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 get_arca_reads(N=None):
"""Return N downsampled reads from ArcA dataset"""
filename = '/home/pat/chip_seq_inference/data/chip_seq_datasets/ArcA_park_et_al/SRR835423/SRR835423.map'
arca_reads = read_map(filename)
sampled_arca_reads = sample(N, arca_reads) if N else arca_reads
sampled_read_fraction = len(sampled_arca_reads)/float(len(arca_reads))
print "sampled %1.2f%% of %s reads" % (sampled_read_fraction*100, len(arca_reads))
return sampled_arca_reads
def frags_from_map(filename,N,mfl=250):
reads = read_map(filename)
fragments = infer_frags(reads,N,mfl)
return fragments
