#!/bin/bash

PATH=/data/results/tools/align/cufflinks-2.2.1.Linux_x86_64:$PATH; export PATH

LABELS[1]="GM-tr-0h-a"
LABELS[2]="GM-tr-0h-b"
LABELS[3]="GM-tr-1h-a"
LABELS[4]="GM-tr-1h-b"



#rm time_Cuff-mm9.txt
CONCUR=1
THREADS=8

echo BEGIN Cufflinks witth $CONCUR Concurrent and $THREADS threads `date` >> time_Cuff-mm9.txt
#for i in `seq 6 16`
#for i in `seq 5 5`
#do
#echo ${LABELS[$i]}


#ls */accepted_hits_ensembl_novel/transcripts.gtf  > assemblies_GM.txt
#cuffmerge -p 8 -s /data/results/reference/hsa/GRCh37/human_g1k_v37.fasta -o merged_asm_GM -g /data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf assemblies_GM.txt
#cd merged_asm_GM
#awk -f /data/results/tools/rnaseq/collect-locus-coords-from-merged-gtf.awk merged.gtf > merged-xloc-coords.csv
# get bt for xlocs
#awk -v f="/data/results/reference/hsa/GRCh37/Homo_sapiens.GRCh37.75.gtf.biotypes" -f /data/results/tools/rnaseq/add-biotype-to-merged-gtf1.awk merged.gtf > merged-biotypes.txt

i=1
j=3
echo ${LABELS[i]},${LABELS[j]}

cuffdiff -L ${LABELS[i]},${LABELS[j]} --no-effective-length-correction --library-type fr-secondstrand --no-update-check --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[j]}  ../merged_asm_GM/merged.gtf ../bams/${LABELS[$i]}.bam2,../bams/${LABELS[$i+1]}.bam2 ../bams/${LABELS[$j]}.bam2,../bams/${LABELS[$j+1]}.bam2  &> cuffdiff_${LABELS[i]}_vs_${LABELS[j]}.log

#awk -v f="/data/images/proton/run90/pairings/merged_asm_GM/merged-xloc-coords.csv" -f /data/results/tools/rnaseq/filter-cuffdiff-genes2.awk gene_exp.diff  > gene_exp.diff.minlen100 
#awk -v f="/data/images/proton/run90/pairings/merged_asm_GM/merged-biotypes.txt" -f /data/results/tools/rnaseq/add-biotype-to-cuffdiff1.awk gene_exp.diff.minlen100 > gene_exp.diff.minlen100.biotype

Rscript /data/results/tools/rnaseq/re_adjust_q_values.r gene_exp.diff.minlen100.biotype



exit 0

#sem -j 2 cuffdiff  -L ${LABELS[i]},${LABELS[j]}  --no-update-check --library-type fr-unstranded --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[j]}  merged_asm_GKlab/merged.gtf ${IN_DIR[i]}/accepted_hits.bam ${IN_DIR[j]}/accepted_hits.bam  &> cuffdiff2_SVT_S_vs_SVT_V.log 

# wt_untr vs wt_LPS
i=10
j=9
sem -j 2 cuffdiff  -L ${LABELS[i]},${LABELS[j]}  --no-update-check --library-type fr-unstranded --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[j]}  merged_asm_GKlab/merged.gtf ${IN_DIR[i]}/accepted_hits.bam,${IN_DIR[i+6]}/accepted_hits.bam ${IN_DIR[j]}/accepted_hits.bam,${IN_DIR[j+6]}/accepted_hits.bam  &> cuffdiff_${LABELS[i]}_${LABELS[j]}.log 


# wt_untr vs wt_IL1b
i=10
j=8

sem -j 2 cuffdiff  -L ${LABELS[i]},${LABELS[j]}  --no-update-check --library-type fr-unstranded --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[j]}  merged_asm_GKlab/merged.gtf ${IN_DIR[i]}/accepted_hits.bam,${IN_DIR[i+6]}/accepted_hits.bam ${IN_DIR[j]}/accepted_hits.bam,${IN_DIR[j+6]}/accepted_hits.bam  &> cuffdiff_${LABELS[i]}_${LABELS[j]}.log 

# wt_untr vs dd_untr
i=10
j=7
sem -j 2 cuffdiff  -L ${LABELS[i]},${LABELS[j]}  --no-update-check --library-type fr-unstranded --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[j]}  merged_asm_GKlab/merged.gtf ${IN_DIR[i]}/accepted_hits.bam,${IN_DIR[i+6]}/accepted_hits.bam ${IN_DIR[j]}/accepted_hits.bam,${IN_DIR[j+6]}/accepted_hits.bam  &> cuffdiff_${LABELS[i]}_${LABELS[j]}.log 

# dd_untr vs dd_LPS
i=7
j=6
sem -j 2 cuffdiff  -L ${LABELS[i]},${LABELS[j]}  --no-update-check --library-type fr-unstranded --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[j]}  merged_asm_GKlab/merged.gtf ${IN_DIR[i]}/accepted_hits.bam,${IN_DIR[i+6]}/accepted_hits.bam ${IN_DIR[j]}/accepted_hits.bam,${IN_DIR[j+6]}/accepted_hits.bam  &> cuffdiff_${LABELS[i]}_${LABELS[j]}.log 

# dd_untr vs dd_IL1b
i=7
j=5
sem -j 2 cuffdiff  -L ${LABELS[i]},${LABELS[j]}  --no-update-check --library-type fr-unstranded --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[j]}  merged_asm_GKlab/merged.gtf ${IN_DIR[i]}/accepted_hits.bam,${IN_DIR[i+6]}/accepted_hits.bam ${IN_DIR[j]}/accepted_hits.bam,${IN_DIR[j+6]}/accepted_hits.bam  &> cuffdiff_${LABELS[i]}_${LABELS[j]}.log 

# wt_LPS vs dd_LPS
i=9
j=6
sem -j 2 cuffdiff  -L ${LABELS[i]},${LABELS[j]}  --no-update-check --library-type fr-unstranded --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[j]}  merged_asm_GKlab/merged.gtf ${IN_DIR[i]}/accepted_hits.bam,${IN_DIR[i+6]}/accepted_hits.bam ${IN_DIR[j]}/accepted_hits.bam,${IN_DIR[j+6]}/accepted_hits.bam  &> cuffdiff_${LABELS[i]}_${LABELS[j]}.log 

# wt_IL1b vs dd_IL1b
i=8
j=5
sem -j 2 cuffdiff  -L ${LABELS[i]},${LABELS[j]}  --no-update-check --library-type fr-unstranded --num-threads $THREADS -q -o cuffdiff_${LABELS[i]}_vs_${LABELS[j]}  merged_asm_GKlab/merged.gtf ${IN_DIR[i]}/accepted_hits.bam,${IN_DIR[i+6]}/accepted_hits.bam ${IN_DIR[j]}/accepted_hits.bam,${IN_DIR[j+6]}/accepted_hits.bam  &> cuffdiff_${LABELS[i]}_${LABELS[j]}.log 


#sem -j $CONCUR cuffcompare -o ${OUT_DIR[$i]}/cuffcompare  -R -s /mnt/raid/data/reference/mmu/nocolor/mm9.fa  -r /mnt/raid/data/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf  ${OUT_DIR[$i]}/accepted_hits3/transcripts.gtf

#done

sem --wait

echo END Cufflinks witth $CONCUR Concurrent and $THREADS threads `date` >> time_Cuff-mm9.txt
echo "************************ " >> time_Cuff-mm9.txt
echo "************************ " >> time_Cuff-mm9.txt
exit