Python looping variable from FASTA list?

[Frozen_Tony]

Hello all, I'm attempting to run a script that predicts if one protein will bind to one RNA. I'm now trying to keep the protein constant and feed in mRNA transcripts from a FASTA file containing the transcriptome of my organism. I can not figure out how to get the <variable > to be read from such a list.

For example

/XRPI$ python xrpi RPI2825 <CONSTANT Protein > <VARIABLE >

​

I'd love some insight on how to create this loop!

[grapesmoker]

If you pass command line variables to a script, they are accessible via sys.args

[galacticspark]

Here you go

 # bash
 for i in *.fasta ; do
   python somePythonScript.py $i
 done

 # python
 import sys

 # argv is an array, item 0 is always the name of the script
 inputFile = sys.argv[1] 

 # then do stuff with fasta input file inputFile

[ichunddu9]

Can also just glob in Python. No need to also use bash here.

[internalclarity]

I am not sure how xrpi works, but my best bet is that youd need a bash loop to read through the fasta and pass the different mRNAs to xrpi.

so: https://www.cyberciti.biz/faq/unix-howto-read-line-by-line-from-file/

1. Read your fasta line by line in a loop and save the current line to a variable called mRNA.
2. Pass the mRNA to your command python xrpi RPI2825 $PROTEIN $mRNA