def loadmotif(infile, trimstart=0, trimend=0):
from TAMO import MotifTools
lines = loadlist(infile)
if lines[0] == "A\tC\tG\tT":
ma = []
for l in lines[1:]:
p = l.split("\t")
ma.append({
'A': float(p[0]),
'C': float(p[1]),
'G': float(p[2]),
'T': float(p[3])
})
if trimend == 0: ma = ma[trimstart:]
else: ma = ma[trimstart:-trimend]
return MotifTools.Motif_from_counts(ma)
elif lines[0][0] in 'ACGT':
if trimend == 0: lines = lines[trimstart:]
else: lines = lines[trimstart:-trimend]
return MotifTools.Motif(lines)
else:
na = []
for line in lines:
na.append(list(map(int, line.split())))
ma = []
for i in range(len(na[0])):
ma.append({
'A': na[0][i],
'C': na[1][i],
'G': na[2][i],
'T': na[3][i]
})
return MotifTools.Motif_from_counts(ma)
def parse_block(name, block):
mat = []
ACGT = {"A": 1, "C": 2, "G": 3, "T": 4}
for i in block:
L = i.strip().split()
D = {'A': 0, 'C': 0, 'T': 0, 'G': 0}
for j in ACGT.keys():
D[j] = float(L[ACGT[j]])
mat.append(D)
m = MotifTools.Motif_from_counts(mat)
m.source = name
#print m._print_p()
return m
motiflist.pop(blankindex)
# Build matrix dictionaries and substitute the strings for the dictionaries
for num in range(len(motiflist)):
# Prepare emtpy list of dictionaries of the length of the motif
tempmotif = []
motiflength = len(motiflist[num][1].strip().split('\t')) - 1
for item in range(motiflength):
tempmotif.append({})
# Start filling in the dictionaries with the information in the matrix
for line in range(1, 5):
nucleotide = motiflist[num][line].strip().split('\t')[0]
problist = motiflist[num][line].strip().split('\t')[1:]
for position in range(motiflength):
tempmotif[position][nucleotide] = float(problist[position])
# Save the list of dictionaries in the general variable
motiflist[num] = tempmotif
#print motiflist
# TAMO CONVERSION
# TAMO formated list of files
tamomotifs = []
# Convert dictionaries found in sigmotifs and store them as TAMO motifs
for motif in motiflist:
tamomotif = MotifTools.Motif_from_counts(motif[:], beta=0.01, bg=bkgrddict)
tamomotifs.append(tamomotif)
MotifTools.save_motifs(tamomotifs, output)
