Shell Script for creating a shortlist of phosphopeptides of Arabidopsis

ShortListArabidopsisPeptides.sh

#!/bin/sh

#####################################################################
# SYNOPSIS
#	The following script was used for the shortlist of
#	the peptides sent for Arabidopsis-specific array
#	synthesis
#
# 	DAPPLE2 Configruation 
#		Target Organism 		: {ANY}
#		PTM Type			: Phosphorylation
#		Database(s)			: All (379,247 sites)
#		Search method			: BLAST
#		Maximum results per PTM site	: 1
#
# IMPLEMENTATION
#	The script was created by Tayab Soomro ([email protected])
#
# VERSION HISTORY
# 	- 18/1/2020 -- Creation of script
#####################################################################


if [ "$#" -ne 2 ]
then
	echo "USAGE: $0 <INPUT_FILE> <OUTPUT_FILE>"
	echo "\t- INPUT_FILE -- This file contains the output from DAPPLE2"
	echo "\t- OUTPUT_FILE -- The file to output the shortlist to"
fi

input=$1
output=$2

# Printing the header
echo "Query Accession\t \
	Query Organism\t \
	Hit Site\t \
	HitSequence\t \
	Hit Protein Rank\t \
	Hit Protein E-value\t \
	RBH?\t \
	High-throughput references\t \
	Hit keywords" >> $output;

# Printing the phosphorylation sites and assocaited data.
awk -F "\t" '{print $1"\t"$3"\t"$6"\t"$9"\t"$14"\t"$15"\t"$16"\t"$18"\t"$22}' \
	DAPPLE2_UtaqTFoldY.txt | \
	grep "arabidopsis" | 	# Only Arabidopsis results were retained \
	grep -v "N/A" | \
	sort -rnk8 | 		# Sorted with highly referenced peptides on top \
	grep ";" | \
	head -n+1200 |		# Select up to 1200 peptides \
	tail -n+2 | \
	sort -rk8,8 | \
	awk -F "\t" '!seen[$9]++' # Remove duplicate peptides \
	>> $output