def do_reduction(subset, args, nrfuzzykey, location):
seen = set()
for i in subset:
seen.add(i)
for j in subset[i]:
seen.add(j)
singles = []
for num in nrfuzzykey:
if num not in seen:
singles.append(num)
#if len(subset.keys()) == 0 and len(compatible.keys()) == 0: return
families = get_subset_evidence(subset, nrfuzzykey, args)
gpdlines = ""
tablelines = ""
for num in singles:
families.append(nrfuzzykey[num])
# find gpds not in the graph...
for fz in families:
info = fz.get_info_string()
gpdline = fz.get_genepred_line()
#print '&&&&&&&&&&&&&&&&'
#print gpdline
#print fz.get_info_string()
#print '&&&&&&&&&&&&&&&&'
gpd = GenePredEntry(gpdline)
if not gpd.is_valid():
sys.stderr.write("WARNING: invalid genepred entry generated\n" +
gpdline + "\n" + fz.get_info_string() + "\n")
gpd = sorted(
fz.gpds, key=lambda x: x.get_exon_count(),
reverse=True)[0] #just grab one that has all the exons
fz = FuzzyGenePred(gpd, juntol=args.junction_tolerance * 2)
gpdline = fz.get_genepred_line()
if not gpd.is_valid():
sys.stderr.write("WARNING: still problem skilling\n")
continue
gpdlines += gpdline + "\n"
if args.output_original_table:
name = gpd.entry['name']
for g in fz.gpds:
tablelines += name + "\t" + g.entry['name'] + "\n"
grng = gpd.get_bed()
grng.direction = None
if not location:
location = grng
location = location.merge(grng)
locstring = ''
if location: locstring = location.get_range_string()
return [gpdlines, tablelines, locstring]
def main():
parser = argparse.ArgumentParser(description="do join of gpd overlaps")
parser.add_argument('gpd_left')
parser.add_argument('gpd_right')
parser.add_argument('-j', '--junction_tolerance', default=5, type=int)
parser.add_argument('--threads', type=int, default=1)
parser.add_argument('--left_outer_join', action='store_true')
parser.add_argument('-o', '--output')
args = parser.parse_args()
global of
of = sys.stdout
if args.output: of = open(args.output, 'w')
#read the left into memory
rightlines = []
z = 0
with open(args.gpd_right) as inf:
for line in inf:
z += 1
if z % 100 == 0:
sys.stderr.write("reading in " + str(z) + " \r")
fgpd = FuzzyGenePred(GPD(line.rstrip()),
juntol=args.junction_tolerance)
rightlines.append(fgpd)
sys.stderr.write("\n")
sys.stderr.write("finished reading in " + str(len(rightlines)) +
" gpd entries\n")
i = 0
if args.threads > 1:
p = Pool(processes=args.threads)
with open(args.gpd_left) as inf:
for line in inf:
i += 1
fgpd1 = FuzzyGenePred(GPD(line.rstrip()),
juntol=args.junction_tolerance)
if args.threads > 1:
p.apply_async(get_compatible,
args=(rightlines, fgpd1, i, args),
callback=do_output)
else:
v = get_compatible(rightlines, fgpd1, i, args)
do_output(v)
if args.threads > 1:
p.close()
p.join()
of.close()
def do_reduction(subset,args,nrfuzzykey,location):
seen = set()
for i in subset:
seen.add(i)
for j in subset[i]: seen.add(j)
singles = []
for num in nrfuzzykey:
if num not in seen:
singles.append(num)
#if len(subset.keys()) == 0 and len(compatible.keys()) == 0: return
families = get_subset_evidence(subset,nrfuzzykey,args)
gpdlines = ""
tablelines = ""
for num in singles:
families.append(nrfuzzykey[num])
# find gpds not in the graph...
for fz in families:
info = fz.get_info_string()
gpdline = fz.get_genepred_line()
#print '&&&&&&&&&&&&&&&&'
#print gpdline
#print fz.get_info_string()
#print '&&&&&&&&&&&&&&&&'
gpd = GenePredEntry(gpdline)
if not gpd.is_valid():
sys.stderr.write("WARNING: invalid genepred entry generated\n"+gpdline+"\n"+fz.get_info_string()+"\n")
gpd = sorted(fz.gpds, key=lambda x: x.get_exon_count(), reverse=True)[0] #just grab one that has all the exons
fz = FuzzyGenePred(gpd,juntol=args.junction_tolerance*2)
gpdline = fz.get_genepred_line()
if not gpd.is_valid():
sys.stderr.write("WARNING: still problem skilling\n")
continue
gpdlines += gpdline+"\n"
if args.output_original_table:
name = gpd.entry['name']
for g in fz.gpds:
tablelines+=name+"\t"+g.entry['name']+"\n"
grng = gpd.get_bed()
grng.direction = None
if not location:
location = grng
location = location.merge(grng)
locstring = ''
if location: locstring = location.get_range_string()
return [gpdlines, tablelines, locstring]
def get_nr_fuzzy(nrlocuskey, args):
global warning_count
global glock
nrfuzzykey = {}
for num in nrlocuskey:
# Create FuzzyGenePreds out of all of the GPDs
# And reduce the sets of many gpds down to just a single fuzzy gpd representing each specific gpd.
v = greedy_combine_down_fuzzies([
FuzzyGenePred(x, juntol=args.junction_tolerance * 2)
for x in nrlocuskey[num]
])
if len(v) > 1:
if args.verbose:
sys.stderr.write("WARNING expected only 1 fuzzy genepred\n")
glock.acquire()
warning_count += 1
glock.release()
nrfuzzykey[num] = v[0]
return nrfuzzykey
def do_prediction(compatible,args,nrfuzzykey,location):
#if len(compatible.keys()) == 0: return None
#all reads could be standing alone version
families = []
for num in nrfuzzykey:
families.append(nrfuzzykey[num])
nrfuzzykey[num].params['proper_set'] = False #partial overlap is enough
#get_compatible_evidence(compatible,nrfuzzykey,args)
for i in compatible:
for j in compatible[i]:
#see if its already in there
g1lines = set()
for g1 in nrfuzzykey[i].gpds: g1lines.add(g1.get_line())
repeat = False
for g2 in nrfuzzykey[j].gpds:
if g2.get_line() in g1lines:
repeat = True
break
if not repeat: continue
together = nrfuzzykey[i].concat_fuzzy_gpd(nrfuzzykey[j])
if together:
families.append(together)
# now we need to find any duplicate entries and combine them
newfam = []
beforefam = len(families)
while len(families) > 0:
fam = families.pop(0)
remaining = []
for i in range(0,len(families)):
if fam.is_equal_fuzzy(families[i]):
added = fam.add_fuzzy_gpd(families[i])
if not added:
sys.stderr.write("WARNING NOT SURE WHY NOT ADDED EQUAL\n")
fam = added
else: remaining.append(families[i])
families = remaining
newfam.append(fam)
families = newfam
afterfam = len(families)
# Replace the family with a set where we haven't used the same gpd line twice
# This may damage the fuzzy object
for i in range(0,len(families)):
gset = set()
for g in families[i].gpds:
gset.add(g.get_line())
families[i].gpds = [GenePredEntry(x) for x in gset]
# sys.stderr.write("\n\ncahnged from "+str(beforefam)+"\t"+str(afterfam)+"\n\n")
gpdlines = ""
tablelines = ""
# find gpds not in the graph...
for fz in families:
info = fz.get_info_string()
gpdline = fz.get_genepred_line()
#print '&&&&&&&&&&&&&&&&'
#print gpdline
#print fz.get_info_string()
#print '&&&&&&&&&&&&&&&&'
gpd = GenePredEntry(gpdline)
if not gpd.is_valid():
sys.stderr.write("WARNING: invalid genepred entry generated\n"+gpdline+"\n"+fz.get_info_string()+"\n")
gpd = sorted(fz.gpds, key=lambda x: x.get_exon_count(), reverse=True)[0] #just grab one that has all the exons
fz = FuzzyGenePred(gpd,juntol=args.junction_tolerance*2)
gpdline = fz.get_genepred_line()
if not gpd.is_valid():
sys.stderr.write("WARNING: still problem skilling\n")
continue
gpdlines += gpdline+"\n"
if args.output_original_table:
name = gpd.entry['name']
for g in fz.gpds:
tablelines+=name+"\t"+g.entry['name']+"\n"
grng = gpd.get_bed()
grng.direction = None
if not location:
location = grng
location = location.merge(grng)
locstring = ''
if location: locstring = location.get_range_string()
return [gpdlines, tablelines, locstring]
def do_prediction(compatible, args, nrfuzzykey, location):
#if len(compatible.keys()) == 0: return None
#all reads could be standing alone version
families = []
for num in nrfuzzykey:
families.append(nrfuzzykey[num])
nrfuzzykey[num].params[
'proper_set'] = False #partial overlap is enough
#get_compatible_evidence(compatible,nrfuzzykey,args)
for i in compatible:
for j in compatible[i]:
#see if its already in there
g1lines = set()
for g1 in nrfuzzykey[i].gpds:
g1lines.add(g1.get_line())
repeat = False
for g2 in nrfuzzykey[j].gpds:
if g2.get_line() in g1lines:
repeat = True
break
if not repeat: continue
together = nrfuzzykey[i].concat_fuzzy_gpd(nrfuzzykey[j])
if together:
families.append(together)
# now we need to find any duplicate entries and combine them
newfam = []
beforefam = len(families)
while len(families) > 0:
fam = families.pop(0)
remaining = []
for i in range(0, len(families)):
if fam.is_equal_fuzzy(families[i]):
added = fam.add_fuzzy_gpd(families[i])
if not added:
sys.stderr.write("WARNING NOT SURE WHY NOT ADDED EQUAL\n")
fam = added
else:
remaining.append(families[i])
families = remaining
newfam.append(fam)
families = newfam
afterfam = len(families)
# Replace the family with a set where we haven't used the same gpd line twice
# This may damage the fuzzy object
for i in range(0, len(families)):
gset = set()
for g in families[i].gpds:
gset.add(g.get_line())
families[i].gpds = [GenePredEntry(x) for x in gset]
# sys.stderr.write("\n\ncahnged from "+str(beforefam)+"\t"+str(afterfam)+"\n\n")
gpdlines = ""
tablelines = ""
# find gpds not in the graph...
for fz in families:
info = fz.get_info_string()
gpdline = fz.get_genepred_line()
#print '&&&&&&&&&&&&&&&&'
#print gpdline
#print fz.get_info_string()
#print '&&&&&&&&&&&&&&&&'
gpd = GenePredEntry(gpdline)
if not gpd.is_valid():
sys.stderr.write("WARNING: invalid genepred entry generated\n" +
gpdline + "\n" + fz.get_info_string() + "\n")
gpd = sorted(
fz.gpds, key=lambda x: x.get_exon_count(),
reverse=True)[0] #just grab one that has all the exons
fz = FuzzyGenePred(gpd, juntol=args.junction_tolerance * 2)
gpdline = fz.get_genepred_line()
if not gpd.is_valid():
sys.stderr.write("WARNING: still problem skilling\n")
continue
gpdlines += gpdline + "\n"
if args.output_original_table:
name = gpd.entry['name']
for g in fz.gpds:
tablelines += name + "\t" + g.entry['name'] + "\n"
grng = gpd.get_bed()
grng.direction = None
if not location:
location = grng
location = location.merge(grng)
locstring = ''
if location: locstring = location.get_range_string()
return [gpdlines, tablelines, locstring]
