#working directory (parent)
wd="/Volumes/web/Mollusk/bs_larvae_exp"
#where is bsmap
bsmap="/Users/Shared/Apps/bsmap-2.73/"
#Where is bsmap file
bsmapfile="/Volumes/web/Mollusk/bs_larvae_exp/AdaptorTrimmed_BSMAP_files/"
#Output for methratio file
methratio="/Volumes/web/Mollusk/bs_larvae_exp/AdapterTrimmed_methratio_files/"
#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"
!python {bsmap}methratio.py -d {genome} -u -z -g -o {methratio}methratio_out_M1.txt -s {bsmap}samtools {bsmapfile}M1/condor-stdout-0.sam
!python {bsmap}methratio.py -d {genome} -u -z -g -o {methratio}methratio_out_M3.txt -s {bsmap}samtools {bsmapfile}M3/condor-stdout-0.sam
!python {bsmap}methratio.py -d {genome} -u -z -g -o {methratio}methratio_out_T1D3.txt -s {bsmap}samtools {bsmapfile}T1D3/condor-stdout-0.sam
!python {bsmap}methratio.py -d {genome} -u -z -g -o {methratio}methratio_out_T1D5.txt -s {bsmap}samtools {bsmapfile}T1D5/condor-stdout-0.sam
!python {bsmap}methratio.py -d {genome} -u -z -g -o {methratio}methratio_out_T3D3.txt -s {bsmap}samtools {bsmapfile}T3D3/condor-stdout-0.sam
!python {bsmap}methratio.py -d {genome} -u -z -g -o {methratio}methratio_out_T3D5.txt -s {bsmap}samtools {bsmapfile}T3D5/condor-stdout-0.sam
#NOTEBOOK NAME
nb='Methratio_AdapterTrimmed_Larvae'
#NOTEBOOK LOCATION
nbloc='/Users/claireolson/Dropbox/Lab\ \(1\)/IPython_nbs/Claire/'
#TIMESTAMP
date=!date +%m%d_%H%M
#LOCATION OF POST DIRECTORY
post='/Volumes/web/Mollusk/iPython_Posts/'
cd {post}
!ipython nbconvert {nbloc}{nb} --to html --template full --output {nb}{date}