runlibrary.sh

#!/bin/bash
set -o pipefail

if [[ "$3" == *"gold"* ]]; then
	ti=`echo "$3" | sed 's/gold/G/g'`
	ptot=20000
	rtot=10000
	cheat="gold"
elif [[ "$3" == *"silver"* ]]; then
	ti=`echo "$3" | sed 's/silver/S/g'`
	ptot=10000
	rtot=5000
	cheat="silver"
elif [[ "$3" == *"iron"* ]]; then
	ti=`echo "$3" | sed 's/iron/I/g'`
	ptot=2000
	rtot=1000
	cheat="iron"
else
	ti=`echo "$3"`
	ptot=500
	rtot=500
	cheat="none"
fi

opt=$4

cd   tmp/$1

	rna=`cat $2 | awk 'BEGIN{s=0}{if(NF==2){c=0;for(i=1;i<=length($2);i++){if(substr($2,i,1)~/A/ || substr($2,i,1)~/T/ || substr($2,i,1)~/U/ || substr($2,i,1)~/C/ || substr($2,i,1)~/G/){c++}} s+=c/length($2)}}END{if(s/NR==1){print 1}else{print 0}}'`
	prot=`echo $rna | awk '{print 1-$1}'`

	if [[ "$rna" -ne 0 && "$prot" -ne 0 ]]; then
		exit 1;
	else

		if [[ "$rna" -eq 1 ]]; then

			bash rungenerator.rna.sh "$2" "$rtot" "$opt"
			echo "http://s.tartaglialab.com/prefills/catrapid_omics_protein/$1" > outputs/link.txt
		fi

		if [[ "$prot" -eq 1 ]]; then

			bash rungenerator.protein.sh "$2" "$ptot" "$opt"
			echo "http://s.tartaglialab.com/prefills/catrapid_omics_transcript/$1" > outputs/link.txt
		fi
	fi

cd ..