def run(blocks, print_table=False):
species = sorted(list(get_set_entries(blocks)))
threaded_genomes = {}
for sp in species:
entries = utils.get_specie_entries(blocks, sp)
threaded_genomes[sp] = utils.thread_specie_genome(entries)
index = create_indices(species, threaded_genomes)
blocks_ids = get_blocks_ids(blocks)
blocks_num = 0
features = {}
if not print_table:
features = build_features_index(blocks)
if print_table:
header = '\t'.join(['breakpoint block']+species)
print header
for b in blocks_ids:
blocks_num += 1
block_inds = filter(lambda x: x[0] == b, index)
if not print_table:
print 'block_id:', b
for ind in block_inds:
print index[ind]
dupls_num, entries_num, neighbours, species_status = build_neighbours(
block_inds, index)
process_block_neighborhood(neighbours, block_inds, species_status,
print_table, features, index)
if not print_table:
print
if print_table:
l = str(b)
if not species_status.keys():
# in case breakpoint is caused by assembly incompleteness
continue
for e in species:
if e not in species_status.keys():
l += '\t' + 'not-in-block'
else:
l += '\t' + species_status[e]
print l
if not print_table:
print 'STAT number of blocks:', blocks_num
print 'STAT number of entries:', entries_num
print 'STAT number of dupls (among entries):', dupls_num
print 'STAT rate of duplications:', float(dupls_num)/entries_num
f_blocks = utils.filter_bed(blocks, args.filter)
elif args.classify_breakpoints:
if args.print_table:
breakpoints_classifier.run(blocks, True)
else:
breakpoints_classifier.run(blocks, False)
#for k in breakpoints.keys():
# k[0].print_out()
# k[1].print_out()
# print breakpoints[k]
elif args.report_duplications:
#TODO: this should be updated because its a rude estimation
#some blocks should be counted as as one duplication
for sp in args.species:
entries = utils.get_specie_entries(blocks, sp)
entries = utils.thread_specie_genome(entries)
for c in entries:
count_dup = 0
dup = rearrangements_type.check_duplications(c, blocks, sp)
for e in dup:
this_prev = e[0]
this_dup = e[1]
if not this_prev in map(lambda x: x[1], dup):
count_dup += 1
print 'duplication:',
this_dup.print_out()
if count_dup:
print 'overall duplications', count_dup
elif args.report_translocations or args.report_transpositions or args.report_reversals\
or args.report_duplications:
def run(blocks, print_table=False):
species = sorted(list(get_set_entries(blocks)))
threaded_genomes = {}
for sp in species:
entries = utils.get_specie_entries(blocks, sp)
threaded_genomes[sp] = utils.thread_specie_genome(entries)
index = create_indices(species, threaded_genomes)
blocks_ids = get_blocks_ids(blocks)
dupls_num = 0
blocks_num = 0
entries_num = 0
if print_table:
header = '\t'.join(['breakpoint block']+species)
print header
for b in blocks_ids:
blocks_num += 1
block_inds = filter(lambda x: x[0] == b, index)
neighbours = []
species_status = {}
if not print_table:
for ind in block_inds:
print index[ind]
#just linearize two-dimensional data
#[(prev1, next1), (prev2, next2)] -> [prev1, next1, prev2, next2]
for ind in block_inds:
entries_num += len(index[ind])
if len(index[ind]) > 1:
dupls_num += len(index[ind])
index[ind] = [(-3,-3)]
species_status[ind[1]] = 'DUP'
#TODO solve duplications!!
#beware of dupl!
neighb = index[ind][0]
neighbours.append(neighb[0])
neighbours.append(neighb[1])
#sort by popularity in descending order
#and leave only non-ending
c = Counter(neighbours).most_common()
c = filter(lambda x:x[0] != -2 and x[0] != -1 and x[0] != -3, c)
#print c
#if len is less or equal than two (most popular from left and from right),
#then breakpoint is likely to be caused by assembly incompleteness
if len(c) > 2:
c2 = Counter(dict(c)).most_common()
if c[2][1] == c[1][1]:
if not print_table:
print 'cant distinguish two most common!'
print
for ind in block_inds:
if not ind[1] in species_status.keys():
#could not resolve breakpoint
species_status[ind[1]] = 'NA'
continue
first_common = c[0][0]
second_common = c[1][0]
nodef = set([-1,-2])
allowable = set([-1,-2,first_common,second_common])
br = False
for ind in block_inds:
#beware of dupl!
prev,next = index[ind][0]
if prev in nodef and next in nodef:
#the whole block is a full scaffold in the specie
species_status[ind[1]] = 'END'
# print 'possible breakpoint', ind[1], prev, '-', ind[0], '-', next
continue
if prev in allowable and next in allowable:
species_status[ind[1]] = '-'
continue
if not prev in allowable:
species_status[ind[1]] = 'BR'
if not print_table:
print 'breakpoint', ind[1], prev, '-', ind[0]
br = True
if not next in allowable:
species_status[ind[1]] = 'BR'
if not print_table:
print 'breakpoint', ind[1], ind[0], '-', next
br = True
#if br:
# print
if not print_table:
print
if print_table:
l = str(b)
if not species_status.keys():
#in case breakpoint is caused by assembly incompleteness
continue
for e in species:
if not e in species_status.keys():
l += '\t'+'not in block'
else:
l+='\t'+species_status[e]
print l
if not print_table:
print 'STAT Also:'
print 'STAT number of blocks:', blocks_num
print 'STAT number of entries:', entries_num
print 'STAT number of dupls (among entries):', dupls_num
print 'STAT rate of duplications:', float(dupls_num)/entries_num
f_blocks = utils.filter_bed(blocks, args.filter)
elif args.classify_breakpoints:
if args.print_table:
breakpoints_classifier.run(blocks, True)
else:
breakpoints_classifier.run(blocks, False)
#for k in breakpoints.keys():
# k[0].print_out()
# k[1].print_out()
# print breakpoints[k]
elif args.report_duplications:
#TODO: this should be updated because its a rude estimation
#some blocks should be counted as as one duplication
for sp in args.species:
entries = utils.get_specie_entries(blocks, sp)
entries = utils.thread_specie_genome(entries)
for c in entries:
count_dup = 0
dup = rearrangements_type.check_duplications(c, blocks, sp)
for e in dup:
this_prev = e[0]
this_dup = e[1]
if not this_prev in map(lambda x:x[1], dup):
count_dup += 1
print 'duplication:',
this_dup.print_out()
if count_dup:
print 'overall duplications', count_dup
elif args.report_translocations or args.report_transpositions or args.report_reversals\
or args.report_duplications: