4 Week 2 Exercises

4.1 In-class exercises

We can run the script on a file (assuming we are in bash_for_bio/):

./scripts/week2/sam_count.sh ./data/my_file.bam

Try out the above script on ./data/CALU1_combined_final.sam.

Make sure you are in the top folder (bash_for_bio) when you do it.

Run run_bwa.sh using:

./scripts/week2/run_bwa.sh ./data/CALU1_combined_final.fasta

Run process_data.R:

module load fhR
Rscript process_data.R input_file="LUSC_clinical.csv"
module purge

Run process_data.py:

module load fhPython
python3 process_file.py lusc_file.csv
module purge

4.2 Homework Exercises

All exercises are required for the badge.

Copy the below script into a file called samtools_count.sh. What does the script do?

#!/bin/bash
module load SAMtools
samtools view -c $1

How would we modify the above script to redirect the output to ${1}.counts.txt?

Make sure you can get scripts/week2/run_bwa.sh to run on rhino.
Modify scripts/week2/run_bwa.sh to
1. Take an additional argument, a folder path
2. Save the SAM file to this folder path

Hint 1: I recommend that you copy run_bwa.sh into a new script and work from there. Put your code into the codeblock below:

Write an example to run your new version of the script below and run it:

For question 4, pick one language to answer.

4R. (R) Modify the below R script and save it to a file called scripts/week2/r_csv_script.R. It should also take an argument called $FILEPATH for read.csv():

library(tidyverse)
csv_file <- read_csv("myfile.csv")
summary(csv_file)

How would you run this on the command line?

module load fhR
-----
module purge

How would you redirect the output of your script to a file?

4Py. (py) Modify the below Python script to be runnable and save it to scripts/week2/py_csv_script.py. Your new version should also take the first position argument (a file path) and process the file:

#| eval: false
import pandas as pd
csv_file = pd.read_csv("my_file.csv")
csv_file.describe()

How would you run this on the command line?

module load fhPython
-----
module purge