def testReader(self):
# test basic format: i.e. for jaspar
wms = [wm for wm in pwm.Reader(StringIO(basicPwm),format="basic", \
background=background,score_correction=False)]
assert len(wms) == 1
# test transfac format
wms = [wm for wm in pwm.Reader(StringIO(transfacPwm),format="transfac", \
background=background,score_correction=False)]
assert len(wms) == 1
wm = wms[0]
dScores = wm.score_seq(dSeq)
assert len(dScores) == 2
assert "%.4f %.4f %.4f %.4f" % (dScores[0][0], dScores[0][1],
dScores[1][0],
dScores[1][1]) == dScoresExpected
qdSeq = []
for (ix, nt) in enumerate(dSeq):
qdSeq.append(dict())
qdSeq[ix][nt] = 1.0
qScores = wm.score_seq(qdSeq)
assert len(qScores) == 2
assert "%.4f %.4f %.4f %.4f" % (qScores[0][0], qScores[0][1],
qScores[1][0],
qScores[1][1]) == dScoresExpected
qScores = wm.score_seq(qSeq)
assert len(qScores) == 1
assert "%.4f %.4f" % (qScores[0][0], qScores[0][1]) == qScoresExpected
def main():
pwm_file = sys.argv[1]
splist = sys.argv[2]
if len(sys.argv) == 4:
inmaf = open(sys.argv[3])
else:
inmaf = sys.stdin
# read alignment species
species = []
for sp in splist.split(','):
species.append(sp)
# read weight matrices
pwm = {}
for wm in pwmx.Reader(open(pwm_file), format='basic'):
pwm[wm.id] = wm
fbunch = {}
for scoremax, index, headers in MafScorer(pwm, species, inmaf):
for k, matrix in scoremax.items():
fname = k + '.mx'
if fname not in fbunch:
fbunch[fname] = open(fname, 'w')
print("Writing", fname, file=sys.stderr)
for i in range(len(matrix)):
for j in range(len(matrix[i])):
print("%.2f" % matrix[i][j], end=' ', file=fbunch[fname])
print(file=fbunch[fname])
for file in fbunch.values():
file.close()
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 main():
if len(sys.argv) < 5:
print >> sys.stderr, "%s transfac|basic pwmfile inmaf threshold [motif]" % sys.argv[
0]
sys.exit(2)
r = pwmx.Reader(open(sys.argv[2]), format=sys.argv[1])
pwm = iter(r).next()
inmaf = open(sys.argv[3])
threshold = float(sys.argv[4])
if len(sys.argv) > 5: motif = sys.argv[5]
else: motif = None
for maf in align_maf.Reader(inmaf):
for mafmotif, pwm_score, motif_score in MafMotifSelect(
maf, pwm, motif, threshold):
#mafwrite( mafmotif,pwm_score,motif_score)
print mafmotif, pwm_score, motif_score
print 'zzzzzzzzzzzzzzzzzzzzzzzzzzzzz'
#FOX 6-mer motif
fm = """>FOX6
0 0 0 100
0 0 100 0
0 100 0 0
100 0 0 0
0 0 0 100
0 0 100 0
"""
background = { 'A':.28,'C':.21, 'G':.24, 'T':.27 } #genome background. not transcriptome :(
FOXwm = [w for w in pwm.Reader(StringIO.StringIO(fm),format="basic", background=background,score_correction=True)][0]
hg19Phylo = hg19Phylogeny()
fasta = pyfasta.Fasta("/home/lovci/data/Genome/hg19/all.fa", flatten_inplace=True)
def alnToPWM(aln, id = "id", background=background, nSpecies = 46.0):
#import StringIO
#s = StringIO.StringIO()
#s.write(">" + id + "\n")
sz = aln.components[0].size
ar = np.ndarray( shape=(sz,4))
for rowN, i in enumerate(aln.column_iter()):
