#!/bin/bash

# 24 June 2011
# Output: /projects/remc_bigdata/miR/TargetSpy/hsa-mir-483


#InstPath="/usr/local/bin/"
# 21 Nov 2010
#InstPath="/Users/grobertson/GENEREG/RNA/miRNA/targets/TargetSpy/TargetSpy/bin/"
#MaxMem="500M"

#java -Xmx${MaxMem} -jar ${InstPath}TargetSpy.jar "$@"

JAVA=/gsc/software/linux-x86_64/jdk1.6.0_18/bin/java

#TSJAR=/projects/remc_bigdata/miR/TargetSpy/bin/TargetSpy.jar
# v1.01
export PATH=/projects/remc_bigdata/miR/TargetSpy/v1.01/TargetSpy/bin:$PATH
TSJAR=/projects/remc_bigdata/miR/TargetSpy/v1.01/TargetSpy/bin/TargetSpy.jar


#MIRFA=/projects/remc_bigdata/miR/TargetSpy/sample/miRNA_isomiRs.23c_0.fa

#UTRFA=/projects/remc_bigdata/miR/TargetSpy/sample/transcripts_demo.fa
#RPT=/Users/grobertson/GENEREG/RNA/miRNA/targets/TargetSpy/TargetSpy/demo.report.20110522.txt


#echo "java -Xmx${MaxMem} -jar ${InstPath}TargetSpy.jar -microRNAs $MIRFA -transcripts $UTRFA -result $RPT"
#java -Xmx${MaxMem} -jar ${InstPath}TargetSpy.jar -microRNAs $MIRFA -transcripts $UTRFA -result $RPT

#echo "java -Xmx${MaxMem} -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA"
#java -Xmx${MaxMem} -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA -result result.isomiRs.20110522.txt

# hsa-mir-483
echo
echo
echo "============================="
echo "2173-5p, NEG corrs"
MIRFA=/projects/grobertson/resources/isomiR_FA/hsa-mir-483.MIMAT0002173.5p.fa
UTRFA=/projects/grobertson/resources/3UTRs/hsa-mir-483.MIMAT-2173.RefSeq-3UTRs.mir_gene.maturestar.c2.txt.filtered.txt.no0slope.25r.pt.mfilter.NEG.rsort.fa
echo
echo "no seed"
#echo "$JAVA -Xmx2g -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0002173-5p.RefSeq-3UTRs.c2.NEG.TargetSpy.no-seed.20110624.txt"
#$JAVA -Xmx2g -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0002173-5p.RefSeq-3UTRs.c2.NEG.TargetSpy.no-seed.20110624.txt
echo
echo "require seed"
#echo "$JAVA -Xmx2g -jar $TSJAR --seed -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0002173-5p.RefSeq-3UTRs.c2.NEG.TargetSpy.seed.20110624.txt"
#$JAVA -Xmx2g -jar $TSJAR --seed -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0002173-5p.RefSeq-3UTRs.c2.NEG.TargetSpy.seed.20110624.txt
echo
echo
echo "============================="
echo "4761-3p, NEG corrs"
MIRFA=/projects/grobertson/resources/isomiR_FA/hsa-mir-483.MIMAT0004761.3p.fa
UTRFA=/projects/grobertson/resources/3UTRs/hsa-mir-483.MIMAT-4761.RefSeq-3UTRs.mir_gene.maturestar.c2.txt.filtered.txt.no0slope.25r.pt.mfilter.NEG.rsort.fa
echo
echo "no seed"
echo "$JAVA -Xmx2g -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0004761-3p.RefSeq-3UTRs.c2.NEG.TargetSpy.no-seed.20110624.txt"
$JAVA -Xmx2g -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0004761-3p.RefSeq-3UTRs.c2.NEG.TargetSpy.no-seed.20110624.txt
echo
echo "require seed"
echo "$JAVA -Xmx2g -jar $TSJAR --seed -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0004761-3p.RefSeq-3UTRs.c2.NEG.TargetSpy.seed.20110624.txt"
$JAVA -Xmx2g -jar $TSJAR --seed -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0004761-3p.RefSeq-3UTRs.c2.NEG.TargetSpy.seed.20110624.txt
echo
echo
echo "============================="
echo "2173-5p, POS corrs"
MIRFA=/projects/grobertson/resources/isomiR_FA/hsa-mir-483.MIMAT0002173.5p.fa
UTRFA=/projects/grobertson/resources/3UTRs/hsa-mir-483.MIMAT-2173.RefSeq-3UTRs.mir_gene.maturestar.c2.txt.filtered.txt.no0slope.25r.pt.mfilter.POS.rsort.fa
echo
echo "no seed"
#echo "$JAVA -Xmx2g -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0002173-5p.RefSeq-3UTRs.c2.NEG.TargetSpy.no-seed.20110624.txt"
#$JAVA -Xmx2g -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0002173-5p.RefSeq-3UTRs.c2.POS.TargetSpy.no-seed.20110624.txt
echo
echo "require seed"
#echo "$JAVA -Xmx2g -jar $TSJAR --seed -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0002173-5p.RefSeq-3UTRs.c2.NEG.TargetSpy.seed.20110624.txt"
#$JAVA -Xmx2g -jar $TSJAR --seed -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0002173-5p.RefSeq-3UTRs.c2.POS.TargetSpy.seed.20110624.txt
echo
echo
echo "============================="
echo "4761-3p, POS corrs"
MIRFA=/projects/grobertson/resources/isomiR_FA/hsa-mir-483.MIMAT0004761.3p.fa
UTRFA=/projects/grobertson/resources/3UTRs/hsa-mir-483.MIMAT-4761.RefSeq-3UTRs.mir_gene.maturestar.c2.txt.filtered.txt.no0slope.25r.pt.mfilter.POS.rsort.fa
echo
echo "no seed"
echo "$JAVA -Xmx2g -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0004761-3p.RefSeq-3UTRs.c2.POS.TargetSpy.no-seed.20110624.txt"
$JAVA -Xmx2g -jar $TSJAR -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0004761-3p.RefSeq-3UTRs.c2.POS.TargetSpy.no-seed.20110624.txt
echo
echo "require seed"
echo "$JAVA -Xmx2g -jar $TSJAR --seed -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0004761-3p.RefSeq-3UTRs.c2.POS.TargetSpy.seed.20110624.txt"
$JAVA -Xmx2g -jar $TSJAR --seed -microRNAs $MIRFA -transcripts $UTRFA -result hsa-mir-483.MIMAT0004761-3p.RefSeq-3UTRs.c2.POS.TargetSpy.seed.20110624.txt
echo "done"










#usage: TargetSpy
# -h,--help             print this message
# -microRNAs <file>     microRNA fasta file
# -result <file>        result file
# -s,--seed             set seed as a requirement
# -threshold <score>    sens, spec or any number in (0,1). Default is sens
# -transcripts <file>   transcript fasta file
# -v,--version          version info