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Reverse monomers as initial monomer #1

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Reverse monomers as initial monomer #1

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86 changes: 48 additions & 38 deletions src/monomer_inference.py
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Original file line number Diff line number Diff line change
Expand Up @@ -139,9 +139,11 @@ def set_blocks_seq(sequences, blocks):
#print("Block read name:", blocks[i].read_name)
#print(records[blocks[i].read_name])
#print(records[blocks[i].read_name][2:6])
blocks[i].seq = records[blocks[i].read_name][blocks[i].lft:blocks[i].rgh + 1]
#print("Set seq: " + blocks[i].seq)

if blocks[i].lft < blocks[i].rgh:
blocks[i].seq = records[blocks[i].read_name][blocks[i].lft:blocks[i].rgh + 1]
else:
blocks[i].seq = records[blocks[i].read_name][blocks[i].rgh:blocks[i].lft + 1]
blocks[i].seq.seq = Seq(rc(str(blocks[i].seq.seq)))

def get_distance(a, b):
result = edlib.align(a, b, mode="NW", task="locations")
Expand Down Expand Up @@ -531,34 +533,34 @@ def init_monomers(monomers_path):
return monomers_list


need_reverse_monomers = -1


def reverse_monomer(args):
global need_reverse_monomers
if need_reverse_monomers != -1:
return need_reverse_monomers
else:
res_tsv = os.path.join(args.outdir, "iter_0", "final_decomposition.tsv")
cnt_need_rev = 0
cnt_dont_need_rev = 0
with open(res_tsv, "r") as f:
csv_reader = csv.reader(f, delimiter='\t')
for row in csv_reader:
if row[2] == "start":
continue
identity = float(row[4])

if identity >= 100 - args.maxDiv:
if row[1][-1] == "'":
cnt_need_rev += 1
else:
cnt_dont_need_rev += 1
if cnt_need_rev > cnt_dont_need_rev:
need_reverse_monomers = 1
else:
need_reverse_monomers = 0
return need_reverse_monomers
#need_reverse_monomers = -1


#def reverse_monomer(args):
# global need_reverse_monomers
# if need_reverse_monomers != -1:
# return need_reverse_monomers
# else:
# res_tsv = os.path.join(args.outdir, "iter_0", "final_decomposition.tsv")
# cnt_need_rev = 0
# cnt_dont_need_rev = 0
# with open(res_tsv, "r") as f:
# csv_reader = csv.reader(f, delimiter='\t')
# for row in csv_reader:
# if row[2] == "start":
# continue
# identity = float(row[4])
#
# if identity >= 100 - args.maxDiv:
# if row[1][-1] == "'":
# cnt_need_rev += 1
# else:
# cnt_dont_need_rev += 1
# if cnt_need_rev > cnt_dont_need_rev:
# need_reverse_monomers = 1
# else:
# need_reverse_monomers = 0
# return need_reverse_monomers


def rc(seq):
Expand Down Expand Up @@ -615,8 +617,8 @@ def update_monomer(args, monomer_record, monomer_resolved_block, iter_outdir, pr
cluster_seqs_path = os.path.join(iter_outdir, monomer_record.id.split('/')[0] + "_seqs.fa")
save_seqs(monomer_resolved_block, cluster_seqs_path)
new_monomer = get_consensus_seq(cluster_seqs_path, monomer_resolved_block, args.threads)
if reverse_monomer(args):
new_monomer = rc(new_monomer)
#if reverse_monomer(args):
# new_monomer = rc(new_monomer)
monomer_record.seq = Seq(new_monomer)
updated_monomers.append(monomer_record.id)

Expand Down Expand Up @@ -752,15 +754,23 @@ def get_unresolved_blocks(res_tsv, monomers_list, args):
identity = float(row[4])
if identity >= 100 - args.resDiv:
resolved_cnt += 1
bgc = int(row[2])
edc = int(row[3])
if row[1][-1] == "'":
row[1] = row[1][:-1]
monomer_resolved[row[1]].append(MonomericBlock(row[0], int(row[2]), int(row[3])))
bgc, edc = edc, bgc
monomer_resolved[row[1]].append(MonomericBlock(row[0], bgc, edc))

if identity <= 100 - args.maxDiv:
non_monomeric_cnt += 1

if (identity > 100 - args.maxDiv) and (identity < 100 - args.resDiv):
unresolved_blocks.append(MonomericBlock(row[0], int(row[2]), int(row[3])))
bgc = int(row[2])
edc = int(row[3])
if row[1][-1] == "'":
row[1] = row[1][:-1]
bgc, edc = edc, bgc
unresolved_blocks.append(MonomericBlock(row[0], bgc, edc))

return unresolved_blocks, monomer_resolved, non_monomeric_cnt, resolved_cnt

Expand Down Expand Up @@ -854,7 +864,7 @@ def main():
f.write(u_mn + "\n")
extra_options = ["--new-monomers", upmn_path]
# run string decomposer
sys_call(["python3", sd_script_path, args.sequences, local_monmers_path, "-t", str(args.threads), "--fast"])
sys_call(["python3", sd_script_path, args.sequences, local_monmers_path, "-t", str(args.threads), "--fast", "--ed_thr", "20"])
log.log("String decomposer is complete. Results save in: " + iter_outdir)

# parse output csv file
Expand Down Expand Up @@ -891,8 +901,8 @@ def main():
new_monomer = get_consensus_seq(cluster_seqs_path, max_cluster[i], args.threads)
radius = get_radius(new_monomer, max_cluster[i])

if reverse_monomer(args):
new_monomer = rc(new_monomer)
#if reverse_monomer(args):
# new_monomer = rc(new_monomer)

dist_to_monomers = get_dist_to_exists_monomers(monomers_list, new_monomer)
log.log("Min Distance to exsisting monomers: " + str(dist_to_monomers))
Expand Down