#trying to get clean version
!date 

#Will go September then Novemeber
!cat /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R1.fastq \
/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L004_R1.fastq > \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R1a.fastq \

!cat /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L007_R2.fastq \
/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM1/filtered_BS_CgM1_ACTTGA_L004_R2.fastq > \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_R2a.fastq \

R1_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L007_R1.fastq"
R1_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L004_R1.fastq"
   
R2_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L007_R2.fastq"
R2_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgM3/filtered_BS_CgM3_GATCAG_L004_R2.fastq"

!cat {R1_A8} \
{R1_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_R1a.fastq \

!cat {R2_A8} \
{R2_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_R2a.fastq \

sample="T1D3"

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L004_R1.fastq.gz

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L004_R2.fastq.gz

R1_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L007_R1.fastq"
R1_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L004_R1.fastq"
   
R2_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L007_R2.fastq"
R2_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D3/filtered_BS_CgLarv_T1D3_TGACCA_L004_R2.fastq"

!cat {R1_A8} \
{R1_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R1a.fastq \



!cat {R2_A8} \
{R2_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R2a.fastq \

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq.gz

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R2.fastq.gz

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R1.fastq.gz

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R2.fastq.gz

R1_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq"
R1_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R1.fastq"
   
R2_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R2.fastq"
R2_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T1D5/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R2.fastq"

sample="T1D5"

!cat {R1_A8} \
{R1_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R1a.fastq \


!cat {R2_A8} \
{R2_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R2a.fastq \

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L007*

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L004*

R1_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R1.fastq"
R1_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R1.fastq"
   
R2_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R2.fastq"
R2_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_Bs_CgLarve_T3D3/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R2.fastq"

sample="T3D3"

!cat {R1_A8} \
{R1_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R1a.fastq \


!cat {R2_A8} \
{R2_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R2a.fastq \

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T3D5/filtered_*

!gunzip /Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T3D5/filtered_*

R1_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T3D5/filtered_BS_CgLarv_T3D5_CAGATC_L007_R1.fastq"
R1_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T3D5/filtered_BS_CgLarv_T3D5_CAGATC_L004_R1.fastq"
   
R2_A8="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCD2CA8_2/Sample_BS_CgLarv_T3D5/filtered_BS_CgLarv_T3D5_CAGATC_L007_R2.fastq"
R2_EM="/Volumes/web/trilobite/Crassostrea_gigas_HTSdata/batterbox/FCC39EM_02/FCC39EM/Sample_BS_CgLarv_T3D5/filtered_BS_CgLarv_T3D5_CAGATC_L004_R2.fastq"

sample="T3D5"

!cat {R1_A8} \
{R1_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R1a.fastq \


!cat {R2_A8} \
{R2_EM} > \
/Volumes/web/cnidarian/BiGo_larvae_merge/Cg{sample}_R2a.fastq \

#file ID
fid="CgM1"

#TIMESTAMP
date=!date +%m%d_%H%M

#working directory (parent)
wd='/Volumes/web/cnidarian/BiGo_larvae_merge/'

#where is bsmap
#bsmap="/Users/Shared/Apps/bsmap-2.73/"
bsmap="/Volumes/Bay3/Software/BSMAP/bsmap-2.74/"

#genome file 
genome="/Volumes/web/whale/ensembl/ftp.ensemblgenomes.org/pub/release-21/metazoa/fasta/crassostrea_gigas/dna/Crassostrea_gigas.GCA_000297895.1.21.dna_sm.genome.fa"

cd {wd} 


mkdir {fid}_{date}  


cd {fid}_{date} 

#option - number of processes 
!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 
!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam 
#command for only obtaining the context '__CG_'
!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> methratio_out_CG.txt 
#5x coverage
!awk '{if ($8 >= 5) print $1,$2-1,$2+1,"CpG",$5}' <methratio_out_CG.txt> filt_methratio_out_CG.igv 
!tr ' ' "\t" <filt_methratio_out_CG.igv> filt_methratio_{fid}.igv


!head filt_methratio_{fid}.igv

#file ID
fid="CgM3"

#TIMESTAMP
date=!date +%m%d_%H%M

#working directory (parent)
wd='/Volumes/web/cnidarian/BiGo_larvae_merge/'

cd {wd}


mkdir {fid}_{date}


cd {fid}_{date}

#option - number of processes 
!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 
!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam 
#command for only obtaining the context '__CG_'
!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> methratio_out_CG.txt 
#5x coverage
!awk '{if ($8 >= 5) print $1,$2-1,$2+1,"CpG",$5}' <methratio_out_CG.txt> filt_methratio_out_CG.igv 
!tr ' ' "\t" <filt_methratio_out_CG.igv> filt_methratio_{fid}.igv


#file ID 
fid="CgT1D3"

#TIMESTAMP
date=!date +%m%d_%H%M

#working directory (parent)
wd="/Volumes/web/cnidarian/BiGo_larvae_merge/"

cd {wd}

mkdir {fid}_{date}

cd {fid}_{date}

#option - number of processes 
!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 
!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam 
#command for only obtaining the context '__CG_'
!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> methratio_out_CG.txt 
#5x coverage
!awk '{if ($8 >= 5) print $1,$2-1,$2+1,"CpG",$5}' <methratio_out_CG.txt> filt_methratio_out_CG.igv 
!tr ' ' "\t" <filt_methratio_out_CG.igv> filt_methratio_{fid}.igv

#file ID
fid="CgT1D5"

#TIMESTAMP
date=!date +%m%d_%H%M

#working directory (parent)
wd="/Volumes/web/cnidarian/BiGo_larvae_merge/"


cd {wd}

mkdir {fid}_{date}

cd {fid}_{date}

#option - number of processes 
!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 
!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam 
#command for only obtaining the context '__CG_'
!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> methratio_out_CG.txt 
#5x coverage
!awk '{if ($8 >= 5) print $1,$2-1,$2+1,"CpG",$5}' <methratio_out_CG.txt> filt_methratio_out_CG.igv 
!tr ' ' "\t" <filt_methratio_out_CG.igv> filt_methratio_{fid}.igv

#file ID
fid="CgT3D3"

#TIMESTAMP
date=!date +%m%d_%H%M

#working directory (parent)
wd="/Volumes/web/cnidarian/BiGo_larvae_merge/"


cd {wd}

mkdir {fid}_{date}

cd {fid}_{date}

#option - number of processes 
!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 
!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam 
#command for only obtaining the context '__CG_'
!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> methratio_out_CG.txt 
#5x coverage
!awk '{if ($8 >= 5) print $1,$2-1,$2+1,"CpG",$5}' <methratio_out_CG.txt> filt_methratio_out_CG.igv 
!tr ' ' "\t" <filt_methratio_out_CG.igv> filt_methratio_{fid}.igv

#file ID
fid="CgT3D5"

#TIMESTAMP
date=!date +%m%d_%H%M

#working directory (parent)
wd="/Volumes/web/cnidarian/BiGo_larvae_merge/"


cd {wd}

mkdir {fid}_{date}

cd {fid}_{date}

#option - number of processes 
!{bsmap}bsmap -a {wd}{fid}_R1a.fastq -b {wd}{fid}_R2a.fastq -d {genome} -o bsmap_out.sam -p 4 
!python {bsmap}methratio.py -d {genome} -u -z -g -o methratio_out.txt -s {bsmap}samtools bsmap_out.sam 
#command for only obtaining the context '__CG_'
!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> methratio_out_CG.txt 
#5x coverage
!awk '{if ($8 >= 5) print $1,$2-1,$2+1,"CpG",$5}' <methratio_out_CG.txt> filt_methratio_out_CG.igv 
!tr ' ' "\t" <filt_methratio_out_CG.igv> filt_methratio_{fid}.igv

!head filt_methratio_{fid}.igv

!head /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1.igv

!awk '{print ($1"_"$2),$1,$2,$3,$4,$5}' </Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1.igv> \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1_id.tab

!head /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1_id.tab

!python {spd}singleupload.py -d filt_methratio_CgM1 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1.igv

!head /Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]/filt_methratio_CgM3.igv

#Location of SQLShare python tools: you can empty ("") if tools are in PATH
spd="/Users/sr320/sqlshare-pythonclient/tools/"

!python {spd}singleupload.py -d filt_methratio_CgM1 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/filt_methratio_CgM1.igv

!python {spd}singleupload.py -d filt_methratio_CgM3 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]/filt_methratio_CgM3.igv

target
!head -2 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/methratio_out_CG.txt
cat /Volumes/web/Mollusk/bs_larvae_exp/methratio.awk.sh
!/Volumes/web/Mollusk/bs_larvae_exp/methratio.awk.sh \
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/methratio_out_CG.txt > \
/Volumes/web/cnidarian/CgM1_[0316_0954]mk.txt
!head /Volumes/web/cnidarian/CgM1_[0316_0954]mk.txt
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_[0316_1306]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_[0316_1346]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_[0316_1436]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_[0316_1532]/


!head -2 /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/methratio_out.txt


cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/

!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> mk_methratio_out_CG.txt 


!awk '{if ($8 >= 5) print $1,$2,$2+1,$3,$8,($7/$8),(1-($7/$8))}' <methratio_out.txt> mk_methratio_out_CG5x.txt 

!head mk_methratio_out_CG5x.txt 

cd 

!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> mk_methratio_out_CG.txt 


!awk '$8 >= 5' <methratio_out_CG.txt> mk_methratio_out_CG5x.txt

cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_[0316_1306]/


!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> mk_methratio_out_CG.txt 


!awk '$8 >= 5' <methratio_out_CG.txt> mk_methratio_out_CG5x.txt

cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_[0316_1346]/


!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> mk_methratio_out_CG.txt 


!awk '$8 >= 5' <methratio_out_CG.txt> mk_methratio_out_CG5x.txt

cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_[0316_1436]/


!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> mk_methratio_out_CG.txt 


!awk '$8 >= 5' <methratio_out_CG.txt> mk_methratio_out_CG5x.txt

cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_[0316_1532]/


!grep "[A-Z][A-Z]CG[A-Z]" <methratio_out.txt> mk_methratio_out_CG.txt 


!awk '$8 >= 5' <methratio_out_CG.txt> mk_methratio_out_CG5x.txt

!head mk_methratio_out_CG5x.txt

/Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgM3_[0316_1207]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D3_[0316_1306]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgT1D5_[0316_1346]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D3_[0316_1436]/
/Volumes/web/cnidarian/BiGo_larvae_merge/CgT3D5_[0316_1532]/


cd /Volumes/web/cnidarian/BiGo_larvae_merge/CgM1_[0316_0954]/


!/Volumes/web/Mollusk/bs_larvae_exp/methratio.awk.sh \
mk_methratio_out_CG5x.txt > mk_CgM1.txt

pwd

!head mk_methratio_out_CG5x.txt