#!/bin/bash
##################################################################################
#Andy Rampersaud, 02.23.16
#This script would be used to summarize Read_Strandness statistics 
#Way to run script:
#Usage: 
#./Read_Strandness_Summary.sh
##################################################################################
#---------------------------------------------------------------------------------
#Source the setup file to initialize variables
source ../00_Setup_Pipeline/01_Pipeline_Setup.sh
#---------------------------------------------------------------------------------
#Check that each variable prints a value to the terminal:
echo "-----------------------"
echo "Start of variable list:"
echo "-----------------------"
echo "Dataset_DIR:"
echo ${Dataset_DIR}
echo "Sample_Labels_DIR:"
echo ${Sample_Labels_DIR}
echo "SCRIPT_DIR:"
echo ${SCRIPT_DIR}
echo "TIME_LIMIT:"
echo ${TIME_LIMIT}
echo "-----------------------"
echo "End of variable list"
echo "-----------------------"
#---------------------------------------------------------------------------------
##################################################################################
#---------------------------------------------------------------------------------
#Retrieve the job name for this step:
Current_DIR=$(pwd)
#Extract the folder name:
DIR_name=`basename ${Current_DIR}`
#---------------------------------------------------------------------------------
OUTPUT_DIR=${Dataset_DIR}/Scripts/${DIR_name}/Job_Summary
###############################
if [ ! -d ${OUTPUT_DIR} ]; then
mkdir -p ${OUTPUT_DIR}
else
#Remove dir:
rm -r ${OUTPUT_DIR}
#Make new dir:
mkdir -p ${OUTPUT_DIR}
fi
###############################
OUTPUT_FILE=$OUTPUT_DIR/Read_Strandness_Stats.txt
######################
if [ -f $OUTPUT_FILE ]
then 
rm $OUTPUT_FILE
else
touch $OUTPUT_FILE
fi
######################
cd ${Current_DIR}
################################################
#A text file (Sample_Labels.txt) is needed to run this script
SCRIPT_DIR=$(pwd)
cp $Sample_Labels_DIR/Sample_Labels.txt $SCRIPT_DIR
################################################
#The text file is formatted like the following:
#----------------------------------------------
#Sample_DIR	Sample_ID	Description
#Sample_Waxman-TP17	G83_M1	Male 8wk-pool 1
#Sample_Waxman-TP18	G83_M2	Male 8wk-pool 2
#Sample_Waxman-TP19	G83_M3	Female 8wk-pool 1
#Sample_Waxman-TP20	G83_M4	Female 8wk-pool 2	
#----------------------------------------------
#The 1st column: The Sample_DIR name
#The 2nd column: Waxman Lab Sample_ID 
#The 3rd column: Sample's description 
################################################
#Text file has a header line to ignore:
tail -n +2 Sample_Labels.txt > Sample_Labels.temp
#Use a while loop to run jobs
while IFS=$'\t' read -r -a myArray
do
#---------------------------
##Check that text file is read in properly:
#echo 'Sample_DIR:'
Sample_DIR=${myArray[0]}
#echo 'Sample_ID:'
Sample_ID=${myArray[1]}
#echo $Sample_ID
#echo 'Description:'
Description=${myArray[2]}
#echo $Description
#---------------------------
echo
echo $Sample_ID
#Need to cd to sample specific Read_Strandness folder
cd ${Dataset_DIR}/$Sample_ID/fastq/tophat2/Read_Strandness
#Print $Sample_ID
echo $Sample_ID':' >> $OUTPUT_FILE
#Concatenate file to $OUTPUT_FILE
cat $Sample_ID'_Read_Strandness.txt' >> $OUTPUT_FILE
#Add a return line
echo >> $OUTPUT_FILE
done < Sample_Labels.temp
cd ${Current_DIR}
#Remove the temp file:
rm Sample_Labels.temp
echo '#--------------------------------------------------------------------------'
echo 'Check out '$OUTPUT_FILE
echo '#--------------------------------------------------------------------------'
##################################################################################