def user_defined_exons(tmp_sg, line):
chr, strand = utils.get_chr(
line[utils.TARGET]), line[utils.TARGET][0] # get chr and strand
upstream_exon = utils.get_pos(
line[utils.UPSTREAM_EXON]) # get user-defined flanking exons
downstream_exon = utils.get_pos(line[utils.DOWNSTREAM_EXON])
first_primer, second_primer = utils.get_primer_coordinates(
line[utils.PRIMER_COORD])
# get possible exons for primer amplification
tmp = sorted(tmp_sg.get_graph().nodes(), key=lambda x: (x[0], x[1]))
first_ex = utils.find_first_exon(first_primer, tmp)
last_ex = utils.find_last_exon(second_primer, tmp)
my_exons = tmp[first_ex:last_ex + 1]
# if tmp_sg.strand == '+':
# my_exons = tmp[tmp.index(upstream_exon):tmp.index(downstream_exon) + 1]
# else:
# my_exons = tmp[tmp.index(downstream_exon):tmp.index(upstream_exon) + 1]
# Use correct tx's and estimate counts/psi
all_paths = algs.AllPaths(
tmp_sg,
my_exons,
utils.get_pos(line[utils.TARGET]), # tuple (start, end)
chr=chr,
strand=strand)
# all_paths.trim_tx_paths()
fexon = upstream_exon if strand == "+" else downstream_exon
lexon = downstream_exon if strand == "+" else upstream_exon
all_paths.trim_tx_paths_using_primers(first_primer, second_primer, fexon,
lexon)
all_paths.set_all_path_coordinates()
paths, counts = all_paths.estimate_counts() # run EM algorithm
return paths, counts
def user_defined_exons(tmp_sg, line):
chr, strand = utils.get_chr(line[utils.TARGET]), line[utils.TARGET][0] # get chr and strand
upstream_exon = utils.get_pos(line[utils.UPSTREAM_EXON]) # get user-defined flanking exons
downstream_exon = utils.get_pos(line[utils.DOWNSTREAM_EXON])
first_primer, second_primer = utils.get_primer_coordinates(line[utils.PRIMER_COORD])
# get possible exons for primer amplification
tmp = sorted(tmp_sg.get_graph().nodes(), key=lambda x: (x[0], x[1]))
first_ex = utils.find_first_exon(first_primer, tmp)
last_ex = utils.find_last_exon(second_primer, tmp)
my_exons = tmp[first_ex:last_ex + 1]
# if tmp_sg.strand == '+':
# my_exons = tmp[tmp.index(upstream_exon):tmp.index(downstream_exon) + 1]
# else:
# my_exons = tmp[tmp.index(downstream_exon):tmp.index(upstream_exon) + 1]
# Use correct tx's and estimate counts/psi
all_paths = algs.AllPaths(tmp_sg,
my_exons,
utils.get_pos(line[utils.TARGET]), # tuple (start, end)
chr=chr,
strand=strand)
# all_paths.trim_tx_paths()
fexon = upstream_exon if strand == "+" else downstream_exon
lexon = downstream_exon if strand == "+" else upstream_exon
all_paths.trim_tx_paths_using_primers(first_primer, second_primer, fexon, lexon)
all_paths.set_all_path_coordinates()
paths, counts = all_paths.estimate_counts() # run EM algorithm
return paths, counts
def trim_tx_paths_using_primers(self, first_primer, second_primer,
first_exon, second_exon):
"""
Get rid of all transcripts which do not contain both the first
and second primer. This method may keep transcripts that do not
contain the exact user defined flanking exons.
"""
self.component = sorted(self.component, key=lambda x:
(x[0], x[1])) # make sure it is sorted
# trim tx_paths to only contain paths within component_subgraph
tmp = set()
for p in self.tx_paths:
first_ex = utils.find_first_exon(first_primer, p)
last_ex = utils.find_last_exon(second_primer, p)
if first_ex is not None and last_ex is not None:
tmp_path = p[first_ex:last_ex + 1]
if tmp_path[0][0] < first_exon[0]:
tmp_path[0] = (first_exon[0], tmp_path[0][1]
) # don't be before user-defined exon
if tmp_path[-1][1] > second_exon[1]:
tmp_path[-1] = (tmp_path[-1][0], second_exon[1]
) # don't be after user-defined exon
tmp.add(tuple(tmp_path)) # make sure no redundancies
# self.tx_paths = sorted(list(tmp), key=lambda x: (x[0], x[1]))
self.tx_paths = list(tmp)
def trim_tx_paths_using_primers(self, first_primer, second_primer, first_exon, second_exon):
"""
Get rid of all transcripts which do not contain both the first
and second primer. This method may keep transcripts that do not
contain the exact user defined flanking exons.
"""
self.component = sorted(self.component, key=lambda x: (x[0], x[1])) # make sure it is sorted
# trim tx_paths to only contain paths within component_subgraph
tmp = set()
for p in self.tx_paths:
first_ex = utils.find_first_exon(first_primer, p)
last_ex = utils.find_last_exon(second_primer, p)
if first_ex is not None and last_ex is not None:
tmp_path = p[first_ex:last_ex+1]
if tmp_path[0][0] < first_exon[0]:
tmp_path[0] = (first_exon[0], tmp_path[0][1]) # don't be before user-defined exon
if tmp_path[-1][1] > second_exon[1]:
tmp_path[-1] = (tmp_path[-1][0], second_exon[1]) # don't be after user-defined exon
tmp.add(tuple(tmp_path)) # make sure no redundancies
# self.tx_paths = sorted(list(tmp), key=lambda x: (x[0], x[1]))
self.tx_paths = list(tmp)