Basic python script structure

Create file

Create file (script.py) in Atom.
Open terminal at side to run script.
Script:

#!/usr/bin/env python
print("this is script.py")

Make it executable

In the terminal, make it executable: chmod +x script.py
Run: ./script.py

Main function

Add def main()
Add “if name” bit at end

#!/usr/bin/env python
print("this is script.py")

def main():
    print("this is the main function")

if __name__ == '__main__':
    main()

Run: ./script.py

Read in the R1.fastq read file

At the top of the script, import the modules argparse and sys
Define a function (any name, here it’s called parse_args())
To read in R1.fastq use add_argument: parser.add_argument(“R1_file”)
Other input args can be added here.

#!/usr/bin/env python
import argparse
import sys
print("this is script.py")

def parse_args():
    parser=argparse.ArgumentParser(description="a script to do stuff")
    parser.add_argument("R1_file")
    args=parser.parse_args()
    return args

def main():
    print("this is the main function")

if __name__ == '__main__':
    main()

Run, but provide file: ./script.py R1.fq

Read the inputs in the main function

Tell the main function to run the parse_args function
and save the output as an object called inputs (or anything)
Access the individual arg with inputs.R1_file

#!/usr/bin/env python
import argparse
import sys
print("this is script.py")

def parse_args():
    parser=argparse.ArgumentParser(description="a script to do stuff")
    parser.add_argument("R1_file")
    args=parser.parse_args()
    return args

def main():
    print("this is the main function")
    inputs=parse_args()
    print(inputs.R1_file)

if __name__ == '__main__':
    main()

Run: ./script.py R1.fq

Make a separate function to process files

Add a line to main function telling it to run another function called process_files()
Also tell it to use the inputs (or whatever they were called) as an argument to this function call
Make the new function: process_files(things) – it doesn’t have to say inputs here, it can say anything (here: things)
Access the R1_file arg in this function, but use “things” not “inputs”

#!/usr/bin/env python
import argparse
import sys
print("this is script.py")

def parse_args():
    parser=argparse.ArgumentParser(description="a script to do stuff")
    parser.add_argument("R1_file")
    args=parser.parse_args()
    return args

def process_files(things):
    print("this is the process files function")
    print(things.R1_file)

def main():
    print("this is the main function")
    inputs=parse_args()
    print(inputs.R1_file)
    process_files(inputs)

if __name__ == '__main__':
    main()

Run a tool to get stats your input R1 file

Use a tool to get stats on this file
e.g. if the command is seqkit stats R1.fq > R1.stats
Break this command into a list of strings, save it as “cmd”
Run the tool with subprocess.run(cmd)
add import subprocess at the top of the script

#!/usr/bin/env python
import argparse
import sys
import subprocess
print("this is script.py")

def parse_args():
    parser=argparse.ArgumentParser(description="a script to do stuff")
    parser.add_argument("R1_file")
    args=parser.parse_args()
    return args

def process_files(things):
    print("this is the process files function")
    print(things.R1_file)
    cmd=["seqkit", "stats", things.R1_file]
    subprocess.run(cmd)

def main():
    print("this is the main function")
    inputs=parse_args()
    print(inputs.R1_file)
    process_files(inputs)

if __name__ == '__main__':
    main()

Put this stats step into its own function

Define a new function called stats that takes in a file - stats(file)
Run this from within the process_files function
Note that in here, we give stats the arg called “things.R1_file”
Then, stats considers this to be “file”

#!/usr/bin/env python
import argparse
import sys
import subprocess
print("this is script.py")

def parse_args():
    parser=argparse.ArgumentParser(description="a script to do stuff")
    parser.add_argument("R1_file")
    args=parser.parse_args()
    return args

def stats(file):
    cmd=["seqkit", "stats", file]
    subprocess.run(cmd)

def process_files(things):
    print("this is the process files function")
    print(things.R1_file)
    # cmd=["seqkit", "stats", things.R1_file]
    # subprocess.run(cmd)
    stats(things.R1_file)

def main():
    print("this is the main function")
    inputs=parse_args()
    print(inputs.R1_file)
    process_files(inputs)

if __name__ == '__main__':
    main()

Add in an optional input

Add number of threads as a new optional arg - note the two dashes
Without these two dashes, it would be a required, positional arg
default type is string, so specify that type=int
can add in a default value
Check you can print the threads arg from the main function

#!/usr/bin/env python
import argparse
import sys
import subprocess
print("this is script.py")

def parse_args():
    parser=argparse.ArgumentParser(description="a script to do stuff")
    parser.add_argument("R1_file")
    parser.add_argument("--threads", type=int, default=16)
    args=parser.parse_args()
    return args

def stats(file):
    cmd=["seqkit", "stats", file]
    subprocess.run(cmd)

def process_files(things):
    print("this is the process files function")
    print(things.R1_file)
    # cmd=["seqkit", "stats", things.R1_file]
    # subprocess.run(cmd)
    stats(things.R1_file)

def main():
    print("this is the main function")
    inputs=parse_args()
    print(inputs.R1_file)
    print(inputs.threads)
    process_files(inputs)

if __name__ == '__main__':
    main() 

Run, and specify threads: ./script.py R1.fq --threads 32

Print all the inputs to the script

We want to print the supplied args, and any default args (if not supplied)
Put this in the parse_args function

#!/usr/bin/env python
import argparse
import sys
import subprocess
print("this is script.py")

def parse_args():
    parser=argparse.ArgumentParser(description="a script to do stuff")
    parser.add_argument("R1_file")
    parser.add_argument("--threads", type=int, default=16)
    args=parser.parse_args()

    print("the inputs are:")
    for arg in vars(args):
        print("{} is {}".format(arg, getattr(args, arg)))

    return args

def stats(file):
    cmd=["seqkit", "stats", file]
    subprocess.run(cmd)

def process_files(things):
    print("this is the process files function")
    print(things.R1_file)
    # cmd=["seqkit", "stats", things.R1_file]
    # subprocess.run(cmd)
    stats(things.R1_file)

def main():
    print("this is the main function")
    inputs=parse_args()
    print(inputs.R1_file)
    print(inputs.threads)
    process_files(inputs)

if __name__ == '__main__':
    main()

Run with and without specifying the --threads