=====================================
= Exercice 1 : Qualité - Nettoyage
=====================================
cp -r /save/sigenae/F13f/TP ~/work/F13f/ 
cd TP 
ls * 

cp /save/sigenae/F13f/Fastq/*fastq data/

foreach i ( data/*.fastq ) 
 echo "bin/FastQC/fastqc -o 1_fastqc $i" >> 1_fastqc.jobs 
end 

qarray -q test.q -o 1_fastqc -e 1_fastqc -N fastqc 1_fastqc.jobs

cutadapt -h 
cd data 
foreach i ( *fastq ) 
echo "(cutadapt -a ATCTCGTATGCCGTCTTCTGCTTG -m 16 -M 28 -o 2_cutadapt/$i.cut.fq data/$i) >& 2_cutadapt/$i.cut.log" >> ../2_cutadapt.jobs 
end
cd .. 
qarray -q test.q -o 2_cutadapt -e 2_cutadapt -N cadapt 2_cutadapt.jobs 

bin/stat1.pl 
qsub -q test.q -b y -o stat/ -e stat/ -N stat   'bin/stat1.pl 2_cutadapt/*fq > 2_cutadapt/2_stat.txt' 

bin/plot1.pl 
bin/plot1.pl 2_cutadapt/2_stat.txt > stat/2_stat.html 

cd 2_cutadapt 
foreach i (*fq) 
echo "bin/fastqnr.pl 2_cutadapt/$i | sort -k1,1 > 3_redundancy/$i.nr" >> ../3_redundancy.jobs 
end 
cd .. 
qarray -q test.q -N redundancy -o 3_redundancy/ -e 3_redundancy/ 3_redundancy.jobs 


bin/join.pl 
qsub -q test.q -b y -o 3_redundancy/ -e 3_redundancy/ -N join    'bin/join.pl 3_redundancy/*.nr > 3_redundancy/ALL.matrix' 

bin/matrix.pl 
qsub -q test.q -b y -o 3_redundancy/ -e 3_redundancy/ -N matrix   'bin/matrix.pl -a 10 -i 3 3_r*/ALL.matrix -o 3_redundancy/ALL.matrix' 

head 3_redundancy/ALL.matrix.* 

bin/plot2.pl 3_redundancy/ALL.mat*.txt > stat/3_stat.html


=====================================
= Exercice 2 : Annotations
=====================================
ln -s /save/sigenae/F13f/Bank/* bank 

cd bank 
foreach i ( *fa *fasta ) 
 echo "bwa aln bank/$i 3_redundancy/ALL.matrix.filter.tfa | bwa samse bank/$i - 3_redundancy/ALL.matrix.filter.tfa | samtools view -bS - | samtools sort - 4_annotation/$i.sort" >> ../4_annotation.jobs 
end 
cd .. 
qarray -q test.q -N bwa -o 4_annotation/ -e 4_annotation/ 4_annotation.jobs 

foreach i (4_annotation/*.sort.bam) 
 samtools view $i | grep 'NM:i:[01]' | awk '$2==0||$2==16' | cut -f1,3 | sort -k1,1 > $i.filter1 
 cut -f1 $i.filter1 > $i.filter2
end 

bin/join.pl 4_annot*/*filter1 > 4_annotation/annot.csv 

bin/lists2venn.pl  4_ann*/euk*filter2   4_ann*/LSU*filter2 4_ann*/SSU*filter2 stat/4_tRNA-rRNA 
cat  4_an*/euk*filter2 4_ann*/LSU*filter2 4_ann*/SSU*filter2 | sort -u > 4_annotation/tRNA-rRNA.filter2 
bin/lists2venn.pl  4_ann*/tRNA-rRNA*2  4_ann*/Rfam*filter2 4_ann*/hairpin*filter2 stat/4_rtRNA-mir-Rfam 

sort -k1,1 3*/*csv > 3_redundancy/ALL.matrix.filter.csv.sort 
join -t 'ctrl-v <tab>' -1 1 -2 1 4*/annot.csv  3*/*.csv.sort > 4_annotation/all.csv 

sort -k8,8nr 4_annotation/all.csv | head 

grep -c '#1#' 4_annotation/all.csv 

perl -lane 'print $_ if($F[2] ne "0" && $F[0]=~/#1#/)' 4_annotation/all.csv | wc -l 

perl -lane 'print $_ if($_ =~ /^#/ || ($F[2] ne "0" && $F[4] ne "0" && $F[7]>100))' 4_annotation/all.csv > 4_annotation/all_filter.csv 

bin/matrix2html.pl 
bin/matrix2html.pl 4_an*/all_filter.csv > stat/4_stat.html


=====================================
= Exercice 3 : Alignement sur réf.
=====================================
ln -s /save/sigenae/F13f/Reference/* 5_reference/ 

qsub -q test.q -b y -o 5_reference/ -e 5_reference/ -N bwa   'bwa aln 5_ref*/V4_454Scaffolds.fna 3_red*/ALL.matrix.filter.tfa | bwa samse -n 100 5_ref*/V4_454Scaffolds.fna - 3_red*/ALL.matrix.filter.tfa | samtools view -bS - | samtools sort - 5_reference/ALL.matrix.filter.sort' 

samtools view 5_reference/ALL.matrix.filter.sort.bam  | bin/bwasam2stat.pl - > 5_reference/5_stat1.txt 
bin/plot3.pl 5_reference/5_stat1.txt > stat/5_stat1.html 

samstat 5*/ALL.matrix.filter.sort.bam -n stat/5_stat 

samtools view -h 5_reference/ALL.matrix.filter.sort.bam | ( bin/bwasamXfilter.pl - -n 1 -0 3 -1 95 -I -o > 5_reference/ALL.matrix.filter.NMX.sam ) >& 5_reference/5_stat2.txt 

bin/plot4.pl 5_reference/5_stat2.txt > stat/5_stat2.html 

bin/bwasam2stat.pl 5*/A*NMX.sam > 5_reference/5_stat3.txt 
bin/plot3.pl 5_reference/5_stat3.txt > stat/5_stat3.html 

bin/samNoXA.pl 5*/ALL.matrix.*.NMX.sam | samtools view -bS - | samtools sort - 5_reference/ALL.matrix.filter.NMX.NOXA 


=====================================
= Exercice 4 : Identification
=====================================
samtools view 5_reference/ALL.matrix.filter.NMX.NOXA.bam | ( bin/sam2locus.pl 5_reference/V4_454Scaffolds.fna > locus_miRNA-miRNAstar ) > & locus 

perl -lne 'BEGIN{$/="\n##\n"} print "##\n$_" if ($_ =~ /locusNumber:2/) ' locus_miRNA-miRNAstar >  locus_miRNA-miRNAstar_2