I'm trying to read arguments with spaces in windows cmd.
So here is the code.
from avl_tree import *
import sys,os
if __name__ == '__main__':
avl = AVLTreeMap()
infile = sys.argv[1] + '.txt'
avl._preprocessing(infile)
avl._interface(infile)
I've written it as sys.argv[1] since I'm gonna type in the cmd as following:
python filename.py textfilename
But then if the text file has spaces in the name it won't work like that.
Any suggestions?
Thanks in advance.
This is a very hacky fix, and I wouldn't necessarily suggest it because it will mess with other arguments you might need to add later but you could do something like this:
infile = " ".join(sys.argv[1:]) + '.txt'
So you if you run the program like this:
python filename.py my file name
infile will equal "my file name.txt"
Related
I am trying to run a bash script multiple times on a cluster. The issue however is I need to grab certain file names to fill the command which I only know how to do via python.
Note:I want to run the the last line (the line that calls the script) in parallel in groups of like two. How can I do this?
I have thought of: outputting all commands to a .txt and catting that in parallel. However, I feel that it is not the most efficient.
Thank you for any help
The script looks like this:
#!/usr/bin/python
import os
import sys
cwd = os.getcwd()
for filename in os.listdir(cwd):
if "_2_" in filename:
continue
elif "_1_" in filename:
in1 = os.path.join(cwd, filename)
secondread = filename.replace("_1.fastq_1_trimmed.fq","_1.fastq_2_trimmed.fq")
in2 = os.path.join(cwd, secondread)
outrename = filename.replace("_1.fastq_1_trimmed.fq",".bam")
out = "/home/blmatsum/working/bamout/" + outrename
cmd = "bbmap.sh ref=/home/blmatsum/working/datafiles/sequence.phages_clustered.fna in={} in2={} out={}".format(in1,in2,out)
os.system(cmd)
an example of the command I want to run would be:
bbmap.sh ref=/home/working/datafiles/sequence.phages_clustered.fna in=/home/working/trimmed/SRR7077355_1.fastq_1_trimmed.fq in2=/home/working/trimmed/SRR7077355_1.fastq_2_trimmed.fq out=/home/working/bamout/SRR7077355.bam'
bbmap.sh ref=/home/working/datafiles/sequence.phages_clustered.fna in=/home/working/trimmed/SRR7077366_1.fastq_1_trimmed.fq in2=/home/working/trimmed/SRR7077366_1.fastq_2_trimmed.fq out=/home/working/bamout/SRR7077366.bam
i am writing an python script. I was having some problems to open the file. The error was always that system just can not find the file.
Because of that i tried get the active path... Replace backslash ... and so on....
Is there any improvements to work with the file in the same folder?
The Code
import os
# The name of the txt file that is in the same folder.
myFile = 'noticia.txt'
# Getting the active script
diretorio = os.path.dirname(os.path.abspath(__file__))
# Replace BackSlash and concatenate myFile
correctPath = diretorio.replace("\\", "/") + "/" + myFile
# Open file
fileToRead = open(correctPath, "r")
# Store text in a variable
myText = fileToRead.read()
# Print
print(myText)
Note:
The script is in the same folder of the txt file.
Is there any improvements to work with the file in the same folder?
First off, please see PEP 8 for standard conventions on variable names.
correctPath = diretorio.replace("\\", "/") + "/" + myFile
While forward slashes are preferred when you specify a new path in your code, there is no need to replace the backslashes in a path that Windows gives you. Python and/or Windows will translate behind the scenes as necessary.
However, it would be better to use os.path.join to combine the path components (something like correct_path = os.path.join(diretorio, my_file)).
fileToRead = open(correctPath, "r")
# Store text in a variable
myText = fileToRead.read()
It is better to use a with block to manage the file, which ensures that it is closed properly, like so:
with open(correct_path, 'r') as my_file:
my_text = my_file.read()
I am working on a code that takes the path of a file and the reads it.
The code is,
import sys
import os
user_input = input("Enter the path of your file: ")
assert os.path.exists(user_input), "I did not find the file at, "+str(user_input)
However, I am on a Windows machine in which, the path names come with a \, like, C:\your\path\and\file.xlsx
Each time I enter the file name to the prompt, I need to manually replace all \ with / and then run the code.
Is there a solution such that I enter C:\your\path\and\file.xlsx but the code takes it as, C:/your/path/and/file.xlsx
Regards.
Use pythons builtin pathlib like this:
from pathlib import Path
# No matter what slash you use in the input path
# I used Raw-Prefix 'r' here because \t would otherwise be interpreted as tab
path_a = Path(r"C:\Temp\test.txt)
path_b = Path(r"C:\Temp/test.txt)
path_c = Path(r"C:/Temp/test.txt)
path_d = Path(r"C:\\Temp\\test.txt)
print(path_a, path_b, path_c, path_d)
# all Paths will be the same:
# out >> C:\Temp\test.txt C:\Temp\test.txt C:\Temp\test.txt C:\Temp\test.txt
Furthermore you can also easily extend a given Path like this:
path_e = Path("C:\Temp")
extended_path = path_e / "Test"
print(extended_path)
# out >> C:\Temp\Test
So in your case simply do it like this:
import sys
import os
from pathlib import Path
user_input = input("Enter the path of your file: ")
file_path = Path(user_input)
if not os.path.exists(file_input):
print("I did not find the file at, " + str(file_path))
Oddly enough, when I use \ in my path it just worked. But for whatever reason if yours is not, here is a way to change backslash to slash. One with a regex and one using replace:
import sys
import os
import re
user_input = input("Enter the path of your file: ")
#with a regex
user_input_regex = re.sub(r"\\", "/", user_input)
print(user_input_regex)
#using replace
user_input_replace = user_input.replace("\\","/")
print(user_input_replace)
I believe that replace is slightly faster but if you want to change other stuff (or just like using regex) the regex will probably offer more options down the road. The key to this is the \ needs to be escaped with a \ since itself is an escape character.
I'm teaching myself Python thanks to a book and nice people i find every day in SO. Thanks all of you.
The question is that i been using VS, because i find it easy, but idk how/where to write commands like "python pythonprogram.py" and make use of the optparse module as i do on a Linux console.
The program i'm working on extracts the metadata from a pdf and it's the code below.
import PyPDF2
import optparse
def printMeta(fileName):
pdfFile = pdfFileReader(file(fileName, 'rb'))
docInfo = pdfFile.getDocumentInfo()
print('[*] PDF Metadata For: ' + str(fileName))
for metaItem in docInfo:
print('[+]' + metaItem + ':' + docInfo[metaItem])
def main():
parser = optparse.OptionParser('usage %prog' + '-F <PDF File Name>')
parser.add_option('-F', dest='fileName', type='string', help='specify PDF file Name')
(options, args) = parser.parse_args()
fileName = options.fileName
if fileName == None:
print(parser.usage)
exit(0)
else:
printMeta(fileName)
if __name__ == '__main__':
fileName = 'pdftest.pdf'
main()
This is a double question, one about VS proper use and the other to ask if my code works. I want to say that the pdftest.pdf is in the python program folder so i don't need a direction if i'm right. Thanks
To make sure where your relative path starts, you might want to use os.chdir
from os import chdir
chdir("path/to/my/python/file")
then, you'll be able to import files in the same directory even if you're running the script from another folder.
Hope that helps
Please bear with me, I've not used python before, and I'm trying to get some rendering done as quick as possible and getting stopped in my tracks with this.
I'm outputting the .ifd files to a network drive (Z:), and they are stored in a folder structure like;
Z:
- \0001
- \0002
- \0003
I need to iterate over the ifd files within a single folder, but the number of files is not static so there also needs to be a definable range (1-300, 1-2500, etc). The script therefore has to be able to take an additional two arguments for a start and end range.
On each iteration it executes something called 'mantra' using this statement;
mantra -f file.FRAMENUMBER.ifd outputFile.FRAMENUMBER.png
I've found a script on the internet that is supposed to do something similar;
import sys, os
#import command line args
args = sys.argv
# get args as string
szEndRange = args.pop()
szStartRange = args.pop()
#convert args to int
nStartRange = int(szStartRange, 10);
nEndRange = int(szEndRange, 10);
nOrd = len(szStartRange);
#generate ID range
arVals = range(nStartRange, nEndRange+1);
for nID in arVals:
szFormat = 'mantra -V a -f testDebris.%%(id)0%(nOrd)dd.ifd' % {"nOrd": nOrd};
line = szFormat % {"id": nID};
os.system(line);
The problem I'm having is that I can't get it to work. It seems to iterate, and do something - but it looks like it's just spitting out ifds into a different folder somewhere.
TLDR;
I need a script which will at least take two arguments;
startFrame
endFrame
and from those create a frameRange, which is then used to iterate over all ifd files executing the following command;
mantra -f fileName.currentframe.ifd fileName.currentFrame.png
If I were able to specify the filename and the files directory and output directory that'd be great too. I've tried manually doing that but there must be some convention to that I don't know as it was coming up with errors when I tried (stopping at the colon).
If anyone could hook me up or point me in the right direction that'd be swell. I know I should try and learn python, but I'm at my wits end with the rendering and need a helping hand.
import os, subprocess, sys
if len(sys.argv) != 3:
print('Must have 2 arguments!')
print('Correct usage is "python answer.py input_dir output_dir" ')
exit()
input_dir = sys.argv[1]
output_dir = sys.argv[2]
input_file_extension = '.txt'
cmd = 'currentframe'
# iterate over the contents of the directory
for f in os.listdir(input_dir):
# index of last period in string
fi = f.rfind('.')
# separate filename from extension
file_name = f[:fi]
file_ext = f[fi:]
# create args
input_str = '%s.%s.ifd' % (os.path.join(input_dir, file_name), cmd)
output_str = '%s.%s.png' % (os.path.join(output_dir + file_name), cmd)
cli_args = ['mantra', '-f', input_str, output_str]
#call function
if subprocess.call(cli_args, shell=True):
print('An error has occurred with command "%s"' % ' '.join(cli_args))
This should be sufficient for you to either use currently or with slight modification.
Instead of specifically inputting a start and end range you could just do:
import os
path, dirs, files = os.walk("/Your/Path/Here").next()
nEndRange = len(files)
#generate ID range
arVals = range(1, nEndRange+1);
The command os.walk() counts the # of files in the folder that you specified.
Although, an even easier way of getting your desired output is like this:
import os
for filename in os.listdir('dirname'):
szFormat = 'mantra -f ' + filename + ' outputFile.FRAMENUMBER.png'
line = szFormat % {"id": filename}; # you might need to play around with this formatting
os.system(line);
Because os.listdir() iterates through the specified directory and filename is every file in that directory, so you don't even need to count them.
a little help building the command.
for nID in arVals:
command = 'mantra -V a -f '
infile = '{0}.{1:04d}.ifd '.format(filename, id)
outfile = '{0}.{1:04d}.png '.format(filename, id)
os.system(command + infile + outfile);
and definitely use os.walk or os.listdir like #logic recommends
for file in os.listdir("Z:"):
filebase = os.path.splitext(file)[0]
command = 'mantra -V a -f {0}.ifd {0}.png'.format(filebase)