Genomic Informatics for Beginners #2

This is a summary of the lecture content for the ourse ‘Shotgun Sequencing – Principle and Experiments’ in IGB, NCHU. This course module is designed to enable students with basic computer skills to utilize some bioinformatics software to perform analysis of genomic data. The second part of this course will explore more in using shell scripts and also scripts using Python.

Lets try some updated Hello World script using variables

vi HelloWorld_today.sh

#!/usr/bin/sh
echo "Hello teacher!"
echo "The current time is $(date -R)."

The variable ($) symbol, hashtag (#) symbol in the script

vi greet.sh

#!/usr/bin/bash
echo "What is your name? "
read name
echo "Hello $name."

Lets try another greeting using ‘whoami’

#!/usr/bin/bash
# This script greets the user by name
name=$(whoami)
echo "Hello, $name! How are you today?"

Python

Work with python

$ python3
Python 3.9.13 (main, Aug 25 2022, 23:26:10) 
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> 

The ‘Hello world!’

>>> print ("Hello World!")
Hello World!

control-D to quit
More practice on editing/running scripts

vi helloworld.py

print("Hello, world!")

run the python script

$ python3 greet.py
Hello, world!

Try this:

name = input("What is your name? ")
print("Hello, " + name + "! Nice to meet you.")

X + Y = ?
Variable types – integers, floating-point numbers, strings

Conda

an open source package management system and environment management system
conda create environment
conda activate
conda install
conda activate

Assembly of shotgun sequencing data

unicycler (another post)

SFTP – file transport

> sftp username@ip.address

Navigating

pwd – Print the working directory on the remote server.
lpwd – Print the working directory on the local machine.
cd – Change the directory on the remote server.
lcd – Change the directory on the local machine.

Listing

ls – List files in the current directory on the remote server.
lls – List files in the current directory on the local machine.

Transfer files

get – Download a file from the remote server to the local machine.
put – Upload a file from the local machine to the remote server.

File management

rm – Remove a file on the remote server.
mkdir – Create a directory on the remote server.
rmdir – Remove a directory on the remote server.

Leaving SFTP

bye or exit – Close the SFTP session.

tar-cvc [archive file] [file | directories]
tar -cvf allgenomes.tar *.gb
tar -tvf allgenomes.tar *.gb
tar -xvf allgenomes.tar *.gb

Handling archive files

tar-cvc [archive file] [file | directories]
tar -cvf allgenomes.tar *.gb
tar -tvf allgenomes.tar *.gb
tar -xvf allgenomes.tar *.gb

gzip, gunzip

Visualization of the assembly results (Windows)

to be continued…