ar_setup_meta.sh

#!/bin/bash

#Generates up/down regulated gene list based on Log2FoldChange and P-adj values 
#results table is generated by DESeq2 and ashr
echo DISCLAIMER: Results table MUST have symbols column and use lfcShrink \(..., type = \"ashr\"\)

#Creates basename "_example" 
name=$(basename "$1" |  sed 's/\.csv\|res//g')

#User inputs L2FC and PADJ threshold
echo Enter Log2FoldChange Threshold
read x

echo Enter P-Adj Threshold
read p

#creates metascape folder for data
mkdir meta${name}
awk -F, -v p=$p '{if(NR != 1 && $6 <= p){print $0}}' $1 >> temp

#generates upregulated and downregulated gene list 
awk -F, -v x=$x '{if($3 >= x){print $1}}' temp | sed 's/"//g' >> ${name}_upreg_input.csv
awk -F, -v x=$x '{if($3 <= -x){print $1}}' temp | sed 's/"//g' >> ${name}_downreg_input.csv
rm temp
exit

#counts the number of genes with gene symbols
upreg=$(awk -F, -v x=$x '{if($3 >= x && $7 != "NA"){print $7}}' temp | wc -l)
downreg=$(awk -F, -v x=$x '{if($3 <= -x && $7 != "NA"){print $7}}' temp | wc -l)

#enters inputted data into text file
printf "Metascape Input Data for ${1} \nLog2FoldChange Threshold = ${x} \nP-Adj Threshhold = ${p} \nDown Regulated Genes with Symbols = ${downreg} \nUp Regulated Genes with Symbols = ${upreg}" >> meta${name}/readme.txt

#counts the total number of ensembl ids 
total_upreg=$(cat meta${name}/meta_input_upreg${name}.csv | wc -l)
total_downreg=$(cat meta${name}/meta_input_downreg${name}.csv | wc -l)

#enters total number of ensembl ids into text file 
printf "\nTotal Down Regulated Gene Ids = ${total_downreg} \nTotal Up Regulated Gene Ids = ${total_upreg} \n" >>  meta${name}/readme.txt

#prints out text file for clarity 
cat meta$name/readme.txt

#removes previous metascape folder if this specific results table has been analyzed
if [ -d "/home/chienlab/Alan/VG 2019 RNASeq/meta${name}" ]; 
    then rm -r "/home/chienlab/Alan/VG 2019 RNASeq/meta${name}"; fi

#moves data folder into metascape home folder (NEEDS TO BE CREATED BEFORE HAND)
mv meta${name} ~/Alan/VG 2019 RNASeq/meta${name}

echo "Results saved to ~/Alan/VG 2019 RNASeq/meta${name}."