I have this file animallog1.txt which contains information that i would like to use to answer questions using python. How would i import the file to python, which would latter be used
I tried
with open('animallog1.txt', 'r') as myfile
but this is not working and just outputs no such file or directory even though i am pretty sure it exists
animal_names, dates, locations = [], [], []
with open('animallog1.txt', 'r') as myfile:
for line in myfile:
animal_name, date, location = line.strip().split(':')
animal_names.append(animal_name)
dates.append(date)
locations.append(location)
print(animal_names)
print(dates)
print(locations)
so this is the code that i have. animallog1.txt is the name of the file that i want to use.
However my output is
Traceback (most recent call last):
File "None", line 3, in <module>
builtins.FileNotFoundError: [Errno 2] No such file or directory: 'animallog1.txt'
how can i fix this?
Make sure you path is corret or try this:
file = open("sample.txt")
sample.txt is present in the current path, in my ubuntu it works.
I would take a look at this. So modifying your code could be like:
f = open('animal data.txt', 'r+');
f.readline(); //Do this until you've read your questions
f.write('Answer to the questions')
Related
I'm trying to have my Python code write everything it does to a log, with a timestamp. But it doesn't seem to work.
this is my current code:
filePath= Path('.')
time=datetime.datetime.now()
bot_log = ["","Set up the file path thingy"]
with open ('bot.log', 'a') as f:
f.write('\n'.join(bot_log)%
datetime.datetime.now().strftime("%d-%b-%Y (%H:%M:%S.%f)"))
print(bot_log[0])
but when I run it it says:
Traceback (most recent call last):
File "c:\Users\Name\Yuna-Discord-Bot\Yuna Discord Bot.py", line 15, in <module>
f.write('\n'.join(bot_log)%
TypeError: not all arguments converted during string formatting
I have tried multiple things to fix it, and this is the latest one. is there something I'm doing wrong or missing? I also want the time to be in front of the log message, but I don't think it would do that (if it worked).
You need to put "%s" somewhere in the input string before string formatting. Here's more detailed explanation.
Try this:
filePath= Path('.')
time=datetime.datetime.now()
bot_log = "%s Set up the file path thingy\n"
with open ('bot.log', 'a') as f:
f.write(bot_log % datetime.datetime.now().strftime("%d-%b-%Y (%H:%M:%S.%f)"))
print(bot_log)
It looks like you want to write three strings to your file as separate lines. I've rearranged your code to create a single list to pass to writelines, which expects an iterable:
filePath= Path('.')
time=datetime.datetime.now()
bot_log = ["","Set up the file path thingy"]
with open ('bot.log', 'a') as f:
bot_log.append(datetime.datetime.now().strftime("%d-%b-%Y (%H:%M:%S.%f)"))
f.writelines('\n'.join(bot_log))
print(bot_log[0])
EDIT: From the comments the desire is to prepend the timestamp to the message and keep it on the same line. I've used f-strings as I prefer the clarity they provide:
import datetime
from pathlib import Path
filePath = Path('.')
with open('bot.log', 'a') as f:
time = datetime.datetime.now()
msg = "Set up the file path thingy"
f.write(f"""{time.strftime("%d-%b-%Y (%H:%M:%S.%f)")} {msg}\n""")
You could also look at the logging module which does a lot of this for you.
The following error message appears when I try to run the following script:
Background: I am trying to split up a large FASTA file (~45Mb) into smaller files based on gene id. I would like to chop it everytime the ">" appears. The following .py script allows me to do so. However, everynow and then I get the following error. Any feedback would be greatly appreciated.
Script:
import os
os.chdir("/vmb/Flavia_All/Python_Commands")
outfile = os.chdir("/vmb/Flavia_All/Python_Commands")
import sys
infile = open(sys.argv[1])
outfile = []
for line in infile:
if line.startswith(">"):
if (outfile != []): outfile.close()
genename = line.strip().split('|')[1]
filename = genename+".fasta"
outfile = open(filename,'w')
outfile.write(line)
else:
outfile.write(line)
outfile.close()
Error Message when script is run:
Traceback (most recent call last):
File "splitting_fasta.py", line 14, in <module>
outfile = open(filename,'w')
IOError: [Errno 2] No such file or directory: 'AY378100.1_cds_AAR07818.1_173 [gene=pbrB/pbrC] [protein=PbrB/PbrC] [protein_id=AAR07818.1] [location=complement(152303..153451)].fasta'
*NOTE: AY378100.1_cds_AAR07818.1 is one of many genes in this FASTA sequence. This is not the only gene i have had the same message appear with. I would like to stop deleting each gene that comes up with this message.
It seems that some of the fasta "names" (the first description line with the >) contains too much. In particular contains some characters not allowed in file names.
If names like the GenBank ID - AY378100 are sufficiently unambiguous then:
genename = line.strip().split('|')[1].split('.')[0]
may be OK. If you have many fasta sequences with the same ID you probably will be OK with:
genename = line.strip().split('|')[1].split('[')[0].strip()
i have the following problem during file open:
Using PyQt QFileDialog I get path for files from user which I would like to read it
def read_file(self):
self.t_file = (QFileDialog.getOpenFileNames(self, 'Select File', '','*.txt'))
Unfortunately I cannot open a file if the path has numbers in it:
Ex:
'E:\test\02_info\test.txt'
I tried
f1 = open(self.t_file,'r')
Could anyone help me to read files from such a path format?
Thank you in advance.
EDIT:
I get the following error:
Traceback (most recent call last):
File "<pyshell#27>", line 1, in <module>
f1 = open(self.t_file,'r')
IOError: [Errno 22] invalid mode ('r') or filename: 'E:\test\x02_info\test.txt'
The problem is caused by your use of getOpenFileNames (which returns a list of files) instead of getOpenFileName (which returns a single file). You also seem to have converted the return value wrongly, but since you haven't shown the relevant code, I will just show you how it should be done (assuming you are using python2):
def read_file(self):
filename = QFileDialog.getOpenFileName(self, 'Select File', '','*.txt')
# convert to a python string
self.t_file = unicode(filename)
I wrote a code using minidom which takes an xml script, opens it as a file object and then parses that file object. Not only that, but I want the script to open multiple files that are all contained in a folder, and parse each one individually.
An example of the xml script is:
<?xml version="1.0"?>
<Data>
<data1>1</data1>
<data2>2</data2>
<data3>3</data3>
<Sub_data>
<sub_data1>0.1111111111111</sub_data1>
<sub_data2>0.2222222222222</sub_data2>
... and so on.
i.e., it's pretty standard.
Now, my code looks like this:
import os
import io
from xml.dom import minidom
#folder where xml files are located
indir = '/foo/bar/docs/'
masterlist = []
for root, dirs, filenames in os.walk(indir):
for f in filenames:
row = []
fsock = io.open(indir + f, mode = 'rt', encoding = 'cp1252')
xmldoc = minidom.parse(fsock)
...
and the error I am getting is:
Traceback (most recent call last): File "kgp_2.py", line 34, in
<module> xmldoc = minidom.parse(fsock) File
"/usr/lib/python2.7/xml/dom/minidom.py", line 1918, in parse return
expatbuilder.parse(file) File
"/usr/lib/python2.7/xml/dom/expatbuilder.py", line 928, in parse
result = builder.parseFile(file) File
"/usr/lib/python2.7/xml/dom/expatbuilder.py", line 211, in parseFile
parser.Parse("", True) xml.parsers.expat.ExpatError: no element found:
line 203, column 1381
Now, when I make the change:
fsock = io.open(indir + filenames[0], mode = 'rt', encoding = 'cp1252')
this works fine, that is, it opens the first file in the folder; but I want to parse all the files in the folder. When I do a loop like:
m = 0
... in loop:
fsock = io.open(indir + filenames[m], mode = 'rt', encoding = 'cp1252')
...
m = m+1
I get the original error.
The reason I am using the io library instead of the usual file open function is that a previous stack overflow article recommended it. Using:
fsock = open(indir + filenames[0])
like before, gets no error, but:
fsock = open(indir + f)
or
#with a loop over m, like above
fsock = open(infir + filenames[m])
get the same error as above.
A strange problem. When I print the filenames they are correct. And they are being opened, there's no error there. It's the parser that just won't parse the object files, even with filenames[m] where m = 0, surely this should be no problem?
EDIT:
Parsing document with python minidom
in this post they had a similar problem, the resolution was to use
xmldoc.seek(0)
however, for me this returns
Traceback (most recent call last):
File "kgp_2.py", line 45, in <module>
xmldoc.seek(0)
AttributeError: Document instance has no attribute 'seek'
EDIT 2: THIS HAS BEEN RESOLVED. IT WAS A CASE OF A CORRUPTED INPUT XML FILE.
Are you sure the XML data contained in all XML files is correct? Perhaps one is empty an you have to handle such Exception. Anyhow I recommend you to use xml.etree doc.
I've been trying to create a python script that edits a file, but if the file is not already there, it has an error like this:
Traceback (most recent call last):
File "openorcreatfile.py", line 56, in <module>
fileHandle = (pathToFile, 'w')
IOError: [Errno 2] No such file or directory: '/home/me/The_File.txt'
It works fine if the file exists. I've also tried this:
fileHandle = (pathToFile, 'w+')
But it comes up with the same error. Do I need to explicitly check if the file is there? If so, how do I create the file?
EDIT: Sorry, I realized the folder was missing. I'm an idiot.
The error says "No such file or directory."
Since you're trying to create a file, that must not be what's missing. So you need to create the /home/me/ directory.
See os.makedirs.
fo = open("myfile.txt", "wb")
fo.write('blah')
fo.close()
That's it, this will do the job.
myfile = open('test.txt','w')
myfile.write("This is my first text file written in python\n")
myfile.close()
To check if the file is there you can do:
import os.path
os.path.isfile(pathToFile)
so you can handle it, only if it exists:
if os.path.isfile(pathToFile):
fileHandle = (pathToFile, 'w')
else:
pass #or other thing
There are several ways to create a file in python, but if you want to create a text file, take a look at numpy.savetxt, which I think is one of the easiest and most effective ways
with open("filename.txt", "w") as f:
f.write("test")