Open and read files in python

deKoch13 · 03-14-2019, 06:35 AM

Hi!

I extracted mapped and unmapped reads of different BAM files using a bash script.
Now, I want to compare which reads are in which BAM files in python.

I imagined to use python sets (union, intersection) to do that.
Unfortunately, I have only little python experience.
I already could write a script that does the job, but without using loops etc for automation.

I tried this:

import glob

path = "/path/to/files/*.txt"
list_of_files=glob.glob(path)

Now, I want to read in all lines of the files using readlines(), and store the output in separate variables to create sets using the .update() function.
Do you have an idea how to do that?

Greetings

luminasapientiae · 03-25-2019, 09:20 AM

Why you are using Python?
You can look for Biopython module. There is a function to import your seq and alignment.

The same can be made (with more options) in linux terminal w/ STAR algorithm.

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03-14-2019, 06:35 AM	#1
deKoch13 Member Location: HD Join Date: Mar 2019 Posts: 12	Open and read files in python Hi! I extracted mapped and unmapped reads of different BAM files using a bash script. Now, I want to compare which reads are in which BAM files in python. I imagined to use python sets (union, intersection) to do that. Unfortunately, I have only little python experience. I already could write a script that does the job, but without using loops etc for automation. I tried this: import glob path = "/path/to/files/*.txt" list_of_files=glob.glob(path) Now, I want to read in all lines of the files using readlines(), and store the output in separate variables to create sets using the .update() function. Do you have an idea how to do that? Greetings

03-25-2019, 09:20 AM	#2
luminasapientiae Junior Member Location: Brazil Join Date: Sep 2017 Posts: 5	Why you are using Python? You can look for Biopython module. There is a function to import your seq and alignment. The same can be made (with more options) in linux terminal w/ STAR algorithm.