def main():
if len(sys.argv) < 6:
print("%s transfac|basic pwmfile inmaf threshold spec1,spec2,... " %
sys.argv[0],
file=sys.stderr)
sys.exit(0)
pwm = {}
format = sys.argv[1]
for wm in pwmx.Reader(open(sys.argv[2]), format=format):
pwm[wm.id] = wm
inmaf = open(sys.argv[3])
threshold = float(sys.argv[4])
species = []
for sp in sys.argv[5].split(','):
species.append(sp)
for maf in align_maf.Reader(inmaf):
mafchrom = maf.components[0].src.split('.')[1]
mafstart = maf.components[0].start
mafend = maf.components[0].end
reftext = maf.components[0].text
# maf block scores for each matrix
for scoremax, width, headers in MafBlockScorer(pwm, species, maf):
blocklength = width
mafsrc, mafstart, mafend = headers[0]
mafchrom = mafsrc.split('.')[1]
# lists of scores for each position in scoremax
for id, mx in scoremax.items():
for offset in range(blocklength):
# scan all species with threshold
for i in range(len(species)):
if mx[i][offset] > threshold:
refstart = mafstart + offset - reftext.count(
'-', 0, offset)
refend = refstart + len(pwm[id])
data = " ".join([
"%.2f" % mx[x][offset]
for x in range(len(species))
])
# underscore spaces in the name
print(mafchrom, refstart, refend,
id.replace(' ', '_'), data)
break
def scoreMaf(maf, motif, sources, sourceDist):
"""
read a single maf and a single motif
return score matrices
"""
pwms = {}
pwms[motif.id] = motif
wtCoef, valCoef = 1, 1
fullSize = maf.text_size
summedWeightedScore = np.zeros(shape=(fullSize, 1))
summedScore = np.zeros(shape=(fullSize, 1))
componentScores = np.zeros(shape=(len(sources), fullSize))
weights = np.zeros(shape=(fullSize, 1))
componentWeightedScores = np.zeros(shape=(len(sources), fullSize))
for scores, width, headers in MafBlockScorer(pwms, sources, maf):
# for scores, width, headers in MafMotifScorer(sources, maf, "TGCATG"):
data = scores[motif.id]
for speciesN, srcName in enumerate(sources):
similarity = scores[motif.id][speciesN]
for pos, val in enumerate(similarity):
if not np.isnan(val):
val = sigmoid(val, .8, 20)
componentScores[speciesN, pos] = val
summedScore[pos] += val
weight = weight_fxn(sourceDist[srcName])
#weightedScore = valCoef*val * wtCoef*weight
weightedScore = (valCoef * val) + wtCoef*(val * weight)
summedWeightedScore[pos] += weightedScore
componentWeightedScores[speciesN, pos] = weightedScore
def main():
if len(sys.argv) < 5:
print >> sys.stderr, "%s bedfile inmaf spec1,spec2,... motif_file " % sys.argv[
0]
sys.exit(0)
# read in intervals
regions = {}
for line in open(sys.argv[1]):
if line.startswith('#'): continue
fields = line.strip().split()
chrom, start, end = fields[0], int(fields[1]), int(fields[2])
try:
name = fields[3]
except:
name = None
if chrom not in regions: regions[chrom] = intervals.Intersecter()
regions[chrom].add(start, end, name)
pwm = {}
for wm in pwmx.Reader(open(sys.argv[4])):
pwm[wm.id] = wm
print >> sys.stderr, wm.id, len(wm)
inmaf = open(sys.argv[2])
threshold = 0.5
species = []
for sp in sys.argv[3].split(','):
species.append(sp)
for maf in align_maf.Reader(inmaf):
mafchrom = maf.components[0].src.split('.')[1]
mafstart = maf.components[0].start
mafend = maf.components[0].end
reftext = maf.components[0].text
# maf block scores for each matrix
for scoremax, width, headers in MafBlockScorer(pwm, species, maf):
#print >>sys.stderr,headers
blocklength = width
mafsrc, mafstart, mafend = headers[0]
mafchrom = mafsrc.split('.')[1]
# lists of scores for each position in scoremax
for mx_name, mx in scoremax.items():
#print >>sys.stderr, mx_name, len(pwm[mx_name])
for offset in range(blocklength):
# scan all species with threshold
for i in range(len(species)):
if mx[i][offset] > threshold:
refstart = mafstart + offset - reftext.count(
'-', 0, offset)
refend = refstart + len(pwm[mx_name])
data = " ".join([
"%.2f" % mx[x][offset]
for x in range(len(species))
])
# quote the motif
r = regions[mafchrom].find(refstart, refend)
if mafchrom in regions and len(r) > 0:
region_label = r[0].value
else:
#region_label = 0
continue
v_name = mx_name.replace(' ', '_')
print mafchrom, refstart, refend, region_label, v_name, data
break