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Shell Script for creating a shortlist of phosphopeptides of Arabidopsis
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| #!/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 (tayab.soomro@usask.ca) | |
| # | |
| # 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 |
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