Practical assignment Module 1_Session 1
Module topic: Linux
Contact session title: Introduction to the command line
Trainers: Sonia Barasa and Lucier Olubayo
[!NOTE]
You may copy and paste this text into a document, or use the file on Vula to complete your assignment.
Participant:
<write your name here>
Date:
<write today’s date here>
Introduction to the command line
Introduction
The aim of this assignment is to practice the command lines we covered
during this first session of the module.
[Tools used in this session]
You’ll be using only your terminal.
[Please note]
- Hand-in information please upload your completed assignment to
the Vula ‘Assignments’ tab. Take note of the final hand-in date for
each assignment, which will be indicated on Vula.
Instructions
To begin, open a new terminal window . For each of the questions, type
the command you used. Remember to always check the content of
directories and files to understand content and formats before starting
to use them and extract information.
- What is your current directory? What’s it’s absolute path?
- How can you check your current working directory?
- Move to the unix directory then complete the exercise below
- Create a directory Assignment under Session1 (remember Session1 is under /unix/practical/)
- Move to the directory you just created
- Copy the file PccAS_v3.gff3 located under ~/course_data/rna_seq_pathogen/data to Assignment. Write 2 different possible commands to do this.
- How can you check that the file has been properly copied?
- What’s the size of the file PccAS_v3.gff3? Type both the command you used to get the information and the size
- How many lines does PccAS_v3.gff3 contain?
- Display the first 15 lines of PccAS_v3.gff3
- Display all the lines containing details of all genes contained in PccAS_v3.gff3?
Please note genes are a type of feature. More details about gff3 format here: https://learn.gencore.bio.nyu.edu/ngs-file-formats/gff3-format/
- Create a new file excluding all the gene features and name this file PccAS_v3_withoutgenes.gff3
- Rename the resulting file PccAS_v3_withoutgenes.gff3 to question_12_results.gff3
-
How many CDS does PccAS_v3.gff3 contain?
a. Write 2 separate commands to do this
b. Combine 2 commands using |
c. Write one single command
- Extract all information sequence ID: PccAS_01_v3 and copy it to a file PccAS_01_v3.gff3
- Write a command to display the names of files ending with .gff3 under the directory Assignment using wildcards
- Create a subdirectory Genomics under Assignment
- Download Plasmodium falciparum fasta file available at: http://plasmodb.org/common/downloads/release-9.0/Pfalciparum/fasta/PlasmoDB-9.0_Pfalciparum_BarcodeIsolates.fasta
- How many lines does the file contain?
- Save all the commands you type to a file named Assignment1_commands
Part 1: participant’s answer
<type your answers here. For most of the questions, you need to enter
the command you used >
________________________________________________________________________________________________________________________________________________