Lesson 3 - Scripting and Permissions

Learning Objectives

• Create simple bash scripts with variables and loops.
• Edit scripts using nano.
• Run scripts using relative paths from different directories.
• Interpret file permissions with ls -l.
• Make a script executable with chmod.

Conceptual Overview

A bash script is a plain text file containing a sequence of commands. Scripts help you repeat analyses, reduce mistakes, and keep a record of what you did. The first line (shebang) tells Linux which interpreter to use. File permissions control who can read, write, or execute a file.

In bioinformatics, scripts often summarize datasets, run tools in loops, or organize outputs into consistent folders.

Worked Examples

1) Inspect permissions

ls -l uses the -l option for a long listing with permissions, size, and timestamps.

ls -l Training/short_reads/paired

Output:

total 109600
drwxrwxrwx 1 bodeoni bodeoni     4096 Jan 16 16:45 SRR1553607
-rwxrwxrwx 1 bodeoni bodeoni 56113290 Jan 16 11:34 SRR1553607_1.fastq
-rwxrwxrwx 1 bodeoni bodeoni 56113290 Jan 16 11:34 SRR1553607_2.fastq

2) Create a script with nano

nano opens a simple text editor in the terminal.

nano Module_1_Linux/summarize_fastq.sh

Paste the script below into nano (save with Ctrl+O, exit with Ctrl+X): This script uses wc -l to count lines and head -n 1 to show the first header line.

#!/usr/bin/env bash

FILES=(
  "Training/short_reads/paired/SRR1553607_1.fastq"
  "Training/long_reads/barcode57.fastq"
)

for f in "${FILES[@]}"; do
  echo "FILE: $f"
  echo "LINES: $(wc -l < "$f")"
  head -n 1 "$f"
  echo ""
done

3) Run the script with bash

bash runs the script using the Bash interpreter.

bash Module_1_Linux/summarize_fastq.sh

Output:

FILE: Training/short_reads/paired/SRR1553607_1.fastq
LINES: 813780
@SRR1553607.1 1 length=101

FILE: Training/long_reads/barcode57.fastq
LINES: 34268
@5832c8b6-696e-46cd-be8d-73b789952b4e  st:Z:2024-06-27T02:52:17.771+00:00  RG:Z:fba2136ff67b57066e5c7e23383eba9e075ff2b2_dna_r10.4.1_e8.2_400bps_sup@v4.3.0

4) Make the script executable

chmod +x adds the execute (x) permission. No output appears when it succeeds.

chmod +x Module_1_Linux/summarize_fastq.sh

Now you can run it directly using a relative path.

./Module_1_Linux/summarize_fastq.sh

Exercises

1. Create a script named fastq_summary.sh in Module_1_Linux/ that loops over all FASTQ files in Training/long_reads and prints:

• filename
• line count
• first header line

2. Run the script from the Module_1_Linux/ directory using a relative path.

3. Make your script executable and run it without calling bash explicitly.

4. Create a results/ folder inside Module_1_Linux/ and redirect the script output to results/long_reads_summary.txt.

5. Challenge: Extend your script to include Training/short_reads/paired/SRR1553607_1.fastq and Training/short_reads/paired/SRR1553607_2.fastq, and print an estimated read count for each (lines / 4).

Solutions

Solution 1

nano opens the file so you can paste the script.

nano Module_1_Linux/fastq_summary.sh

Script content:

#!/usr/bin/env bash

for f in Training/long_reads/*.fastq; do
  echo "FILE: $f"
  echo "LINES: $(wc -l < "$f")"
  head -n 1 "$f"
  echo ""
done

Solution 2

./ runs a script from the current directory.

cd Module_1_Linux
bash ./fastq_summary.sh

Solution 3

chmod +x makes the script executable.

chmod +x Module_1_Linux/fastq_summary.sh
./fastq_summary.sh

Solution 4

mkdir -p creates the folder, and > redirects output to a file.

mkdir -p Module_1_Linux/results
Module_1_Linux/fastq_summary.sh > Module_1_Linux/results/long_reads_summary.txt

Solution 5

Use wc -l for lines and divide by 4 for reads.

#!/usr/bin/env bash

FILES=(
  "Training/long_reads/barcode57.fastq"
  "Training/long_reads/barcode58.fastq"
  "Training/long_reads/sample3.fastq"
  "Training/short_reads/paired/SRR1553607_1.fastq"
  "Training/short_reads/paired/SRR1553607_2.fastq"
)

for f in "${FILES[@]}"; do
  lines=$(wc -l < "$f")
  reads=$((lines / 4))
  echo "FILE: $f"
  echo "READS: $reads"
  head -n 1 "$f"
  echo ""
done