def run(bidirfile, fimodir):
distances = dict()
directorylist = [fimodir + '/' + item for item in os.listdir(fimodir) if 'fimo_out' in item]
bidirsites = Functions.create_site_bidir(bidirfile)
for item in directorylist:
print item
TF = item.split('/')[5].split('_')[0]
fimodict = Functions.create_tup_fimo(item + "/fimo.cut.txt", True)
for key in bidirsites:
start,stop,chrom = key
fimotree = fimodict[chrom]
fimotree = node.tree(fimotree)
intervalsearch = []
for item in fimotree.searchInterval(key):
start2,stop2,pval = item
i = (start+stop)/2
x = (start2+stop2)/2
intervalsearch.append((i-x,pval))
bidirsites[key].append((TF,intervalsearch))
x = Functions.get_distances_pad_v3(bidirfile, item + "/fimo.cut.txt", True, 1500)
if len(x) != 0:
start = min(x)
stop = max(x)
sigma = np.std(x)
mu = np.mean(x)
N = len(x)
#y = np.random.uniform(start, stop, N)
y = np.linspace(start,stop,N)
z = mu/(sigma/math.sqrt(N))
p = 1 - scipy.special.ndtr(z)
k = scipy.stats.ks_2samp(x,y)
m = scipy.stats.mode(x)[0][0]
if -0.25 < m < 0.25:
m = 0
else:
m = 1
distances[TF] = [k[1],p,m]
return distances,bidirsites
def run(bidirfile, fimodir):
directorylist = [fimodir + '/' + item for item in os.listdir(fimodir) if 'fimo_out' in item]
bidirsites = Functions.create_site_bidir(bidirfile)
for item in directorylist:
print item
TF = item.split('/')[5].split('_')[0]
fimodict = Functions.create_tup_fimo(item + "/fimo.cut.txt", True)
for key in bidirsites:
start,stop,chrom = key
fimotree = fimodict[chrom]
fimotree = node.tree(fimotree)
intervalsearch = []
for item in fimotree.searchInterval(key):
start2,stop2,info = item
i = (start+stop)/2
x = (start2+stop2)/2
intervalsearch.append((i-x,info))
bidirsites[key].append((TF,intervalsearch))
return bidirsites
