#!/bin/bash

if [ "$#" -ne 2 ]; then
	echo "Usage: $0 [NAME] [SEQ]"
	exit 1
fi

if [ -d $1 ]; then
	echo "Directory $1 should not already exist. Quitting."
	exit 1
fi

mkdir -p $1/$1.nvp/datasets $1/$1.nvp/list $1/$1.nvp/state $1/$1.nvp/star $1/$1.nvp/structures $1/$1.nvp/win $1/$1.nvp/tcl

echo "loadStar 1" >> $1/$1.nvp/project.txt
echo "loadDatasets 1" >> $1/$1.nvp/project.txt
echo "useIUPAC 1" >> $1/$1.nvp/project.txt

mkdir -p $1/peaklists

mkdir -p $1/sequences

echo ">$1" > $1/sequences/$1.fasta
echo $2 >> $1/sequences/$1.fasta

mkdir -p $1/figures

#mkdir -p $1/cyana
#mkdir -p $1/amber

path_to_executable=$(which mfold_umbc)

if [ -x "$path_to_executable" ] ; then
	mfold_umbc $1/sequences/$1.fasta
else
	echo "Local mfold not found. Visit the website instead for secondary structure prediction or ask Jan for help."
fi

exit 0