def make_rectangles_from_genome(options):
k = options.k
ingraph = Graph()
_, genome = fastaparser.read_fasta(options.genome).next()
ingraph.make_graph(genome, int(k))
edges_before_loop_DG = ingraph.find_loops(10, 1000)
ingraph.save(os.path.join(options.out_dir,"graph"))
rs = RectangleSet(ingraph, int(options.d))
rs.filter_without_prd()
f_left = open(os.path.join(options.out_dir, "paired_genom_contigs_1.fasta"),"w") # TODO: what is it?
f_right = open(os.path.join(options.out_dir, "paired_genom_contigs_2.fasta"),"w") # TODO: what is it?
contigs_id = 0
for key, rect in rs.rectangles.items():
for key, diag in rect.diagonals.items():
e1 = rect.e1.seq
e2 = rect.e2.seq
f_left.write(">" + str(contigs_id) + "/1\n")
f_left.write(e1[diag.offseta:diag.offsetc])
f_left.write("\n")
f_right.write(">"+str(contigs_id) + "/2\n")
f_right.write(e2[diag.offsetb:diag.offsetd])
f_right.write("\n")
contigs_id += 1
bgraph = rs.bgraph_from_genome()
bgraph.condense()
outgraph = bgraph.project(options.out_dir, False)
outgraph.fasta(open(os.path.join(options.out_dir, 'rectangles.fasta'), 'w'))
def resolve(input_path, output_path, test_utils, genome, is_sc):
if not os.path.exists(output_path):
os.mkdir(output_path)
grp_filename = os.path.join(input_path, 'late_pair_info_counted.grp')
sqn_filename = os.path.join(input_path, 'late_pair_info_counted.sqn')
cvr_filename = os.path.join(input_path, 'late_pair_info_counted.cvr')
first_prd_filename = os.path.join(input_path, 'late_pair_info_counted.prd')
prd_filename = os.path.join(input_path, 'late_pair_info_counted.prd' if experimental.filter != experimental.Filter.spades else 'distance_filling_cl.prd')
pst_filename = os.path.join(input_path, 'distance_estimation.pst') if experimental.filter == experimental.Filter.pathsets else None
inf_filename = os.path.join(input_path, 'late_pair_info_counted_est_params.info')
log_filename = os.path.join(output_path, 'rectangles.log')
config = saveparser.config(inf_filename)
d = config.median - config.RL
makelogger(log_filename)
logger = logging.getLogger('rectangles')
logger.info("Rectangle Resolving %s..." % input_path)
logger.info("d = %d..." % d)
#################################
# PARSE INITIAL BE BRUIJN GRAPH #
#################################
ingraph = Graph()
ingraph.load(grp_filename, sqn_filename, cvr_filename)
ingraph.check()
edges_before_loop_DG = ingraph.find_loops(10, 1000)
maxN50 = 0
maxgraph = None
maxbgraph = None
maxthreshold = 0
rs = RectangleSet(ingraph, d, test_utils, prd_filename, first_prd_filename, config)
if experimental.filter == experimental.Filter.pathsets:
rs.pathsets(pst_filename)
else:
rs.filter(prd_filename, config)
logger.info(" RectangleSet built.")
if experimental.filter == experimental.Filter.spades:
thresholds = [0.0] # everything supported by paired info
elif experimental.filter == experimental.Filter.pathsets:
thresholds = [-1] # everything from pathsets file
else:
thresholds = rs.percentiles()
logger.info(" Checking thresholds %s..." % thresholds)
for threshold in set(thresholds):
logger.info(" Checking threshold %f..." % threshold)
bgraph = rs.bgraph(threshold)
if not bgraph.diagonals:
continue
bgraph.build_missing_rectangles(ingraph.K, rs)
bgraph.condense()
outgraph = bgraph.project(output_path, is_sc)
maxgraph = outgraph
maxbgraph = bgraph
maxthreshold = threshold
maxgraph.fasta(open(os.path.join(output_path, 'begin_rectangles.fasta'), 'w'))
#maxgraph.save(os.path.join(output_path, 'rectangles'))
maxbgraph.save(output_path, ingraph.K)
maxbgraph.check_tips(ingraph.K)
outgraph = maxbgraph.project(output_path, is_sc)
outgraph.fasta(open(os.path.join(output_path, 'delete_tips.fasta'), 'w'))
edges_before_loop = maxbgraph.delete_loops(ingraph.K, 1000, 10)
maxbgraph.condense()
outgraph = maxbgraph.project(output_path, is_sc)
outgraph.fasta(open(os.path.join(output_path,"delete_tips_delete_loops_1000.fasta"),"w"))
to_del = set()
for eid in edges_before_loop_DG:
if eid in edges_before_loop:
to_del.add(eid)
print "to_del", len(to_del)
for eid in to_del:
del edges_before_loop_DG[eid]
maxbgraph.delete_missing_loops(edges_before_loop_DG, ingraph.K, 1000, 10)
maxbgraph.condense()
outgraph = maxbgraph.project(output_path, is_sc)
outgraph.fasta(open(os.path.join(output_path, 'delete_tips_delete_all_loops_1000.fasta'), 'w'))
edges_before_loop_DG = ingraph.find_loops(4, 10000)
edges_before_loop_DG = edges_before_loop_DG or maxbgraph.delete_missing_loops(ingraph.K, 10000,10)
to_del = set()
for eid in edges_before_loop_DG:
if eid in edges_before_loop:
to_del.add(eid)
print "to_del", len(to_del)
for eid in to_del:
del edges_before_loop_DG[eid]
maxbgraph.delete_missing_loops(edges_before_loop_DG, ingraph.K, 10000, 10)
maxbgraph.condense()
outgraph = maxbgraph.project(output_path, is_sc)
outgraph.fasta(open(os.path.join(output_path, "after_deleting_big_loops.fasta"), "w"))
additional_paired_info = dict()
should_connect = maxbgraph.edges_expand(5000)
should_connect_by_first_pair_info = maxbgraph.use_scaffold_paired_info(2 * maxbgraph.d, rs.additional_prd)
for (e1id, e2id) in should_connect_by_first_pair_info:
if e1id not in additional_paired_info and maxbgraph.es[e1id].conj.eid not in additional_paired_info and e2id not in additional_paired_info:
additional_paired_info[e1id] = [maxbgraph.es[e1id], maxbgraph.es[e2id]]
additional_paired_info[maxbgraph.es[e1id].conj.eid] = [maxbgraph.es[e2id].conj, maxbgraph.es[e1id].conj]
outgraph.fasta_for_long_contigs(ingraph.K, maxbgraph.d, is_sc, open(os.path.join(output_path,"rectangles_extend.fasta"),"w"), should_connect, additional_paired_info)
outgraph.fasta_for_long_contigs(ingraph.K, maxbgraph.d, is_sc, open(os.path.join(output_path,"rectangles_extend_before_scaffold.fasta"),"w"), should_connect, dict())
maxbgraph.print_about_edges([20586, 23014, 23806, 19630,23350], ingraph.K)
outgraph.save(os.path.join(output_path,"last_graph"))
if genome:
check_diags.check(genome, maxbgraph, maxgraph.K, open(os.path.join(output_path, "check_log.txt"), "w"), test_utils)
logger.info("Best Threshold = %d" % maxthreshold)
logger.info("Best N50 = %d" % maxN50)
def resolve(input_path, output_path, test_utils, genome, is_sc, is_careful):
grp_filename = os.path.join(input_path, 'late_pair_info_counted.grp')
sqn_filename = os.path.join(input_path, 'late_pair_info_counted.sqn')
cvr_filename = os.path.join(input_path, 'late_pair_info_counted.cvr')
first_prd_filename = os.path.join(input_path, 'late_pair_info_counted_0.prd')
if experimental.filter != experimental.Filter.spades:
prd_filename = first_prd_filename
else:
prd_filename = os.path.join(input_path, 'distance_estimation_0_cl.prd')
if experimental.filter == experimental.Filter.pathsets:
pst_filename = os.path.join(input_path, 'distance_estimation.pst')
inf_filename = os.path.join(input_path, 'late_pair_info_counted_est_params.info')
log_filename = os.path.join(output_path, 'rectangles.log')
config = saveparser.config(inf_filename)
d = config['median'] - config['RL']
if d <= 0:
print "Read length", config ['RL'], "is smaller than insert size", config['median'],", can't do anything"
return
makelogger(log_filename)
logger = logging.getLogger('rectangles')
logger.info("Rectangle Resolving %s..." % input_path)
logger.info("d = %d..." % d)
#################################
# PARSE INITIAL BE BRUIJN GRAPH #
#################################
ingraph = Graph()
ingraph.load(grp_filename, sqn_filename, cvr_filename)
ingraph.check()
logger.info("init rectangles set")
rs = RectangleSet(ingraph, d, test_utils, prd_filename, first_prd_filename, config)
if experimental.filter == experimental.Filter.pathsets:
rs.pathsets(pst_filename)
else:
logger.info("begin filter")
rs.filter(prd_filename, config)
logger.info(" RectangleSet built.")
threshold = 0.0
logger.info(" Checking threshold %f..." % threshold)
maxbgraph = rs.bgraph(threshold)
save_fasta(maxbgraph, output_path, is_sc, 'begin_rectangles.fasta', is_careful)
logger.info("outputed begin rectangles")
maxbgraph.check_tips(ingraph.K)
save_fasta(maxbgraph, output_path, is_sc, 'delete_tips.fasta', is_careful)
logger.info("outputed delete tips")
edges_before_loop = maxbgraph.delete_loops(ingraph.K, 1000, 10)
save_fasta(maxbgraph, output_path, is_sc, "delete_tips_delete_loops_1000.fasta", is_careful)
logger.info("outputed delete loops")
edges_before_loop_DG = ingraph.find_loops(10, 1000, rs)
logger.info("find DG 1000 loops")
to_del = set(edges_before_loop_DG.keys()) & edges_before_loop
for eid in to_del:
del edges_before_loop_DG[eid]
maxbgraph.delete_missing_loops(edges_before_loop_DG, ingraph.K, 1000, 10)
logger.info("delete missing loops")
save_fasta(maxbgraph, output_path, is_sc, 'delete_tips_delete_all_loops_1000.fasta', is_careful)
edges_before_loop_DG = ingraph.find_loops(4, 10000, rs)
to_del = set(edges_before_loop_DG.keys()) & edges_before_loop
for eid in to_del:
del edges_before_loop_DG[eid]
maxbgraph.delete_missing_loops(edges_before_loop_DG, ingraph.K, 10000, 10)
outgraph = save_fasta(maxbgraph, output_path, is_sc, "after_deleting_big_loops.fasta", is_careful)
additional_paired_info = dict()
should_connect = maxbgraph.edges_expand(5000)
should_connect_by_first_pair_info = maxbgraph.use_scaffold_paired_info(2 * maxbgraph.d, rs.prd_for_scaffold)
for (e1id, e2id) in should_connect_by_first_pair_info:
if e1id not in additional_paired_info and maxbgraph.es[
e1id].conj.eid not in additional_paired_info and e2id not in additional_paired_info:
additional_paired_info[e1id] = [maxbgraph.es[e1id], maxbgraph.es[e2id]]
additional_paired_info[maxbgraph.es[e1id].conj.eid] = [maxbgraph.es[e2id].conj, maxbgraph.es[e1id].conj]
outgraph.fasta_for_long_contigs(ingraph.K, maxbgraph.d, is_sc, is_careful,
open(os.path.join(output_path, "rectangles_extend.fasta"), "w"), should_connect, additional_paired_info)
outgraph.fasta_for_long_contigs(ingraph.K, maxbgraph.d, is_sc, is_careful,
open(os.path.join(output_path, "rectangles_extend_before_scaffold.fasta"), "w"), should_connect, dict())
outgraph.save(os.path.join(output_path, "last_graph"))
if genome:
check_diags.check(genome, maxbgraph, maxgraph.K, open(os.path.join(output_path, "check_log.txt"), "w"),
test_utils)
def resolve(input_path, output_path, test_utils, genome, is_sc, is_careful):
grp_filename = os.path.join(input_path, 'late_pair_info_counted.grp')
sqn_filename = os.path.join(input_path, 'late_pair_info_counted.sqn')
cvr_filename = os.path.join(input_path, 'late_pair_info_counted.cvr')
first_prd_filename = os.path.join(input_path,
'late_pair_info_counted_0.prd')
if experimental.filter != experimental.Filter.spades:
prd_filename = first_prd_filename
else:
prd_filename = os.path.join(input_path, 'distance_estimation_0_cl.prd')
if experimental.filter == experimental.Filter.pathsets:
pst_filename = os.path.join(input_path, 'distance_estimation.pst')
inf_filename = os.path.join(input_path,
'late_pair_info_counted_est_params.info')
log_filename = os.path.join(output_path, 'rectangles.log')
config = saveparser.config(inf_filename)
d = config['median'] - config['RL']
if d <= 0:
print "Read length", config[
'RL'], "is smaller than insert size", config[
'median'], ", can't do anything"
return
makelogger(log_filename)
logger = logging.getLogger('rectangles')
logger.info("Rectangle Resolving %s..." % input_path)
logger.info("d = %d..." % d)
#################################
# PARSE INITIAL BE BRUIJN GRAPH #
#################################
ingraph = Graph()
ingraph.load(grp_filename, sqn_filename, cvr_filename)
ingraph.check()
logger.info("init rectangles set")
rs = RectangleSet(ingraph, d, test_utils, prd_filename, first_prd_filename,
config)
if experimental.filter == experimental.Filter.pathsets:
rs.pathsets(pst_filename)
else:
logger.info("begin filter")
rs.filter(prd_filename, config)
logger.info(" RectangleSet built.")
threshold = 0.0
logger.info(" Checking threshold %f..." % threshold)
maxbgraph = rs.bgraph(threshold)
save_fasta(maxbgraph, output_path, is_sc, 'begin_rectangles.fasta',
is_careful)
logger.info("outputed begin rectangles")
maxbgraph.check_tips(ingraph.K)
save_fasta(maxbgraph, output_path, is_sc, 'delete_tips.fasta', is_careful)
logger.info("outputed delete tips")
edges_before_loop = maxbgraph.delete_loops(ingraph.K, 1000, 10)
save_fasta(maxbgraph, output_path, is_sc,
"delete_tips_delete_loops_1000.fasta", is_careful)
logger.info("outputed delete loops")
edges_before_loop_DG = ingraph.find_loops(10, 1000, rs)
logger.info("find DG 1000 loops")
to_del = set(edges_before_loop_DG.keys()) & edges_before_loop
for eid in to_del:
del edges_before_loop_DG[eid]
maxbgraph.delete_missing_loops(edges_before_loop_DG, ingraph.K, 1000, 10)
logger.info("delete missing loops")
save_fasta(maxbgraph, output_path, is_sc,
'delete_tips_delete_all_loops_1000.fasta', is_careful)
edges_before_loop_DG = ingraph.find_loops(4, 10000, rs)
to_del = set(edges_before_loop_DG.keys()) & edges_before_loop
for eid in to_del:
del edges_before_loop_DG[eid]
maxbgraph.delete_missing_loops(edges_before_loop_DG, ingraph.K, 10000, 10)
outgraph = save_fasta(maxbgraph, output_path, is_sc,
"after_deleting_big_loops.fasta", is_careful)
additional_paired_info = dict()
should_connect = maxbgraph.edges_expand(5000)
should_connect_by_first_pair_info = maxbgraph.use_scaffold_paired_info(
2 * maxbgraph.d, rs.prd_for_scaffold)
for (e1id, e2id) in should_connect_by_first_pair_info:
if e1id not in additional_paired_info and maxbgraph.es[
e1id].conj.eid not in additional_paired_info and e2id not in additional_paired_info:
additional_paired_info[e1id] = [
maxbgraph.es[e1id], maxbgraph.es[e2id]
]
additional_paired_info[maxbgraph.es[e1id].conj.eid] = [
maxbgraph.es[e2id].conj, maxbgraph.es[e1id].conj
]
outgraph.fasta_for_long_contigs(
ingraph.K, maxbgraph.d, is_sc, is_careful,
open(os.path.join(output_path, "rectangles_extend.fasta"), "w"),
should_connect, additional_paired_info)
outgraph.fasta_for_long_contigs(
ingraph.K, maxbgraph.d, is_sc, is_careful,
open(
os.path.join(output_path,
"rectangles_extend_before_scaffold.fasta"), "w"),
should_connect, dict())
outgraph.save(os.path.join(output_path, "last_graph"))
if genome:
check_diags.check(
genome, maxbgraph, maxgraph.K,
open(os.path.join(output_path, "check_log.txt"), "w"), test_utils)