I am going to start of by showing the code I have thus far:
def err(em):
print(em)
exit
def rF(f):
s = ""
try:
fh = open(f, 'r')
except IOError:
e = "Could not open the file: " + f
err(e)
try:
with fh as ff:
next(ff)
for l in ff:
if ">" in l:
next(ff)
else:
s += l.replace('\n','').replace('\t','').replace('\r','')
except:
e = "Unknown Exception"
err(e)
fh.close()
return s
For some reason the python shell (I am using 3.2.2) freezes up whenever I tried to read a file by typing:
rF("mycobacterium_bovis.fasta")
The conditionals in the rF function are to prevent reading each line that starts with a ">" token. These lines aren't DNA/RNA code (which is what I am trying to read from these files) and should be ignored.
I hope anyone can help me out with this, I don't see my error.
As per the usual, MANY thanks in advance!
EDIT:
*The problem persists!*
This is the code I now use, I removed the error handling which was a fancy addition anyway, still the shell freezes whenever attempting to read a file. This is my code now:
def rF(f):
s = ""
try:
fh = open(f, 'r')
except IOError:
print("Err")
try:
with fh as ff:
next(ff)
for l in ff:
if ">" in l:
next(ff)
else:
s += l.replace('\n','').replace('\t','').replace('\r','')
except:
print("Err")
fh.close()
return s
You didn't ever define e.
So you'll get a NameError that is being hidden by the naked except:.
This is why it is good and healthy to specify the exception, e.g.:
try:
print(e)
except NameError as e:
print(e)
In cases like yours, though, when you don't necessarily know what the exception will be you should at least use this method of displaying information about the error:
import sys
try:
print(e)
except: # catch *all* exceptions
e = sys.exc_info()[1]
print(e)
Which, using the original code you posted, would have printed the following:
name 'e' is not defined
Edit based on updated information:
Concatenating a string like that is going to be quite slow if you have a large file.
Consider instead writing the filtered information to another file, e.g.:
def rF(f):
with open(f,'r') as fin, open('outfile','w') as fou:
next(fin)
for l in fin:
if ">" in l:
next(fin)
else:
fou.write(l.replace('\n','').replace('\t','').replace('\r',''))
I have tested that the above code works on a FASTA file based on the format specification listed here: http://en.wikipedia.org/wiki/FASTA_format using Python 3.2.2 [GCC 4.6.1] on linux2.
A couple of recommendations:
Start small. Get a simple piece working then add a step.
Add print() statements at trouble spots.
Also, consider including more information about the contents of the file you're attempting to parse. That may make it easier for us to help.
Related
Recently I've been practicing lessions by Jason Cannon on O'reilly: https://learning.oreilly.com/videos/python-for-beginners/9781789617122/9781789617122-video10_3/
At 6:55 of the 'Files, Part II' section, I have a problem practicing error catch following the idea in the video. My code:
with open('data.txt') as file:
try:
file_content = file.read()
except:
file_content = ''
print(len(file_content))
The idea is to catch error when the file is not found, the try block runs but the except block not. I expected the file_content has length of 0 instead of error shows up. Please tell me where I did wrong. Thank you very much
If the file isn't found, it's open that raises the error, not the attempt to read from it.
try:
with open('data.txt') as file:
file_content = file.read()
except (FileNotFoundError, IOError):
file_content = ''
Note that if open raises a FileNotFound error, then no context manager will actually be created, and so there is no need for the with statement to try to execute an __exit__ method before control passes to the exception handler.
I'm trying to control exceptions when reading files, but I have a problem. I'm new to Python, and I am not yet able to control how I can catch an exception and still continue reading text from the files I am accessing. This is my code:
import errno
import sys
class Read:
#FIXME do immutables this 2 const
ROUTE = "d:\Profiles\user\Desktop\\"
EXT = ".txt"
def setFileReaded(self, fileToRead):
content = ""
try:
infile = open(self.ROUTE+fileToRead+self.EXT)
except FileNotFoundError as error:
if error.errno == errno.ENOENT:
print ("File not found, please check the name and try again")
else:
raise
sys.exit()
with infile:
content = infile.read()
infile.close()
return content
And from another class I tell it:
read = Read()
print(read.setFileReaded("verbs"))
print(read.setFileReaded("object"))
print(read.setFileReaded("sites"))
print(read.setFileReaded("texts"))
Buy only print this one:
turn on
connect
plug
File not found, please check the name and try again
And no continue with the next files. How can the program still reading all files?
It's a little difficult to understand exactly what you're asking here, but I'll try and provide some pointers.
sys.exit() will terminate the Python script gracefully. In your code, this is called when the FileNotFoundError exception is caught. Nothing further will be ran after this, because your script will terminate. So none of the other files will be read.
Another thing to point out is that you close the file after reading it, which is not needed when you open it like this:
with open('myfile.txt') as f:
content = f.read()
The file will be closed automatically after the with block.
I am browsing URL using txt file follow.txt and doing click on specific button in website.But the problem is that sometime I am getting error of unable to locate element and unable to click button.
I want that if that error come, it should read second line of txt file and ignore the error.I also tried the code to overcome the problem.But it is still not working properly.I think my code have some problem.How i can solve this problem.Here is my code that i used for error handling.
try:
f = open('follow.txt', 'r', encoding='UTF-8', errors='ignore')
line = f.readline()
while line:
line = f.readline()
browser.get(line)
browser.find_element_by_xpath(""".//*[#id='react-root']/section/main/article/header/div[2]/div[1]/span/button""").click()
time.sleep(50)
f.close();
except Exception as e:
f = open('follow.txt', 'r', encoding='UTF-8', errors='ignore')
line = f.readline()
while line:
line = f.readline()
browser.get(line)
browser.find_element_by_xpath(""".//*[#id='react-root']/section/main/article/header/div[2]/div[1]/span/button""").click()
time.sleep(20)
browser.find_element_by_tag_name("body").send_keys(Keys.ALT + Keys.NUMPAD2)
browser.switch_to_window(main_window)
time.sleep(10)
f.close();
In the way you have written the answer to a question like... "What happens when there is an error even in the second line?" would be scary. You definitely do NOT want to write as many nested try except blocks as the number of lines in the file.
So, you will need to have the try except on the statement where you would expect an error, which will allow you to use the opened file object without the necessity to reopen the file. Something similar to the following:
f = open('follow.txt', 'r', encoding='UTF-8', errors='ignore')
line = f.readline()
while line:
line = f.readline()
browser.get(line)
try:
browser.find_element_by_xpath(""".//*[#id='react-root']/section/main/article/header/div[2]/div[1]/span/button""").click()
except Exception as e:
print e # Or better log the error
time.sleep(50)
browser.find_element_by_tag_name("body").send_keys(Keys.ALT + Keys.NUMPAD2)
browser.switch_to_window(main_window)
time.sleep(10)
f.close();
This should let you to continue with the next line even though there is an error at the time of ".click()". Note that you do not want to close the file when you are not done with reading all that you want from file.
My intention of moving "try except" deep into the logic doesn't mean that you shouldn't use "try except" else where for example while opening file. The more better way is to use 'with' in which case you don't even need to worry about closing the file and handling exceptions while opening the file.
with open('follow.txt', 'r', encoding='UTF-8', errors='ignore') as f:
....
I have a directory that has bunch of sub directories, each subdir has many csv files, but I am only interest in certain csv file. So I wrote following python method, but I am unable to capture the file name, if I do *.csv it will find all the file but I don't want to all the files to be read in:
def gatherStats(template_file, csv_file):
for lang in getLanguageCodes(csv_file):
lang_dir = os.path.join(template_file, lang)
try:
for file in os.listdir(lang_dir):
if fnmatch.fnmatch(file, '*-*-template-users-data.csv'):
t_file = open(file, 'rb').read()
reader = csv.reader()
for row in reader:
print row
else:
print "didn't find the file"
except Exception, e:
logging.exception(e)
What am I doing wrong here? Is it a regular expression issue? Can we use regular expression with fnmath?
There are several problems with your code. Fix them first, then we might get to the bottom of what your issue really is.
First of all, don't use built-in names as variables, such as file. Rather replace it with filename.
Then os.path.join(lang_dir, filename) before opening the file. Meaning:
t_file = open(os.path.join(lang_dir, filename), 'rb').read()
How do you expect reader = csv.reader() to read your file if you don't reference your open file object in this line?
Your try/except block is a bit too wide for my taste. Take your time and narrow down the errors that actually can happen. Then decide which of them you want to ignore and which should crash your program. Take a close look at the exceptions actually thrown in this block. You'll probably find your issue there.
With the help provided by another user, I manage to fix the problem. I am putting this answer here for future reference for community.
def gatherStats(template_file, csv_file):
for lang in getLanguageCodes(csv_file):
lang_dir = os.path.join(template_file, lang)
try:
for filename in os.listdir(lang_dir):
path = os.path.join(lang_dir, filename)
if re.search(r'-.+-template-users-data.csv$',filename):
with open(path, 'rb') as template_user_data_file:
reader = csv.reader(template_user_data_file)
try:
for row in reader:
print row
except csv.ERROR as e:
logging.error(e)
else:
print "didn't find the file"
except Exception, e:
logging.exception(e)
Why is else clause needed for try statement in python ?
Taking it forward:
try:
f = open('foo', 'r')
except IOError as e:
error_log.write('Unable to open foo : %s\n' % e)
else:
data = f.read()
f.close()
It occurs to me that the corner case solved by else clause still can be avoided by a nested try...except avoiding the need of else? :
try:
f = open('foo', 'r')
try:
data = f.read()
f.close()
except:
pass
except IOError as e:
error_log.write('Unable to open foo : %s\n' % e)
try..except..else may not be needed, but it can be nice. In this case, the try..except..else form is distinctly nicer, in my opinion.
Just because you can do without an element of syntax, doesn't make it useless. Decorator syntax is purely syntax sugar (the most obvious example, I think), for loops are just glorified while loops, et cetera. There's a good place for try..except..else and I would say this is one such place.
Besides, those two blocks of code are far from equivalent. If f.read() raises an exception (disk read error, data corruption inside the file or some other such problem), the first will raise an exception as it should but the second will lose it and think that everything has worked. For myself, I would prefer something more along these lines, which is shorter and still easier to understand:
try:
with open('foo', 'r') as f:
data = f.read()
except IOError as e:
error_log.write('Unable to open foo : %s\n' % e)
(This assumes that you want to catch errors in file.read and file.close. And I can't really see why you wouldn't.)
Actually, is not always needed you can simply do:
f = None
try:
f = open('foo', 'r')
except IOError:
error_log.write('Unable to open foo\n')
if f:
data = f.read()
f.close()