ls

ls *.dens

nobias = numpy.loadtxt('reads-nobias.dens')
bias_rand = numpy.loadtxt('reads-bias-random.dens')
bias_nonrand = numpy.loadtxt('reads-bias-nonrandom.dens')

plot(nobias[:,0], nobias[:,3], label='no bias')
plot(bias_rand[:,0], bias_rand[:,3], label='random errors, with bias')
plot(bias_nonrand[:,0], bias_nonrand[:,3], label='random errors, bias')
axis(ymin=0)
xlabel("Position in read")
ylabel("Average graph density within 10 steps")
title("Effects of errors on assembly graph density")
legend(loc='lower right')
savefig('/tmp/bias.png')

bias_rand_r1 = numpy.loadtxt('reads-bias-random.r1.dens')
bias_rand_r3 = numpy.loadtxt('reads-bias-random.r3.dens')
bias_rand_r5 = numpy.loadtxt('reads-bias-random.r5.dens')


plot(bias_rand_r1[:,0], bias_rand_r1[:,3], label='r1')
plot(bias_rand_r3[:,0], bias_rand_r3[:,3], label='r3')
plot(bias_rand_r5[:,0], bias_rand_r5[:,3], label='r5')
plot(bias_rand[:,0], bias_rand[:,3], label='r10')
axis(ymin=0)
legend(loc='lower left')
xlabel("Position in read")
ylabel("Average graph density within given radius")
title("Effects of errors density for different radii")
savefig('/tmp/foo.png')

posns = [ int(line) for line in open('biased-random-positions.out') ]
hist(posns)
xlabel('Error position within read')
ylabel('Number of errors')
savefig('/tmp/foo2.png')

bias_rand_rep = numpy.loadtxt('repreads-bias-random.dens')


plot(bias_rand_rep[:,0], bias_rand_rep[:,3], label='w/repeats')
plot(bias_rand[:,0], bias_rand[:,3], label='no repeats')
axis(ymin=0)
xlabel("Position in read")
ylabel("Average graph density within 10 steps")
title("Effects of errors on assembly graph density")
legend(loc='lower right')
savefig('/tmp/bias2.png')