Perl & Genomics

Bioinformatics for Genomics Course – University of Padua

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Apr 07 2014

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quiz

Lab02/0: First quiz

This post is a part of the second laboratory session. Please refer to the main post.

First quiz for the practical: check how much did you learn about the terminal and its commands

The following command:

mkdir My Directory

Will create a new directory called “My Directory”

If I wanted to create a “My Directory” new directory, I had to add quotes around the two words.

Will create a directory called “My”

Will move “My” to “Directory”

In your home you have two directories: lab1 and lab2. You are currently working on lab1 and want to list files present in the lab2 directory. Choose the right command(s):

ls lab2

cat /home/lab2

ls ../lab2

cat ../lab2

cat lab2

The following command:

grep > genome.fasta

Print only lines containing the > in a file called genome.fasta

Will redirect the output of the “grep” command into a file

The genome.fasta file will contain some lines after the execution

If the genome.fasta exists before the command, will change after the command execution

The command head will print the first 10 lines of a file. To print the first 100:

head filename -n 100

head -n 100 filename

head -n100 filename

head filename | tail -n 100

To count how many sequences you have in “genome.fasta”, you can:

cat genomes.fasta | grep “>” | wc -l

grep > genomes.fasta | wc -l

grep “>” genomes.fasta | wc -l

wc -l “>” genomes.fasta

grep “>” genomes.fasta > lines (and then) wc -l lines

less “>” genomes.fasta

If you want to see how many files (or directories) you have in your home folder:

ls ~ | wc -l

ls /home | wc -l

ls ~ > wc -l

ls ~ > ls (and then) wc -l ls

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