def populate_graph(self):
"""
Add edges from acceptors to donors, donors to acceptors,
on distinct strands.
Record the exon number within the transcript.
"""
print "Populating graph..."
t1 = time.time()
for table_name in self.tables:
print "Adding splice edges from table %s" %(table_name)
for item in self.tables[table_name]:
chrom, startvals, endvals, strand, gene = item
startvals = map(int, startvals.split(",")[:-1])
# Adds +1 since downloaded UCSC tables are 0-based start!
startvals = map(str, [x + 1 for x in startvals])
endvals = endvals.split(",")[:-1]
indices = range(len(startvals))
if strand == "-":
# If it's a minus strand event, walk the transcript from
# end (in order of transcription)
startvals = startvals[::-1]
endvals = endvals[::-1]
# Zero-based exon number
curr_exon_num = 0
for curr_i, next_i in utils.iter_by_pair(indices, step=1):
# Splice from end of current exon to start of next exonp
donor_unit = Unit((chrom, startvals[curr_i], strand),
(chrom, endvals[curr_i], strand))
acceptor_unit = Unit((chrom, startvals[next_i], strand),
(chrom, endvals[next_i], strand))
if strand == "-":
# Reverse start/end of donor and acceptor units
# if it's a minus strand event
donor_unit = Unit((chrom, endvals[curr_i], strand),
(chrom, startvals[curr_i], strand))
acceptor_unit = Unit((chrom, endvals[next_i], strand),
(chrom, startvals[next_i], strand))
# donor_unit, acceptor_unit = acceptor_unit, donor_unit
## Record the exon number for donor and acceptor
# Donor is exon number N
self.add_unit_number(donor_unit, curr_exon_num, strand)
# Acceptor is exon number N+1
self.add_unit_number(donor_unit, curr_exon_num + 1,
strand=strand)
self.add_edge(donor_unit, acceptor_unit,
strand=strand)
curr_exon_num += 1
t2 = time.time()
print "Populating graph took %.2f seconds" %(t2 - t1)
def prob_score(self, subseq):
"""
Score probability of subseq in sequence.
"""
if len(subseq) == 0:
return 0
# Score first base
total_logscore = np.log(self.base_freqs[subseq[0]])
for prev_base, next_base in utils.iter_by_pair(subseq, 1):
# Score current dinucleotide
curr_dinuc = "%s%s" %(prev_base, next_base)
# Divide by sum of all other transitions from the previous base
curr_dinuc_freq = self.du[curr_dinuc]
denom_dinuc_freqs = np.sum(self.get_dinuc_freqs_from(prev_base))
total_logscore += (np.log(curr_dinuc_freq) - \
np.log(denom_dinuc_freqs))
total_score = np.exp(total_logscore)
return total_score
def prob_score(self, subseq):
"""
Score probability of subseq in sequence.
"""
if len(subseq) == 0:
return 0
# Score first base
total_logscore = np.log(self.base_freqs[subseq[0]])
for prev_base, next_base in utils.iter_by_pair(subseq, 1):
# Score current dinucleotide
curr_dinuc = "%s%s" % (prev_base, next_base)
# Divide by sum of all other transitions from the previous base
curr_dinuc_freq = self.du[curr_dinuc]
denom_dinuc_freqs = np.sum(self.get_dinuc_freqs_from(prev_base))
total_logscore += (np.log(curr_dinuc_freq) - \
np.log(denom_dinuc_freqs))
total_score = np.exp(total_logscore)
return total_score
def populate_graph(self):
"""
Add edges from acceptors to donors, donors to acceptors,
on distinct strands.
"""
print "Populating graph..."
t1 = time.time()
for table_name in self.tables:
print "Adding splice edges from table %s" %(table_name)
for item in self.tables[table_name]:
chrom, startvals, endvals, strand, gene = item
startvals = map(int, startvals.split(",")[:-1])
# Adds +1 since downloaded UCSC tables are 0-based start!
startvals = map(str, [x + 1 for x in startvals])
endvals = endvals.split(",")[:-1]
indices = range(len(startvals))
if strand == "-":
# If it's a minus strand event, walk the transcript from
# end (in order of transcription)
startvals = startvals[::-1]
endvals = endvals[::-1]
for curr_i, next_i in utils.iter_by_pair(indices, step=1):
# Splice from end of current exon to start of next exonp
donor_unit = Unit((chrom, startvals[curr_i], strand),
(chrom, endvals[curr_i], strand))
acceptor_unit = Unit((chrom, startvals[next_i], strand),
(chrom, endvals[next_i], strand))
if strand == "-":
# Reverse start/end of donor and acceptor units
# if it's a minus strand event
donor_unit = Unit((chrom, endvals[curr_i], strand),
(chrom, startvals[curr_i], strand))
acceptor_unit = Unit((chrom, endvals[next_i], strand),
(chrom, startvals[next_i], strand))
# donor_unit, acceptor_unit = acceptor_unit, donor_unit
# Record splice site as edge
self.add_edge(donor_unit, acceptor_unit,
strand=strand)
t2 = time.time()
print "Populating graph took %.2f seconds" %(t2 - t1)