bash.md

Dataset processing bash codes!

step 1: get only the protine names

$awk '{ print $2 $4 }' filename.txt //$1 for first column,$2 for second column

Step 2: get only the unique portine names

https://stackoverflow.com/questions/618378/select-unique-or-distinct-values-from-a-list-in-unix-shell-script
$./yourscript.ksh | sort | uniq //FYI, yes, the sort is necessary in this command line, uniq only strips duplicate lines that are 										immediately after each other

setp 3: get my own written shell script to get all the protin fasta from UNIPROT used in fasta/getFasta.sh

count all the K :

$cat proteinB protinlistA | tr -cd 'K' | wc -c

replace multiple spaces with one

$tr -s " " < file

comparing two files

While $grep -v -f 1.txt 2.txt > 3.txt gives you the differences of two files (what is in 2.txt and not in 1.txt), you could easily do a

$grep -f 1.txt 2.txt > 3.txt to collect all common lines, which should provide an easy solution to your problem. If you have sorted files, you should take comm nonetheless. Regards!

replace:

https://www.cyberciti.biz/faq/howto-delete-word-using-sed-under-unix-linux-bsd-appleosx/

• $sed -e 's/<regex-for-word>//g' input > output
• $sed -e 's/<[a-zA-Z0-9]*[g|G]>//g' input
• $sed 's/[[]]//g' /path/to/file
• $sed 's/[//g;s/]//g' /path/to/file