How to convert fasta file to uppercase/lowercase, without altering the annotation line

This awk-oneliner converts all lines which do not contain a '>' in the beginning to upper case:

$ awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' name.fasta

Bash Shell: Check if a file exists

To check, whether a file exists use this expression:

First, create the file thisFileExists.txt:
touch thisFileExists.txt

Now, check if it exists:
if [ -f thisFileExists.txt ]
then
  echo It is there
fi

This is what it looks like in terminal:

Bash Shell: Repeat a command every x seconds, e.g. to update list of files

When running a command that changes/creates files and takes a while, one might be interested in seeing how progress is going.
For this the "watch" command can be useful:


watch -n 2 ls *file

This will print the output of "ls *file" every 2 seconds.


watch -n 2 -d ls *file

Adding -d will highlight all the changes in comparison to the last time the command was performed