# perpare mmu mirbase hairpins
zcat hairpin.fa.gz  | awk -f /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/get-mmu-hairpins1.awk > hairpin-mmu.fa
zcat mature.fa.gz  | awk -f /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/get-mmu-hairpins1.awk > mature-mmu.fa
cd /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21
 export SHRIMP_FOLDER=/mnt/raid/tools/align/shrimp
 export SHRIMP_FOLDER=/data/results/tools/align/SHRiMP_2_2_3
$SHRIMP_FOLDER/utils/project-db.py --h-flag  --shrimp-mode ls hairpin-mmu.fa 
$SHRIMP_FOLDER/utils/project-db.py --h-flag  --shrimp-mode ls mature-mmu.fa 

cd /data/images/proton/GKlab/run150/shrimp
for i in *_1_seq*txt*gz
do
echo $i
zcat $i  | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/hairpin-mmu-ls - --positive -N 6 -o 1 -n 2  -r 30% -h 50% --local -Q --sam --isize-hist > $i"-vs-mat.sam" 2>  $i"-vs-mat.log"
done
bam2fastx -A -o /dev/stdout  -q  /data/images/proton/run150/bowtie2_002/sort_uniq.bam | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/hairpin-mmu-ls - --positive -N 6 -o 1 -n 2  -r 30% -h 50% --local -Q --sam --isize-hist > "vs-hp.sam" 2>  "vs-hp.log"

bam2fastx -A -o /dev/stdout  -q  /data/images/proton/run150/bowtie2_002/sort_uniq.bam | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls - --positive -N 6 -o 1 -n 2  -r 30% -h 50% --local -Q --sam --isize-hist --no-qv-check > "vs-mat.sam" 2>  "vs-mat.log"

bam2fastx -A -o /dev/stdout  -q  /data/images/proton/run150/bowtie2_002/sort_uniq.bam | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 2  -r 30% -h 50% --local -Q --sam --isize-hist --no-qv-check --ignore-qvs  > "vs-mat.sam" 2>  "vs-mat.log"
        Reads Matched:          9,430    (0.2467%)

bam2fastx -A -o /dev/stdout  -q  /data/images/proton/run150/bowtie2_002/sort_uniq.bam | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 2  -r 15% -h 50% --local -Q --sam --isize-hist --no-qv-check --ignore-qvs  > "vs-mat.sam" 2>  "vs-mat.log"
        Reads Matched:          9,430    (0.2467%)

bam2fastx -A -o /dev/stdout  -q  /data/images/proton/run150/bowtie2_002/sort_uniq.bam | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 1  -r 15% -h 50% --local -Q --sam --isize-hist --no-qv-check --ignore-qvs  > "vs-mat.sam" 2>  "vs-mat.log"
        Reads Matched:          12,130    (0.3173%)


bam2fastx -A -o /dev/stdout  -q  /data/images/proton/run150/bowtie2_002/sort_uniq.bam | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 1  -r 5% -h 25% --local -Q --sam --isize-hist --no-qv-check --ignore-qvs  > "vs-mat.sam" 2>  "vs-mat.log"
        Reads Matched:          49,167    (1.2863%)

GKmR7-wt1late	/data/images/proton/run150/bowtie2_007/sort_uniq.bam	WT	single	yes
GKmR8-DARE1lata	/data/images/proton/run150/bowtie2_008/sort_uniq.bam	DARE	single	yes
GKmR1-wt1early	/data/images/proton/run150/bowtie2_011/sort_uniq.bam	WT	single	yes


cat R_2015_02_25_11_26_27_user_ION-150-GKlab_miRNAseq_150225_GKmR1-2-7-8.GKmR2-DARE1early.IonXpressRNA_002.fastq | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 1  -r 5% -h 25% --local -Q --sam --isize-hist --no-qv-check --ignore-qvs  > "vs-mat.sam" 2>  "vs-mat.log"
        Reads Matched:          50,537    (1.1237%)

awk -f /data/results/tools/formats/shrimp-sam2mirstat1.awk  vs-mat.sam  | sort -r -k2,2n > DARE1early-stats.csv


bam2fastx -A -o /dev/stdout  -q /data/images/proton/run150/bowtie2_007/sort_uniq.bam  | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 1  -r 5% -h 25% --local -Q --sam --isize-hist --no-qv-check --ignore-qvs  > "vs-mat.sam" 2>  "vs-mat.log"
        Reads Matched:          302,873    (1.8228%)


bam2fastx -A -o /dev/stdout  -q /data/images/proton/run150/bowtie2_007/sort_uniq.bam  | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 1  -r 5% -h 30% --local -Q --sam --isize-hist --no-qv-check --ignore-qvs  > "vs-mat.sam" 2>  "vs-mat.log"
        Reads Matched:          65,226    (0.3926%)


cat R_2015_02_25_11_26_27_user_ION-150-GKlab_miRNAseq_150225_GKmR1-2-7-8.GKmR2-DARE1early.IonXpressRNA_002.fastq | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 1  -r 5% -h 25% --local -Q --sam --no-qv-check --ignore-qvs  > "vs-mat.sam" 2>  "vs-mat.log"
awk -f /data/results/tools/formats/shrimp-sam2mirstat1.awk  vs-mat.sam  | sort -r -k2,2n > DARE1early-stats.csv

cat R_2015_02_25_11_26_27_user_ION-150-GKlab_miRNAseq_150225_GKmR1-2-7-8.GKmR8-DARE1late.IonXpressRNA_008.fastq  | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 1  -r 5% -h 25% --local -Q --sam --no-qv-check --ignore-qvs  > DARE1late-vs-mat.sam 2>  DARE1late-vs-mat.log
awk -f /data/results/tools/formats/shrimp-sam2mirstat1.awk  DARE1late-vs-mat.sam  | sort -r -k2,2n > DARE1late-stats.csv

cat R_2015_02_25_11_26_27_user_ION-150-GKlab_miRNAseq_150225_GKmR1-2-7-8.GKmR1-wt1early.IonXpressRNA_011.fastq  | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 1  -r 5% -h 25% --local -Q --sam --no-qv-check --ignore-qvs  > WT1early-vs-mat.sam 2>  WT1early-vs-mat.log
awk -f /data/results/tools/formats/shrimp-sam2mirstat1.awk  WT1early-vs-mat.sam   | sort -r -k2,2n > WT1early-vs-mat-stats.csv

cat R_2015_02_25_11_26_27_user_ION-150-GKlab_miRNAseq_150225_GKmR1-2-7-8.GKmR7-wt1late.IonXpressRNA_007.fastq | $SHRIMP_FOLDER/bin/gmapper-ls -L /data/results/reference/rna/mirna/mirbase.org/pub/mirbase/21/mature-mmu-ls -  -N 6 -o 1 -n 1  -r 5% -h 25% --local -Q --sam --no-qv-check --ignore-qvs  > WT1late-vs-mat.sam 2>  WT1late-vs-mat.log
awk -f /data/results/tools/formats/shrimp-sam2mirstat1.awk  WT1late-vs-mat.sam   | sort -r -k2,2n > WT1late-vs-mat-stats.csv