def test_frags_from_map():
filename = "../data/chip_seq_datasets/ArcA_park_et_al/SRR835423/SRR835423.map"
reads = read_map(filename)
num_frags = 10000
frags = frags_from_map(filename,num_frags,mfl=250)
plot_reads(reads)
plot_reads(map(lambda (start,stop):('+',start,stop),frags))
def sanity_check():
G = 10000
config = [G/2]
mfl = 250
lamb = 1.0/mfl
num_frags = 10000
frags = concat([chip(G,config,mfl) for i in xrange(num_frags)])
min_seq_length = 75
sequenced_frags = filter(lambda (start,stop):stop - start > min_seq_length,frags)
fd_frags,bk_frags = separate(lambda x:random.random() < 0.5,sequenced_frags)
fd_reads = [('+',start,start+min_seq_length) for (start,stop) in fd_frags]
bk_reads = [('-',stop-min_seq_length,stop) for (start,stop) in bk_frags]
reads = fd_reads + bk_reads
inferred_frags = exp_reconstruction(reads,lamb,G)
plot_reads(reads,G=G)
plt.plot(frag_density(frags,G=G),label="all frags")
plt.plot(frag_density(sequenced_frags,G=G),label="seq frags")
plt.plot((inferred_frags),label="inferred frags")
plt.legend()