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:
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.