise I would check to file to see if you have the string in the file/ check the location for any spelling mistakes and try to narrow down the problem.
f = open(datafile, 'r')
lines = f.read()
answer = lines.find(buildSucceeded)
Also note that if it does not find the string answer would be -1.
As explained, the problem happening was related to encoding. In the below website there is a very good explanation on how to convert between files with one encoding to some other.
I used the last example (with Python 3 which is my case) it worked as expected:
buildSucceeded = "Build succeeded."
datafile = 'C:\\PowerBuild\\logs\\Release\\BuildAllPart2.log'
# Open both input and output streams.
#input = open(datafile, "rt", encoding="utf-16")
input = open(datafile, "r", encoding="utf-16")
output = open("output.txt", "w", encoding="utf-8")
# Stream chunks of unicode data.
with input, output:
while True:
# Read a chunk of data.
chunk = input.read(4096)
if not chunk:
break
# Remove vertical tabs.
chunk = chunk.replace("\u000B", "")
# Write the chunk of data.
output.write(chunk)
with open('output.txt', 'r') as f:
for line in f:
if buildSucceeded in line:
print(line)
Source: http://blog.etianen.com/blog/2013/10/05/python-unicode-streams/
I'm currently have an issue with my python 3 code.
replace_line('Products.txt', line, tenminus_str)
Is the line I'm trying to turn into utf-8, however when I try to do this like I would with others, I get errors such as no attribute ones and when I try to add, for example...
.decode("utf8")
...to the end of it, I still get errors that it is using ascii. I also tried other methods that worked with other lines such as adding io. infront and adding a comma with
encoding = 'utf8'
The function that I am using for replace_line is:
def replace_line(file_name, line_num, text):
lines = open(file_name, 'r').readlines()
lines[line_num] = text
out = open(file_name, 'w')
out.writelines(lines)
out.close()
How would I fix this issue? Please note that I'm very new to Python and not advanced enough to do debugging well.
EDIT: Different fix to this question than 'duplicate'
EDIT 2:I have another error with the function now.
File "FILELOCATION", line 45, in refill replace_line('Products.txt', str(line), tenminus_str)
File "FILELOCATION", line 6, in replace_line lines[line_num] = text
TypeError: list indices must be integers, not str
What does this mean and how do I fix it?
Change your function to:
def replace_line(file_name, line_num, text):
with open(file_name, 'r', encoding='utf8') as f:
lines = f.readlines()
lines[line_num] = text
with open(file_name, 'w', encoding='utf8') as out:
out.writelines(lines)
encoding='utf8' will decode your UTF-8 file correctly.
with automatically closes the file when its block is exited.
Since your file started with \xef it likely has a UTF-8-encoding byte order mark (BOM) character at the beginning. The above code will maintain that on output, but if you don't want it use utf-8-sig for the input encoding. Then it will be automatically removed.
codecs module is just what you need. detail here
import codecs
def replace_line(file_name, line_num, text):
f = codecs.open(file_name, 'r', encoding='utf-8')
lines = f.readlines()
lines[line_num] = text
f.close()
w = codecs.open(file_name, 'w', encoding='utf-8')
w.writelines(lines)
w.close()
Handling coding problems You can try adding the following settings to your head
import sys
reload(sys)
sys.setdefaultencoding('utf-8')
Type = sys.getfilesystemencoding()
Try adding encoding='utf8' if you are reading a file
with open("../file_path", encoding='utf8'):
# your code
I was trying to read a file in python2.7, and it was readen perfectly. The problem that I have is when I execute the same program in Python3.4 and then appear the error:
'utf-8' codec can't decode byte 0xf2 in position 424: invalid continuation byte'
Also, when I run the program in Windows (with python3.4), the error doesn't appear. The first line of the document is:
Codi;Codi_lloc_anonim;Nom
and the code of my program is:
def lectdict(filename,colkey,colvalue):
f = open(filename,'r')
D = dict()
for line in f:
if line == '\n': continue
D[line.split(';')[colkey]] = D.get(line.split(';')[colkey],[]) + [line.split(';')[colvalue]]
f.close
return D
Traduccio = lectdict('Noms_departaments_centres.txt',1,2)
In Python2,
f = open(filename,'r')
for line in f:
reads lines from the file as bytes.
In Python3, the same code reads lines from the file as strings. Python3
strings are what Python2 call unicode objects. These are bytes decoded
according to some encoding. The default encoding in Python3 is utf-8.
The error message
'utf-8' codec can't decode byte 0xf2 in position 424: invalid continuation byte'
shows Python3 is trying to decode the bytes as utf-8. Since there is an error, the file apparently does not contain utf-8 encoded bytes.
To fix the problem you need to specify the correct encoding of the file:
with open(filename, encoding=enc) as f:
for line in f:
If you do not know the correct encoding, you could run this program to simply
try all the encodings known to Python. If you are lucky there will be an
encoding which turns the bytes into recognizable characters. Sometimes more
than one encoding may appear to work, in which case you'll need to check and
compare the results carefully.
# Python3
import pkgutil
import os
import encodings
def all_encodings():
modnames = set(
[modname for importer, modname, ispkg in pkgutil.walk_packages(
path=[os.path.dirname(encodings.__file__)], prefix='')])
aliases = set(encodings.aliases.aliases.values())
return modnames.union(aliases)
filename = '/tmp/test'
encodings = all_encodings()
for enc in encodings:
try:
with open(filename, encoding=enc) as f:
# print the encoding and the first 500 characters
print(enc, f.read(500))
except Exception:
pass
Ok, I did the same as #unutbu tell me. The result was a lot of encodings one of these are cp1250, for that reason I change :
f = open(filename,'r')
to
f = open(filename,'r', encoding='cp1250')
like #triplee suggest me. And now I can read my files.
In my case I can't change encoding because my file is really UTF-8 encoded. But some rows are corrupted and causes the same error:
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd0 in position 7092: invalid continuation byte
My decision is to open file in binary mode:
open(filename, 'rb')
I'm trying to scrape some stuff off a page using selenium. But this some of the text has ascii text in it.. so I get this.
f.write(database_text.text)
UnicodeEncodeError: 'ascii' codec can't encode character u'\xed' in position 1462: ordinal not in range(128)
I was wondering, is there anyway to just simpley ascii?
Thanks!
print("â")
I'm not looking to write it in my text file, but ignore it.
note: It's not just "â" it has other chars like that also.
window_before = driver.window_handles[0]
nmber_one = 1
f = open(str(unique_filename) + ".txt", 'w')
for i in range(5, 37):
time.sleep(3)
driver.find_element_by_xpath("""/html/body/center/table[2]/tbody/tr[2]/td/table/tbody/tr""" + "[" + str(i) + "]" + """/td[2]/a""").click()
time.sleep(3)
driver.switch_to.window(driver.window_handles[nmber_one])
nmber_one = nmber_one + 1
database_text = driver.find_element_by_xpath("/html/body/pre")
f = open(str(unique_filename) + ".txt", 'w',)
f.write(database_text.text)
driver.switch_to.window(window_before)
import uuid
import io
unique_filename = uuid.uuid4()
which generates a new filename, well it should anyway, it worked before.
The problem is that some of the text is not ascii. database_text.text is likely unicode text (you can do print type(database_text.text) to verify) and contains non-english text. If you are on windows it may be "codepage" text which depends on how your user account is configured.
Often, one wants to store text like this as utf-8 so open your output file accordingly
import io
text = u"â"
with io.open('somefile.txt', 'w', encoding='utf-8') as f:
f.write(text)
If you really do want to just drop the non-ascii characters from the file completely you can setup a error policy
text = u"ignore funky â character"
with io.open('somefile.txt', 'w', encoding='ascii', errors='ignore') as f:
f.write(text)
In the end, you need to choose what representation you want to use for non-ascii (roughly speaking, non-English) text.
A Try Except block would work:
try:
f.write(database_text.text)
except UnicodeEncodeError:
pass
I'm using the following code to unzip and save a CSV file:
with gzip.open(filename_gz) as f:
file = open(filename, "w");
output = csv.writer(file, delimiter = ',')
output.writerows(csv.reader(f, dialect='excel', delimiter = ';'))
Everything seems to work, except for the fact that the first characters in the file are unexpected. Googling around seems to indicate that it is due to BOM in the file.
I've read that encoding the content in utf-8-sig should fix the issue. However, adding:
.read().encoding('utf-8-sig')
to f in csv.reader fails with:
File "ckan_gz_datastore.py", line 16, in <module>
output.writerows(csv.reader(f.read().encode('utf-8-sig'), dialect='excel', delimiter = ';'))
File "/usr/lib/python2.7/encodings/utf_8_sig.py", line 15, in encode
return (codecs.BOM_UTF8 + codecs.utf_8_encode(input, errors)[0], len(input))
UnicodeDecodeError: 'ascii' codec can't decode byte 0xef in position 0: ordinal not in range(128)
How can I remove the BOM and just save the content in correct utf-8?
First, you need to decode the file contents, not encode them.
Second, the csv module doesn't like unicode strings in Python 2.7, so having decoded your data you need to convert back to utf-8.
Finally, csv.reader is passed an iteration over the lines of the file, not a big string with linebreaks in it.
So:
csv.reader(f.read().decode('utf-8-sig').encode('utf-8').splitlines())
However, you might consider it simpler / more efficent just to remove the BOM manually:
def remove_bom(line):
return line[3:] if line.startswith(codecs.BOM_UTF8) else line
csv.reader((remove_bom(line) for line in f), dialect = 'excel', delimiter = ';')
That is subtly different, since it removes a BOM from any line that starts with one, instead of just the first line. If you don't need to keep other BOMs that's OK, otherwise you can fix it with:
def remove_bom_from_first(iterable):
f = iter(iterable)
firstline = next(f, None)
if firstline is not None:
yield remove_bom(firstline)
for line in f:
yield f