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MGJW Problem Set 1

Useful Unix Commands

Command Description
pwd Command to see where you are "Parent Working Directory"
cd /go_to_path/ Change current working directory
ls Lists files in a directory. ls -l (long listing), ls -lh (human-readable format, must be used with -l), ls -a (all, including hidden files).
mv filename1 filename2 Move or rename a file or directory.
cp filename1 filename2 Copy a file. Use -R for copying directories recursively
chmod Change the read, write, and execute permissions of a file or directory. Use ls -l to show the permissions of files in a directory
mkdir Make a directory.
head View the first few lines of a file. You can control how many lines to view.
cat Can be used to concatenate multiple files together into a single file, or to view the contents of a file in the terminal.
less A version of more with more features.
wc filename Count -w words, -l lines and/or -m characters in a file. This can be used for knowing how many reads are in a fastq file
grep Print lines matching a specified pattern or that don't match a specified pattern. grep -c '>' file.fasta will print number of > in a file which is a proxy for number of contigs in a fasta file
gzip (gunzip) Compress (uncompress) a file.
tar Archive or unarchive an entire directory into a single file. You may receive your run from a sequencing core in this format
emacs Run the Emacs text editor. It needs to be installed first.
echo Print a copy of some text to the screen. E.g. echo 'Microbial Genomics'
history Show all the commands that were run recently

Part 1

  • Check your parent working directory
  • Change your directory to home directory
  • Change your directory to your MGJW directory or create it if it does not exist
  • Make a new file using vi and name the file script.sh and type in it
echo "Hello Microbes"
echo "Hello Bacteria"
echo "Hello Viruses"
echo "Hello Bacteria"

This is quick manual of how to use vi (https://www.marquette.edu/mathematical-and-statistical-sciences/basic-vi-editor-commands.php). You will need to use letter i to start inserting in the file. After editing, you will need to use esc button and then type :wq to save and exit.

  • Count the number of lines in script.sh and redirect output to a new file called number_of_lines.txt
  • Try to run this shell script using ./script.sh, did it work?
  • Change permissions of the file to be readable, writable and executable for everyone (google chmod 777)
  • Try to rerun the file ./script.sh, did it work this time?

Part 2

  • Install wget using conda in a new environment (optional)
  • Download this file from this dropbox URL problem_set1.tar.gz and put it in MGJW or using wget -O problem_set1.tar.gz https://www.dropbox.com/s/fel9pq2hxj58gmo/problem_set1.tar.gz?dl=0 --no-check-certificate
  • Make a new directory called problem_set1 in MGJW
  • Unarchive the file (tar -xf problem_set1.tar.gz -C ./problem_set1)
  • What do you see after you unarchived the file? Do you have one directory/file or multiple?
  • List all fasta files with the extension ".fasta.gz" in the fasta folder
  • Uncompress all files ending with .fasta.gz
  • Use a command to count how many '>' characters are in each fasta file?
  • Make a new directory in your current directory and name it project1
  • Copy genome2.fasta in the same directory to a file called genome2_copy.fasta
  • Move genome2_copy.fasta to project1 folder
  • Save your history of commands in a file called commands_notes.txt