i'm attempting to read a plain text file and resolve each IP address and (for now) just spit them back out on-screen.
import socket
f = open("test.txt")
num_line = sum(1 for line in f)
f.close()
with open("test.txt", "r") as ins:
array = []
for line in ins:
array.append(line)
for i in range(0,num_line):
x = array[i]
print x
data = socket.gethostbyname_ex(x)
print data
Currently I'm getting the following:
me#v:/home/# python resolve-list2.py
test.com
Traceback (most recent call last):
File "resolve-list2.py", line 15, in <module>
data = socket.gethostbyname_ex(x)
socket.gaierror: [Errno -2] Name or service not known
Googling that error doesn't seem to help me...
The text file only contains one line at the moment (test.com) but i get the same error even with multiple lines/different hosts.
Any suggestions?
Thanks!
import socket
with open("test.txt", "r") as ins:
for line in ins:
print socket.gethostbyname(line.strip())
Related
The goal was to import the infile, read it, and print only two lines into the outfile.This is the code I had in IDLE:
def main():
infile = open('names.py', "r")
outfile = open('orgnames.py', "w")
for i in range (2):
line = ("names.py".readlines())
print (line[:-1], infile = outfile)
infile.close()
outfile.close()
main()
This is the error message I keep getting:
Traceback (most recent call last):
File "C:/Python33/studentnames6.py", line 11, in <module>
main()
File "C:/Python33/studentnames6.py", line 6, in main
line = ("names.py".readlines())
AttributeError: 'str' object has no attribute 'readlines'
I have used the function readlines in a similar situation before and it had worked fine. I don't understand why it's having an error now, or how to fix it.
The error is because names.py is a string, and not a file object. The following code should work for you:
def main():
infile = open('names.py', "r")
outfile = open('orgnames.py', "w")
# Prints the first two lines in outfile
for line in infile.readlines()[:2]:
outfile.write(line)
infile.close()
outfile.close()
main()
Ok well i have another question. I implemented the error checking but for some reason it still isn't working. I still get a python error instead of the error i just wrote in the program.
Traceback (most recent call last):
File "E:/python/copyfile.py", line 31, in <module>
copyFile()
File "E:/python/copyfile.py", line 8, in copyFile
file1 = open(source,"r")
IOError: [Errno 2] No such file or directory: 'C:/Users/Public/asdf.txt'
check out the shutil module in standard library:
shutil.copyfile(src, dst)
http://docs.python.org/2/library/shutil.html#shutil.copyfile
I would rather ask you to write your own:
import os
import hashlib
def md5ChkSum(_file): # Calculates MD5 CheckSum
with open(_file, 'rb') as fp:
hash_obj = hashlib.md5()
line = fp.readline()
while line:
hash_obj.update(line)
line = fp.readline()
return hash_obj.hexdigest()
def copier(_src, _dst):
if not os.path.exists(_src):
return False
_src_fp = open(_src, "r")
_dst_fp = open(_dst, "w")
line = _src_fp.readline()
while line:
_dst_fp.write(line)
line = _src_fp.readline()
_src_fp.close()
_dst_fp.close()
if md5ChkSum(_src) == md5ChkSum(_dst):
return "Copy: SUCCESSFUL"
return "Copy: FAILED"
res = copier(r"/home/cnsiva/6.jpg", r"/home/cnsiva/6_copied.jpg")
if not res:
print "FILE Does not Exists !!!"
else: print res
OUTPUT:
Copy: SUCCESSFUL
Can Someone Explain to me what is wrong with my code? I get the following error:
Traceback (most recent call last): File "C:\LineRep.py", line
15, in module:
for line in File2: ValueError: I/O operation on closed file
My Code:
import os, Tkinter, tkFileDialog
root = Tkinter.Tk()
root.withdraw()
dirprompt = tkFileDialog.askopenfilename()
File = open (dirprompt, 'r')
File2 = open (dirprompt + 'temp', 'w')
for line in File:
File2.write(line.replace(',', ' '))
File.close()
File2.close()
names = []
for line in File2:
names.append(line)
print names
You are iterating over File2 after you call File2.close()
I'm new to python and bioinformatics field. I'm using python-2.6. Now I'm trying to select all fastq.gz files, then gzip.open(just a few lines because it's too huge and time-wasting), then count 'J' , then pick out those files with 'J' count NOT equal to 0.
The following is my code:
#!/usr/bin/python
import os,sys,re,gzip
path = "/home/XXX/nearline"
for file in os.listdir(path):
if re.match('.*\.recal.fastq.gz', file):
text = gzip.open(file,'r').readlines()[:10]
word_list = text.split()
number = word_list.count('J') + 1
if number !== 0:
print file
But I got some errors:
Traceback (most recent call last):
File "fastqfilter.py", line 9, in <module>
text = gzip.open(file,'r').readlines()[:10]
File "/share/lib/python2.6/gzip.py", line 33, in open
return GzipFile(filename, mode, compresslevel)
File "/share/lib/python2.6/gzip.py", line 79, in __init__
fileobj = self.myfileobj = __builtin__.open(filename, mode or 'rb')
IOError: [Errno 2] No such file or directory: 'ERR001268_1.recal.fastq.gz'
What's this traceback: File......
Is there anything wrong with gzip here?
And why can't it find ERR001268_1.recal.fastq.gz? It's the first fastq file in the list, and DOES exist there.
Hope give me some clues, and any point out any other errors in the script.
THanks a lot.
Edit: thx everyone. I followed Dan's suggestion. And I tried on ONE fastq file first. My script goes like:
#!/usr/bin/python
import os,sys
import gzip
import itertools
file = gzip.open('/home/xug/nearline/ERR001274_1.recal.fastq.gz','r')
list(itertools.islice(file.xreadlines(),10))
word_list = list.split()
number = word_list.count('J') + 1
if number != 0:
print 'ERR001274_1.recal.fastq.gz'
Then errors are:
Traceback (most recent call last):
File "try2.py", line 8, in <module>
list(itertools.islice(text.xreadlines(),10))
AttributeError: GzipFiles instance has no attribute 'xreadlines'
Edit again: Thx Dan, I've solved the problem yesterday. Seems GzipFiles don't support xreadlines. So I tried the similar way as you suggested later. And it works. See below:
#!/usr/bin/python
import os,sys,re
import gzip
from itertools import islice
path = "/home/XXXX/nearline"
for file in os.listdir(path):
if re.match('.*\.recal.fastq.gz', file):
fullpath = os.path.join(path, file)
myfile = gzip.open(fullpath,'r')
head = list(islice(myfile,1000))
word_str = ";".join(str(x) for x in head)
number = word_str.count('J')
if number != 0:
print file
on this line:
text = gzip.open(file,'r').read()
file is a filename not a full path so
fullpath = os.path.join(path, file)
text = gzip.open(fullpath,'r').read()
about F.readlines()[:10] will read the whole file in to a list of lines and then take the first 10
import itertools
list(itertools.islice(F.xreadlines(),10))
this will not read the whole file into memory and will only read the first 10 lines into a list
but as gzip.open returns an object that doesn't have .xreadlines() and but as files are iterable on their lines just:
list(itertools.islice(F,10))
would work as this test shows:
>>> import gzip,itertools
>>> list(itertools.islice(gzip.open("/home/dan/Desktop/rp718.ps.gz"),10))
['%!PS-Adobe-2.0\n', '%%Creator: dvips 5.528 Copyright 1986, 1994 Radical Eye Software\n', '%%Title: WLP-94-int.dvi\n', '%%CreationDate: Mon Jan 16 16:24:41 1995\n', '%%Pages: 6\n', '%%PageOrder: Ascend\n', '%%BoundingBox: 0 0 596 842\n', '%%EndComments\n', '%DVIPSCommandLine: dvips -f WLP-94-int.dvi\n', '%DVIPSParameters: dpi=300, comments removed\n']
Change your code to:
#!/usr/bin/python
import os,sys,re,gzip
path = "/home/XXX/nearline"
for file in os.listdir(path):
if re.match('.*\.recal.fastq.gz', file):
text = gzip.open(os.path.join(path,file),'r').readlines()[:10]
word_list = text.split()
number = word_list.count('J') + 1
if number !== 0:
print file
It's trying to open ERR001268_1.recal.fastq.gz from the working directory, not from /home/XXX/nearline.
If I try executing the following code
f = file('test','rb')
fout = file('test.out','wb')
for i in range(10):
a = f.read(1)
fout.write(a)
f.close()
f = fout
f.seek(4)
print f.read(4)
Where 'test' is any arbitrary file, I get:
Traceback (most recent call last):
File "testbad.py", line 12, in <module>
print f.read(4)
IOError: [Errno 9] Bad file descriptor
If however, I change just the fout line to use a temporary file:
import tempfile
f = file('test','rb')
fout = tempfile.NamedTemporaryFile()
for i in range(10):
a = f.read(1)
fout.write(a)
f.close()
f = fout
f.seek(4)
print f.read(4)
There are no errors. Does anyone know why this is? I would have expected the first case to work, but I must be doing something wrong.
Thanks in advance for any help!
you've only opened the file fout for writing, not reading. To open for both use
fout = file('test.out','r+b')