How to turn a python script into a command-line program

Using the argparse package, you can turn any Python script into a program you can run from the command-line in bash (terminal, shell, etc. on Mac or Linux). This video shows how to use argparse with an example of turning a fasta file into a fastq file.

[miryamadvanced]

please my dear can you make one clip write code with python for auto installer application
or hide apk in image

when open image that apk is runing automatic

[shubhamaggarwal]

Nicely Explained: Keep doing the good work.
Got the

[System-brtx]

I just want terminal to automatically run a command when i run the .py script

[tandavme]

You ain have to install argparse, its comes with python3 's standard library

[voytechj]

hello,

one small improvement would be getting rid off file.close() statements, using "with" statement:

with open(args.input) as f, open(args.output, 'w') as fout:
f.read()
fout.write(...)

in Python "with" will take care of closing files automatically

[NadiasTravelTales]

How you submit this kind of script to cluster?

[bossman]

Yeah i need this to make an hashing algorithm program...




Thx VERY much!

[arto_]

exactly what I was searching for thank you so much

[Davidemmanuelkatz]

Awesome Video. Love seeing Python used in wide variety of sciences.

[stringsc]

for a more native flavor you need to move your script to any of the bin folders like /usr/bin or local/bin so it is available system wide and then to use $command arg arg ...n instead of ./script.py arg ...n syntax

[mohammedahmed]

Thanks for the clear and concise demonstration.

[bsyo]

can i do this without the command prompt?

[gatherswag]

Hi Maria,

I'm wondering if there is a similar package for R scripts?

Cheers

[medhabhat]

can you suggest vice versa if i want to try

[starwords]

I think I installed argparse. But how do I open it so it is in a cool window on the right side like the one in the video and I can type things into it . (I am using a pc)

[napier]

Hi, how do you make the dollar sign appear on a new line in terminal (or iTerm2)?

[sudhanshukumar]

Wow! That's what I was searching for.
Kudos to you!!!

[haroldovivallo]

Didn't know about argparse, thanks.

[DanielFPaulo]

Hi Maria,

Nice video, thank you so much!
I'm starting learn python for bioinformatics, as I would like to write my own scripts.
I'm woundering if you could explain what seq = "" and fout.write("@" + line[1:]) means in your script.
Also, I found that if you move:

fout.write("@" + line[1:])
seq = ""

to one space before, the script crash. Why that?
Thank you again!
Dani.

[brendannolan]

Whenever I want to do something with Python or Bash and I find an OMGenomics video about it I'm like "This is going to be great. It's going to be clear and tell me everything I need"; that just happened again.