def parse(self, fo):
motifs = []
p = re.compile(
r'^\d+\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)')
pwm = []
motif_id = ""
for line in fo.readlines():
if line.startswith("Motif #"):
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
motif_id = line.split("#")[1].split(":")[0]
pwm = []
else:
m = p.search(line)
if m:
pwm.append(
[float(m.group(x)) / 100.0 for x in range(1, 5)])
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
return motifs
def match(args):
sample = dict([(m.id, m) for m in pwmfile_to_motifs(args.pwmfile)])
db = dict([(m.id, m) for m in pwmfile_to_motifs(args.dbpwmfile)])
mc = MotifComparer()
result = mc.get_closest_match(sample.values(), db.values(), "partial", "wic", "mean")
print("Motif\tMatch\tScore\tP-value")
for motif, match in result.items():
pval, pos, orient = mc.compare_motifs(sample[motif], db[match[0]], "partial", "wic", "mean", pval=True)
print("%s\t%s\t%0.2f\t%0.3e" % (motif, match[0], match[1][0], pval))
if args.img:
plotdata = []
for query, match in result.items():
motif = sample[query]
dbmotif = db[match[0]]
pval, pos, orient = mc.compare_motifs(motif, dbmotif, "partial", "wic", "mean", pval=True)
if orient == -1:
tmp = dbmotif.id
dbmotif = dbmotif.rc()
dbmotif.id = tmp
if pos < 0:
tmp = motif.id
motif = Motif([[0.25,0.25,0.25,0.25]] * -pos + motif.pwm)
motif.id = tmp
elif pos > 0:
tmp = dbmotif.id
dbmotif = Motif([[0.25,0.25,0.25,0.25]] * pos + dbmotif.pwm)
dbmotif.id = tmp
plotdata.append((motif, dbmotif, pval))
match_plot(plotdata, args.img)
def test6_pcc(self):
pfm1 = [[5, 0, 0, 0], [0, 5, 0, 0], [0, 5, 0, 0], [0, 0, 0, 5]]
pfm2 = [[5, 0, 0, 0], [0, 5, 0, 0], [0, 5, 0, 0], [0, 0, 0, 5]]
m1 = Motif(pfm1)
m2 = Motif(pfm2)
self.assertEqual(4, m1.max_pcc(m2)[0])
def parse(self, fo):
"""
Convert MDmodule output to motifs
Parameters
----------
fo : file-like
File object containing MDmodule output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
nucs = {"A": 0, "C": 1, "G": 2, "T": 3}
p = re.compile(
r"(\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)")
pf = re.compile(r">.+\s+[bf]\d+\s+(\w+)")
pwm = []
pfm = []
align = []
m_id = ""
for line in fo.readlines():
if line.startswith("Motif"):
if m_id:
motifs.append(Motif())
motifs[-1].id = m_id
motifs[-1].pwm = pwm
motifs[-1].pfm = pfm
motifs[-1].align = align
pwm = []
pfm = []
align = []
m_id = line.split("\t")[0]
else:
m = p.search(line)
if m:
pwm.append([float(m.group(x)) / 100 for x in [2, 3, 4, 5]])
m = pf.search(line)
if m:
if not pfm:
pfm = [[0 for x in range(4)]
for x in range(len(m.group(1)))]
for i in range(len(m.group(1))):
pfm[i][nucs[m.group(1)[i]]] += 1
align.append(m.group(1))
if pwm:
motifs.append(Motif())
motifs[-1].id = m_id
motifs[-1].pwm = pwm
motifs[-1].pfm = pfm
motifs[-1].align = align
return motifs
def test8_pwm_to_str_hash(self):
pwm = [[0.01, 0.01, 0.01, 0.97], [0.123, 0.456, 0.222, 0.199]]
m = Motif(pwm)
h = "1f260320cac8c26a"
self.assertEqual(h, m.hash())
pwm = [
[0.010000, 0.010000, 0.010000, 0.970000],
[0.12300, 0.45600, 0.22200, 0.19900],
]
m = Motif(pwm)
self.assertEqual(h, m.hash())
def test_motif_export_import(self):
pfm = [
[120, 0, 0, 0],
[120, 0, 0, 0],
[0, 60, 60, 0],
[0, 0, 0, 120],
[0, 0, 0, 120],
]
motif = Motif(pfm)
motif.id = "test_motif"
f = StringIO(motif.to_transfac())
motif_from_file = read_motifs(f, fmt="transfac")[0]
self.assertEqual("AASTT", motif_from_file.to_consensus().upper())
self.assertEqual("test_motif", motif_from_file.id)
f = StringIO(motif.to_meme())
motif_from_file = read_motifs(f, fmt="meme")[0]
self.assertEqual("AASTT", motif_from_file.to_consensus().upper())
self.assertEqual("test_motif", motif_from_file.id)
f = StringIO(motif.to_motevo())
motif_from_file = read_motifs(f, fmt="transfac")[0]
self.assertEqual("AASTT", motif_from_file.to_consensus().upper())
self.assertEqual("test_motif", motif_from_file.id)
def parse(self, fo):
"""
Convert ChIPMunk output to motifs
Parameters
----------
fo : file-like
File object containing ChIPMunk output.
Returns
-------
motifs : list
List of Motif instances.
"""
line = fo.readline()
if not line:
return []
while not line.startswith("A|"):
line = fo.readline()
matrix = []
for _ in range(4):
matrix.append(
[float(x) for x in line.strip().split("|")[1].split(" ")])
line = fo.readline()
# print matrix
matrix = [[matrix[x][y] for x in range(4)]
for y in range(len(matrix[0]))]
# print matrix
m = Motif(matrix)
m.id = "ChIPMunk_w%s" % len(m)
return [m]
def parse(self, fo):
"""
Convert MotifSampler output to motifs
Parameters
----------
fo : file-like
File object containing MotifSampler output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
pwm = []
info = {}
for line in fo.readlines():
if line.startswith("#"):
vals = line.strip()[1:].split(" = ")
if len(vals) > 1:
info[vals[0]] = vals[1]
elif len(line) > 1:
pwm.append([float(x) for x in line.strip().split("\t")])
else:
motifs.append(Motif())
motifs[-1].consensus = info["Consensus"]
motifs[-1].width = info["W"]
motifs[-1].id = info["ID"]
motifs[-1].pwm = pwm[:]
pwm = []
return motifs
def parse(self, fo):
motifs = []
nucs = {"A": 0, "C": 1, "G": 2, "T": 3}
p = re.compile(
r'(\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)')
pf = re.compile(r'>.+\s+[bf]\d+\s+(\w+)')
pwm = []
pfm = []
align = []
id = ""
for line in fo.readlines():
if line.startswith("Motif"):
if id:
motifs.append(Motif())
motifs[-1].id = id
motifs[-1].pwm = pwm
motifs[-1].pfm = pfm
motifs[-1].align = align
pwm = []
pfm = []
align = []
id = line.split("\t")[0]
else:
m = p.search(line)
if m:
pwm.append([float(m.group(x)) / 100 for x in [2, 3, 4, 5]])
m = pf.search(line)
if m:
if not pfm:
pfm = [[0 for x in range(4)]
for x in range(len(m.group(1)))]
for i in range(len(m.group(1))):
pfm[i][nucs[m.group(1)[i]]] += 1
align.append(m.group(1))
if pwm:
motifs.append(Motif())
motifs[-1].id = id
motifs[-1].pwm = pwm
motifs[-1].pfm = pfm
motifs[-1].align = align
return motifs
def test9_logodds_matrix(self):
pwm = [[0.5, 0.4, 0.1, 0.0], [0.25, 0.25, 0.25, 0.25]]
logodds = np.array([
[0.69813, 0.47623, -0.89160, -4.60517],
[0.00995, 0.00995, 0.00995, 0.00995],
])
m = Motif(pwm)
np.testing.assert_almost_equal(logodds, np.array(m.logodds), decimal=5)
def match(args):
sample = dict([(m.id, m) for m in read_motifs(args.pfmfile)])
db = dict([(m.id, m) for m in read_motifs(args.dbpfmfile)])
mc = MotifComparer()
result = mc.get_best_matches(
sample.values(), args.nmatches, db.values(), "partial", "seqcor", "mean"
)
plotdata = []
print("Motif\tMatch\tScore\tP-value")
for motif_name, matches in result.items():
for match in matches:
pval, pos, orient = mc.compare_motifs(
sample[motif_name], db[match[0]], "partial", "seqcor", "mean", pval=True
)
print("%s\t%s\t%0.2f\t%0.3e" % (motif_name, match[0], match[1][0], pval))
motif = sample[motif_name]
dbmotif = db[match[0]]
if args.img:
if orient == -1:
tmp = dbmotif.id
dbmotif = dbmotif.rc()
dbmotif.id = tmp
if pos < 0:
tmp = motif.id
motif = Motif([[0.25, 0.25, 0.25, 0.25]] * -pos + motif.pwm)
motif.id = tmp
elif pos > 0:
tmp = dbmotif.id
dbmotif = Motif([[0.25, 0.25, 0.25, 0.25]] * pos + dbmotif.pwm)
dbmotif.id = tmp
diff = len(motif) - len(dbmotif)
if diff > 0:
dbmotif = Motif(dbmotif.pwm + [[0.25, 0.25, 0.25, 0.25]] * diff)
else:
motif = Motif(motif.pwm + [[0.25, 0.25, 0.25, 0.25]] * -diff)
plotdata.append((motif, dbmotif, pval))
if args.img:
match_plot(plotdata, args.img)
def parse(self, fo):
motifs = []
m = [[float(x) for x in fo.readline().strip().split(" ")]
for i in range(4)]
matrix = [[m[0][i], m[1][i], m[2][i], m[3][i]]
for i in range(len(m[0]))]
motifs = [Motif(matrix)]
motifs[-1].id = self.name
return motifs
def test5_motif_to_img(self):
""" Motif to img """
seqlogo = which("seqlogo")
if seqlogo:
m = Motif(self.pfm)
m.to_img("test/test.png", fmt="png", seqlogo=seqlogo)
self.assertTrue(os.path.exists("test/test.png"))
os.unlink("test/test.png")
else:
print("seqlogo not found, skipping.")
def test8_pwm_to_str(self):
pwm = [[0.01, 0.01, 0.01, 0.97], [0.123, 0.456, 0.222, 0.199]]
m = Motif(pwm)
s2 = "0.01\t0.01\t0.01\t0.97\n0.12\t0.46\t0.22\t0.20"
s3 = "0.010\t0.010\t0.010\t0.970\n0.123\t0.456\t0.222\t0.199"
self.assertEqual(s2, m._pwm_to_str(precision=2))
self.assertEqual(s3, m._pwm_to_str(precision=3))
def parse(self, fo):
"""
Convert GADEM output to motifs
Parameters
----------
fo : file-like
File object containing GADEM output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
nucs = {"A": 0, "C": 1, "G": 2, "T": 3}
lines = fo.readlines()
for i in range(0, len(lines), 5):
align = []
pwm = []
pfm = []
m_id = ""
line = lines[i].strip()
m_id = line[1:]
number = m_id.split("_")[0][1:]
if os.path.exists("%s.seq" % number):
with open("%s.seq" % number) as f:
for line in f:
if "x" not in line and "n" not in line:
line = line.strip().upper()
align.append(line)
if not pfm:
pfm = [[0 for x in range(4)]
for x in range(len(line))]
for p in range(len(line)):
pfm[p][nucs[line[p]]] += 1
m = [
line.strip().split(" ")[1].split("\t")
for line in lines[i + 1:i + 5]
]
pwm = [[float(m[x][y]) for x in range(4)]
for y in range(len(m[0]))]
motifs.append(Motif(pwm))
motifs[-1].id = "{}_{}".format(self.name, m_id)
# motifs[-1].pwm = pwm
if align:
motifs[-1].pfm = pfm
motifs[-1].align = align
return motifs
def parse(self, fname):
"""
Convert RPMCMC output to motifs
Parameters
----------
fname : str
File containing RPMCMC output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
pfm = []
name = ""
for line in open(fname):
line = line.strip()
if line.startswith("PFM"):
continue
if line.startswith("Motif"):
if len(pfm) > 0:
motif = Motif(pfm)
motif.id = name
motifs.append(motif)
name = line
pfm = []
else:
if line != ("A C G T"):
row = line.split(" ")
if len(row) == 4:
row = [float(x) for x in row]
pfm.append(row)
motif = Motif(pfm)
motif.id = name
motifs.append(motif)
return motifs
def parse(self, fo):
"""
Convert MEME output to motifs
Parameters
----------
fo : file-like
File object containing MEME output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
nucs = {"A": 0, "C": 1, "G": 2, "T": 3}
p = re.compile(
r"MOTIF.+MEME-(\d+)\s*width\s*=\s*(\d+)\s+sites\s*=\s*(\d+)")
pa = re.compile(r"\)\s+([A-Z]+)")
line = fo.readline()
while line:
m = p.search(line)
align = []
pfm = None
if m:
# print(m.group(0))
id = "%s_%s_w%s" % (self.name, m.group(1), m.group(2))
while not line.startswith("//"):
ma = pa.search(line)
if ma:
# print(ma.group(0))
match = ma.group(1)
align.append(match)
if not pfm:
pfm = [[0 for x in range(4)]
for x in range(len(match))]
for pos in range(len(match)):
if match[pos] in nucs:
pfm[pos][nucs[match[pos]]] += 1
else:
for i in range(4):
pfm[pos][i] += 0.25
line = fo.readline()
motifs.append(Motif(pfm[:]))
motifs[-1].id = id
motifs[-1].align = align[:]
line = fo.readline()
return motifs
def parse_out(self, fo):
"""
Convert MotifSampler output to motifs
Parameters
----------
fo : file-like
File object containing MotifSampler output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
nucs = {"A": 0, "C": 1, "G": 2, "T": 3}
pseudo = 0.0 # Should be 1/sqrt(# of seqs)
aligns = {}
for line in fo.readlines():
if line.startswith("#"):
pass
elif len(line) > 1:
vals = line.strip().split("\t")
m_id, site = [
x.strip().split(" ")[1].replace('"', "")
for x in vals[8].split(";")
if x
]
# if vals[6] == "+":
if site.upper().find("N") == -1:
aligns.setdefault(m_id, []).append(site)
# else:
# print site, rc(site)
# aligns.setdefault(id, []).append(rc(site))
for m_id, align in aligns.items():
# print id, len(align)
width = len(align[0])
pfm = [[0 for x in range(4)] for x in range(width)]
for row in align:
for i in range(len(row)):
pfm[i][nucs[row[i]]] += 1
total = float(len(align))
pwm = [[(x + pseudo / 4) / total + (pseudo) for x in row] for row in pfm]
m = Motif()
m.align = align[:]
m.pwm = pwm[:]
m.pfm = pfm[:]
m.id = m_id
motifs.append(m)
return motifs
def parse(self, fo):
"""
Convert BioProspector output to motifs
Parameters
----------
fo : file-like
File object containing BioProspector output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
p = re.compile(
r"^\d+\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)")
pwm = []
motif_id = ""
for line in fo.readlines():
if line.startswith("Motif #"):
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
motif_id = line.split("#")[1].split(":")[0]
pwm = []
else:
m = p.search(line)
if m:
pwm.append(
[float(m.group(x)) / 100.0 for x in range(1, 5)])
if pwm:
m = Motif(pwm)
m.id = "BioProspector_w%s_%s" % (len(m), motif_id)
motifs.append(m)
return motifs
def parse(self, fo):
motifs = []
#160: 112 CACGTGC 7.25 chr14:32308489-32308689
p = re.compile(r'\d+\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)')
wm = []
name = ""
for line in fo.readlines():
if line.startswith("Motif") and line.strip().endswith(":"):
if name:
motifs.append(Motif(wm))
motifs[-1].id = name
name = ""
wm = []
name = "%s_%s" % (self.name, line.split(":")[0])
else:
m = p.search(line)
if m:
wm.append([float(m.group(x)) for x in range(1, 5)])
motifs.append(Motif(wm))
motifs[-1].id = name
return motifs
def parse(self, fo):
"""
Convert AMD output to motifs
Parameters
----------
fo : file-like
File object containing AMD output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
# 160: 112 CACGTGC 7.25 chr14:32308489-32308689
p = re.compile(r"\d+\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)\s+([\d.]+)")
wm = []
name = ""
for line in fo.readlines():
if line.startswith("Motif") and line.strip().endswith(":"):
if name:
motifs.append(Motif(wm))
motifs[-1].id = name
name = ""
wm = []
name = "%s_%s" % (self.name, line.split(":")[0])
else:
m = p.search(line)
if m:
wm.append([float(m.group(x)) for x in range(1, 5)])
motifs.append(Motif(wm))
motifs[-1].id = name
return motifs
def get_gimmemotif(self): """ Get gimmemotif object for motif Reads counts from self.counts """ from gimmemotifs.motif import Motif self.length = len(self.counts[0]) motif_rows = [] for pos_id in range(self.length): row = [self.counts[letter][pos_id] for letter in range(4)] # each row represents one position in motif ( A C G T ) motif_rows.append(row) self.gimme_obj = Motif(motif_rows) # generate gimmemotif motif instance self.gimme_obj.id = self.id + " " + self.name return(self)
def test11_slice_motif(self):
pfm = [
[120, 0, 0, 0],
[120, 0, 0, 0],
[0, 60, 60, 0],
[0, 0, 0, 120],
[0, 0, 0, 120],
]
m = Motif(pfm)
m.to_consensus()
# take slice
m2 = m[1:-1]
self.assertEqual("AST", m2.consensus.upper())
self.assertEqual(pfm[1:-1], m2.pfm)
def parse(self, fo):
motifs = []
nucs = {"A": 0, "C": 1, "G": 2, "T": 3}
lines = [fo.readline() for x in range(6)]
while lines[0]:
matrix = [[float(x) for x in line.strip().split("\t")]
for line in lines[2:]]
matrix = [[matrix[x][y] for x in range(4)]
for y in range(len(matrix[0]))]
m = Motif(matrix)
m.id = lines[0].strip().split(" ")[-1]
motifs.append(m)
lines = [fo.readline() for x in range(6)]
for i, motif in enumerate(motifs):
motif.id = "%s_%s" % (self.name, i + 1)
motif.trim(0.25)
return motifs
def parse(self, fo):
motifs = []
pwm = []
info = {}
for line in fo.readlines():
if line.startswith("#"):
vals = line.strip()[1:].split(" = ")
if len(vals) > 1:
info[vals[0]] = vals[1]
elif len(line) > 1:
pwm.append([float(x) for x in line.strip().split("\t")])
else:
motifs.append(Motif())
motifs[-1].consensus = info["Consensus"]
motifs[-1].width = info["W"]
motifs[-1].id = info["ID"]
motifs[-1].pwm = pwm[:]
pwm = []
return motifs
def parse(self, fo):
"""
Convert HMS output to motifs
Parameters
----------
fo : file-like
File object containing HMS output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
m = [[float(x) for x in fo.readline().strip().split(" ")] for i in range(4)]
matrix = [[m[0][i], m[1][i], m[2][i], m[3][i]] for i in range(len(m[0]))]
motifs = [Motif(matrix)]
motifs[-1].id = self.name
return motifs
def parse(self, fo):
motifs = []
nucs = {"A": 0, "C": 1, "G": 2, "T": 3}
lines = fo.readlines()
for i in range(0, len(lines), 5):
align = []
pwm = []
pfm = []
id = ""
line = lines[i].strip()
id = line[1:]
number = id.split("_")[0][1:]
if os.path.exists("%s.seq" % number):
for l in open("%s.seq" % number).readlines():
if not "x" in l and not "n" in l:
l = l.strip().upper()
align.append(l)
if not pfm:
pfm = [[0 for x in range(4)]
for x in range(len(l))]
for p in range(len(l)):
pfm[p][nucs[l[p]]] += 1
m = [
l.strip().split(" ")[1].split("\t") for l in lines[i + 1:i + 5]
]
pwm = [[float(m[x][y]) for x in range(4)]
for y in range(len(m[0]))]
motifs.append(Motif(pwm))
motifs[-1].id = id
#motifs[-1].pwm = pwm
if align:
pass
motifs[-1].pfm = pfm
motifs[-1].align = align
return motifs
def parse(self, fo):
motifs = []
nucs = {"A": 0, "C": 1, "G": 2, "T": 3}
p = re.compile(r'(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)')
pa = re.compile(r'(\s*\d+\s+.\s+([ACGT]+)\s+.+\))')
pwm = []
align = []
c = 1
for line in fo.readlines():
m = p.search(line)
if m:
pwm.append([int(m.group(x)) for x in [2, 3, 4, 5]])
m = pa.search(line)
if m:
align.append(m.group(2))
elif line.startswith("===="):
motifs.append(Motif())
#total = float(pwm[0][0] + pwm[0][1] + pwm[0][2] + pwm[0][3])
#motifs[-1].pwm = [[x / total for x in row] for row in pwm]
motifs[-1].id = "Weeder_%s" % c
motifs[-1].align = align[:]
width = len(align[0])
pfm = [[0 for x in range(4)] for x in range(width)]
for row in align:
for i in range(len(row)):
pfm[i][nucs[row[i]]] += 1
total = float(len(align))
pwm = [[((x) / total) for x in row] for row in pfm]
motifs[-1].pwm = pwm[:]
motifs[-1].pfm = pfm[:]
align = []
c += 1
pwm = []
return motifs
def parse(self, fo):
#KDIC|6.124756232026243
#A|517.9999999999999 42.99999999999999 345.99999999999994 25.999999999999996 602.9999999999999 155.99999999999997 2.9999999999999996 91.99999999999999
#C|5.999999999999999 4.999999999999999 2.9999999999999996 956.9999999999999 91.99999999999999 17.999999999999996 22.999999999999996 275.99999999999994
#G|340.99999999999994 943.9999999999999 630.9999999999999 6.999999999999999 16.999999999999996 48.99999999999999 960.9999999999999 14.999999999999998
#T|134.99999999999997 7.999999999999999 19.999999999999996 9.999999999999998 287.99999999999994 776.9999999999999 12.999999999999998 616.9999999999999
#N|999.9999999999998
line = fo.readline()
while not line.startswith("A|"):
line = fo.readline()
matrix = []
for i in range(4):
matrix.append(
[float(x) for x in line.strip().split("|")[1].split(" ")])
line = fo.readline()
#print matrix
matrix = [[matrix[x][y] for x in range(4)]
for y in range(len(matrix[0]))]
#print matrix
m = Motif(matrix)
m.id = "ChIPMunk_w%s" % len(m)
return [m]
def parse(self, fo):
"""
Convert Improbizer output to motifs
Parameters
----------
fo : file-like
File object containing Improbizer output.
Returns
-------
motifs : list
List of Motif instances.
"""
motifs = []
p = re.compile(r"\d+\s+@\s+\d+\.\d+\s+sd\s+\d+\.\d+\s+(\w+)$")
line = fo.readline()
while line and line.find("Color") == -1:
m = p.search(line)
if m:
pwm_data = {}
for _i in range(4):
vals = [
x.strip() for x in fo.readline().strip().split(" ")
if x
]
pwm_data[vals[0].upper()] = vals[1:]
pwm = []
for i in range(len(pwm_data["A"])):
pwm.append(
[float(pwm_data[x][i]) for x in ["A", "C", "G", "T"]])
motifs.append(Motif(pwm))
motifs[-1].id = "%s_%s" % (self.name, m.group(1))
line = fo.readline()
return motifs