# Change what's inside the quotes into your MBL STAMPS server username, or something else unique
# reminder! hit shift-ENTER to execute cell & move onto next cell
username="CHANGEME"

# configure paths etc.
import sys
import os
os.environ['PYTHONPATH'] = '/usr/local/share/khmer/python'
sys.path.insert(0, '/usr/local/share/khmer/python')

import khmer
import screed

cd /mnt

mkdir -p $username

cd $username

import random
random.seed(1)

x = ["A"] + ["G"] + ["C"] + ["T"]
x = x*1000
random.shuffle(x)
x = "".join(x)

y = ["A"] + ["G"] + ["C"] + ["T"]
y = y*1000
random.shuffle(y)
y = "".join(y)

print 'x is', x[:100]
print 'y is', y[:100]

outfp = open('metagenome.fa', 'w')
print >>outfp, ">x 1"
print >>outfp, x
print >>outfp, ">y 2"
print >>outfp, y
outfp.close()

!python /usr/local/share/2012-paper-diginorm/pipeline/make-biased-reads.py metagenome.fa | head -100000 > reads.fa

!/usr/local/share/khmer/scripts/abundance-dist-single.py -k 20 -x 1e8 reads.fa reads.hist

histdata = numpy.loadtxt('reads.hist')

plot(histdata[:,0], histdata[:,1])
xlabel("k-mer abundance")
ylabel("N of k-mers with that abundance")

plot(histdata[:,0], histdata[:,1])
axis(ymax=500)
xlabel("k-mer abundance")
ylabel("N of k-mers with that abundance")

plot(histdata[:,0], histdata[:,1])
axis(xmax=10)