%load_ext rpy2.ipython

directory='/mnt/borage/nick/nanopore/data/Flowcell6/downloads'

!find $directory -maxdepth 1 -name "*.fast5" | wc -l

!poretools

!poretools -h

!poretools stats -q $directory

!poretools stats -q --type fwd $directory

!poretools stats -q --type rev $directory

!poretools stats -q --type 2D $directory

!poretools readstats -q $directory > readstats.txt

!wc -l readstats.txt

!head -10 readstats.txt

%R stats=read.table("readstats.txt", sep="\t")
%R stats=subset(stats, V4 < 20000 & V5 < 20000)

%R smoothScatter(stats$V4,stats$V5)

!poretools winner -q --type 2D $directory > winner.fasta

!head -1 winner.fasta | sed 's/>.* //' | xargs poretools squiggle --saveas png --num-facets 12

squiggle=!head -1 winner.fasta | sed 's/>.* //'
squiggle=squiggle[0] + '.png'
Image(squiggle)

!poretools yield_plot -q --theme-bw --saveas yield_plot.png --plot-type reads $directory 

!poretools yield_plot -q --theme-bw --saveas yield_plot.pdf --plot-type reads $directory 

Image("yield_plot.png")

!poretools hist -q --theme-bw --min-length 1000 --max-length 40000 --saveas hist.png $directory

!poretools hist -q --theme-bw --min-length 1000 --max-length 40000 --saveas hist.pdf $directory

Image("hist.png")

!poretools nucdist -q $directory

!poretools qualdist -q $directory