# prep. index
$SHRIMP_FOLDER/utils/project-db.py --h-flag  --shrimp-mode ls mature-hsa.fa

# align fwd. reads
for i in *_1_seq*txt*gz
do
echo $i
zcat $i  | $SHRIMP_FOLDER/bin/gmapper-ls -L /mnt/raid/data/reference/rna/mirna/r19/mature-hsa-ls - --positive -N 6 -o 1 -n 2  -r 30% -h 50% --local -Q --sam > $i"-vs-mat.sam" 2>  $i"-vs-mat.log"
done

# align rev. reads
for i in *_2_seq*txt*gz
do
echo $i
zcat $i  | $SHRIMP_FOLDER/bin/gmapper-ls -L /mnt/raid/data/reference/rna/mirna/r19/mature-hsa-ls - --negative -N 6 -o 1 -n 2  -r 30% -h 50% --local -Q --sam > $i"-vs-mat.sam" 2>  $i"-vs-mat.log"
done

# collect matches
for i in *-vs-mat.sam
do
echo $i
awk -f ~/tools/formats/shrimp-sam2mirstat1.awk   $i | sort -r -k2,2n > $i"-stats.csv"
done

ls *-mat.sam-stats.csv >  mat-stats.txt

# group samples according to:   f="sample3.txt";
awk -f combine-stats.awk mat-stats.txt > hg19-mat-hyp-vs-norm-statsSLKK.csv

Rscript ~/tools/align/scripts/mirSeqDiffExp1.R hg19-mat-hyp-vs-norm-statsSLKK.csv HYP 6 NORM 6

# same for kshv
cd /mnt/raid/data/reference/rna/mirna/r19
$SHRIMP_FOLDER/utils/project-db.py --h-flag  --shrimp-mode ls mature-kshv.fa

cd ~/raid/data/results/ragoussis/miRNA/shiraz.well.ox.ac.uk/130307_SN685_0289_AD1NG0ACXX/
# align fwd. reads
for i in *_1_seq*txt*gz
do
echo $i
zcat $i  | $SHRIMP_FOLDER/bin/gmapper-ls -L /mnt/raid/data/reference/rna/mirna/r19/mature-kshv-ls - --positive -N 6 -o 1 -n 2  -r 30% -h 50% --local -Q --sam > $i"-vs-KSHV-mat.sam" 2>  $i"-vs-KSHV-mat.log"
done

# align rev. reads
for i in *_2_seq*txt*gz
do
echo $i
zcat $i  | $SHRIMP_FOLDER/bin/gmapper-ls -L /mnt/raid/data/reference/rna/mirna/r19/mature-kshv-ls - --negative -N 6 -o 1 -n 2  -r 30% -h 50% --local -Q --sam > $i"-vs-KSHV-mat.sam" 2>  $i"-vs-KSHV-mat.log"
done

# collect matches
for i in *-vs-KSHV-mat.sam
do
echo $i
awk -f ~/tools/formats/shrimp-sam2mirstat1.awk   $i | sort -r -k2,2n > $i"-stats.csv"
done

ls *KSHV-mat.sam-stats.csv >  KSHV-mat-stats.txt

# group samples according to:   f="sample3.txt";
awk -f combine-stats.awk KSHV-mat-stats.txt > KSHV-mat-hyp-vs-norm-statsSLKK.csv

Rscript ~/tools/align/scripts/mirSeqDiffExp1.R KSHV-mat-hyp-vs-norm-statsSLKK.csv HYP 6 NORM 6