def fix_contigs(k):
perfect_contig_num = 0
for contig_id in range(len(contig_find_trans_list)):
all_ok = 1
# 如前文所言，没有找错的
n_of_kmer_in_curr_contig = contig_list[contig_id].n_of_kmer
for each_trans_info in contig_find_trans_list[contig_id]:
if each_trans_info.start_in_tran != 0 or each_trans_info.stop_in_tran != n_of_kmer_in_curr_contig:
all_ok = 0
# 说明这里有找错的
if all_ok:
perfect_contig_num = perfect_contig_num + 1
else:
tmp_list = []
for each_trans_info in contig_find_trans_list[contig_id]:
tmp_list.append(each_trans_info.start_in_tran)
tmp_list.append(each_trans_info.stop_in_tran)
break_points = sorted(list(set(tmp_list)))
old_contig_seq = contig_list[contig_id].seq
old_trans_info = contig_find_trans_list[contig_id]
new_contig = Contig()
for j in range(len(break_points) - 1):
new_contig.seq = old_contig_seq[
break_points[j]:break_points[j + 1] - break_points[j] + k -
1]
new_contig.n_of_kmer = break_points[j + 1] - break_points[j]
if j == 0:
new_contig.id = contig_id
contig_list[contig_id] = new_contig
else:
new_contig.id = len(contig_list)
contig_list.append(new_contig)
ecs_list.append(-1)
for m in range(len(new_contig.seq) - k + 1):
curr_kmer_in_contig = new_contig.seq[m:m + k]
curr_rep = kmer_rep(curr_kmer_in_contig)
if curr_rep in kmer_str_dict:
kmer_str_dict[curr_rep].contig_id = new_contig.id
kmer_str_dict[curr_rep].pos_in_contig = m
kmer_str_dict[
curr_rep].n_of_kmer_in_contig = new_contig.n_of_kmer
else:
program_stop("ecs.py-4")
new_trans_info_list = []
for each_trans_info in old_trans_info:
if not (each_trans_info.start_in_tran >=
break_points[j + 1] or
each_trans_info.stop_in_tran <= break_points[j]):
new_trans_info = ContigFindTrans()
new_trans_info.sense_in_tran = each_trans_info.sense_in_tran
new_trans_info.tran_id = each_trans_info.tran_id
new_trans_info.start_in_tran = 0
new_trans_info.stop_in_tran = new_contig.n_of_kmer
new_trans_info_list.append(new_trans_info)
if j == 0:
contig_find_trans_list[contig_id] = new_trans_info_list
else:
contig_find_trans_list.append(new_trans_info_list)
def write_em_tsv(file_name, alpha_list, eff_lens):
tran_name = transcript_info.tran_name
tran_len = transcript_info.tran_len
try:
fp = open(file_name, 'w')
except IOError:
print("cannot open", file_name)
program_stop("em.py")
fp.write("tran_name\ttran_len\teff_len\tcounts" + "\n")
for ec in range(len(alpha_list)):
fp.write(tran_name[ec] + "\t" + str(tran_len[ec]) + "\t" +
str(round(eff_lens[ec], 4)) + "\t" +
str(round(alpha_list[ec], 8)) + "\n")
fp.close()
def read_tran_files(file_name):
seqs = []
try:
if ".gz" in file_name:
fp = gzip.open(file_name, 'rt')
else:
fp = open(file_name, 'r')
except IOError:
print(file_name, "is not exist!")
program_stop("read_tran.py")
for seq_record in SeqIO.parse(fp, "fasta"):
transcript_info.tran_name.append(seq_record.id)
transcript_info.tran_len.append(len(seq_record.seq))
seq = replace_base(seq_record.seq)
seq = check_poly_a_tail(seq)
seqs.append(seq)
transcript_info.tran_num = len(transcript_info.tran_name)
fp.close()
return seqs
def start(args):
if not os.path.exists(args.index_path):
print("the index_file is not exist.please check.")
program_stop("quant.py")
else:
begin = datetime.datetime.now()
load_k = load_idx(args.index_path)
end = datetime.datetime.now()
print("load_idx:", end - begin)
if args.kmer_len != load_k:
print("the k value is inconsistent.")
program_stop("quant.py")
def_args.k = args.kmer_len
def_args.index = args.index_path
if args.single_mode:
def_args.len_frag = args.fragment_len
def_args.sd = args.sd_len
def_args.fq_file_single = args.fa_or_fq_file
if not os.path.exists(def_args.fq_file_single):
print("fq_or_fa_files is required.please check.")
program_stop("quant.py")
else:
def_args.fq_file_1 = args.fa_or_fq_files_1
def_args.fq_file_2 = args.fa_or_fq_files_2
if not (os.path.exists(def_args.fq_file_1)
or os.path.exists(def_args.fq_file_2)):
print("fq_or_fa_files is required.please check.")
program_stop("quant.py")
output_path_list = os.path.split(args.output_path)
if len(output_path_list[0]) == 0:
output_path = os.path.join(os.getcwd(), output_path_list[1])
else:
output_path = args.output_path
if not os.path.exists(output_path):
os.makedirs(output_path)
def_args.output = output_path
def_args.threads = args.threads
def_args.single_mode = args.single_mode
read_fq_fa_files(def_args)
def start(args):
if args.kmer_len % 2 == 0:
print("k value must be odd.")
program_stop("index.py")
if args.input_fna_path == "null":
print("the input_fna_path is required.")
program_stop("index.py")
else:
if not os.path.isfile(args.input_fna_path):
print("the input_fna_path is wrong.please check.")
program_stop("index.py")
index_out_dir = os.path.split(args.index_path)
if len(index_out_dir[0]) == 0:
index_path = os.path.join(os.getcwd(), index_out_dir[1])
else:
if not os.path.exists(index_out_dir[0]):
print("the index_out_DIR is not exist.please check.")
program_stop("index.py")
else:
index_path = args.index_path
def_args.k = args.kmer_len
def_args.index = index_path
def_args.fna_file = args.input_fna_path
begin = datetime.datetime.now()
seqs = read_tran_files(def_args.fna_file)
end = datetime.datetime.now()
print("read_tran:", end - begin)
begin = datetime.datetime.now()
build_dbg(seqs, def_args.k)
end = datetime.datetime.now()
print("build_contig:", end - begin)
begin = datetime.datetime.now()
build_ecs(seqs, def_args.k)
end = datetime.datetime.now()
print("build_ecs:", end - begin)
begin = datetime.datetime.now()
write_idx(def_args.index, def_args.k)
end = datetime.datetime.now()
print("write_idx:", end - begin)
def read_fq_fa_files(args):
global k, f_len_goal
k = args.k
pool = Pool(processes=args.threads)
begin = datetime.datetime.now()
if args.single_mode:
file_name = args.fq_file_single
file_suffix = os.path.splitext(file_name)[1]
try:
if ".gz" == file_suffix:
fp = gzip.open(file_name, 'rt')
file_suffix_suffix = os.path.splitext(os.path.splitext(file_name)[0])[1]
else:
fp = open(file_name, 'r')
file_suffix_suffix = file_suffix
except IOError:
print(file_name, "is not exist!")
program_stop("process_read.py")
if ".fasta" == file_suffix_suffix or ".fa" == file_suffix_suffix:
res = pool.map(do_something_with_record, to_fasta(fp))
pool.close()
pool.join()
elif ".fastq" == file_suffix_suffix or ".fq" == file_suffix_suffix:
res = pool.map(do_something_with_record, convert_to_fasta(fp))
pool.close()
pool.join()
else:
print("cannot find .fa(.fasta) or .fq(.fastq).please check.")
program_stop("process_read.py")
print(len(res))
print("please waite single mode.")
else:
# paired_mode
file_name_1 = args.fq_file_1
file_suffix_1 = os.path.splitext(file_name_1)[1]
file_name_2 = args.fq_file_2
file_suffix_2 = os.path.splitext(file_name_2)[1]
try:
if ".gz" in file_name_1:
fp1 = gzip.open(file_name_1, 'rt')
file_suffix_suffix_1 = os.path.splitext(os.path.splitext(file_name_1)[0])[1]
else:
fp1 = open(file_name_1, 'r')
file_suffix_suffix_1 = file_suffix_1
if ".gz" in file_name_2:
fp2 = gzip.open(file_name_2, 'rt')
file_suffix_suffix_2 = os.path.splitext(os.path.splitext(file_name_2)[0])[1]
else:
fp2 = open(file_name_2, 'r')
file_suffix_suffix_2 = file_suffix_2
except IOError:
print(file_name_1, "or", file_name_2, "is not exist!")
program_stop("process_read.py")
if file_suffix_suffix_1 != file_suffix_suffix_2:
print("suffix is not inconsistent.please check.")
program_stop("process_read.py")
else:
if ".fasta" == file_suffix_suffix_1 or ".fa" == file_suffix_suffix_1:
res = pool.starmap(do_something_with_record_paired, zip(to_fasta(fp1), to_fasta(fp2)))
pool.close()
pool.join()
elif ".fastq" == file_suffix_suffix_1 or ".fq" == file_suffix_suffix_1:
res = pool.starmap(do_something_with_record_paired, zip(convert_to_fasta(fp1), convert_to_fasta(fp2)))
pool.close()
pool.join()
else:
print("cannot find .fa(.fasta) or .fq(.fastq).please check.")
program_stop("process_read.py")
fp1.close()
fp2.close()
end = datetime.datetime.now()
print("process_reads:", end - begin)
begin = datetime.datetime.now()
for each_u, each_tl in res:
ec = find_ec(each_u)
if ec == -1 or ec >= len(counts):
new_ecs.append(each_u)
else:
counts[ec] = counts[ec] + 1
if f_len_goal > 0 and 0 <= ec < transcript_info.tran_num:
if 0 < each_tl < len(f_lens):
f_lens[each_tl] = f_lens[each_tl] + 1
f_len_goal = f_len_goal - 1
res.clear()
print("counts:", counts)
end = datetime.datetime.now()
print("match_ecs:", end - begin)
begin = datetime.datetime.now()
mean_f_lens = compute_mean_flg_lens(f_lens)
f_lens.clear()
tran_lens_estimated = get_each_tran_len(mean_f_lens)
mean_f_lens.clear()
alpha_list, eff_lens = em_run(counts, tran_lens_estimated)
output_file = os.path.join(args.output, "dualisto_quant.tsv")
write_em_tsv(output_file, alpha_list, eff_lens)
end = datetime.datetime.now()
print("em_run:", end - begin)
def build_ecs(seqs, k):
contig_find_trans_dict = {}
for i in range(len(contig_list)):
contig_find_trans_dict[i] = []
# 遍历基因序列
for i in range(len(seqs)):
each_ec = [i]
ec_map.append(each_ec)
ec_inv_dict[i] = each_ec
seq = seqs[i]
n_of_kmers_of_seq = len(seq) - k + 1
j = 0
while j < n_of_kmers_of_seq:
curr_kmer = seq[j:j + k]
curr_kmer = str(curr_kmer)
curr_rep = kmer_rep(curr_kmer)
curr_twin = kmer_twin(curr_kmer)
if curr_rep in kmer_str_dict:
curr_contig_id = kmer_str_dict[curr_rep].contig_id
curr_contig = contig_list[curr_contig_id]
kmers_in_contig = []
# 遍历curr_contig里面的每一个kmer
for m in range(len(curr_contig.seq) - k + 1):
curr_kmer_in_contig = curr_contig.seq[m:m + k]
kmers_in_contig.append(curr_kmer_in_contig)
kmers_in_contig_len = len(kmers_in_contig)
contig_find_trans = ContigFindTrans()
contig_find_trans.tran_id = i
if (curr_kmer == curr_rep
) == kmer_str_dict[curr_rep].sense_in_contig:
contig_find_trans.sense_in_tran = 1
contig_find_trans.start_in_tran = kmers_in_contig.index(
curr_kmer)
if kmers_in_contig_len - contig_find_trans.start_in_tran > n_of_kmers_of_seq - j:
# 说明这个contig不来自这个seq
contig_find_trans.stop_in_tran = contig_find_trans.start_in_tran + n_of_kmers_of_seq - j
# [start,stop)这里这个长度肯定是错误的，正好后面要用到
j = n_of_kmers_of_seq
# 到末尾，也就是结束
else:
contig_find_trans.stop_in_tran = kmers_in_contig_len
# contig属于这个seq，而且长度就是contig的长度
j = j + contig_find_trans.stop_in_tran - contig_find_trans.start_in_tran
# 下一个从紧接着当前contig的下一个contig开始
else:
contig_find_trans.sense_in_tran = 0
contig_find_trans.stop_in_tran = kmers_in_contig.index(
curr_twin) + 1
# 因为[start,stop) stop代表的是长度，取不到stop，实际取的是stop-1
if contig_find_trans.stop_in_tran > n_of_kmers_of_seq - j:
contig_find_trans.start_in_tran = contig_find_trans.stop_in_tran - n_of_kmers_of_seq + j
j = n_of_kmers_of_seq
else:
contig_find_trans.start_in_tran = 0
j = j + contig_find_trans.stop_in_tran - contig_find_trans.start_in_tran
contig_find_trans_dict[curr_contig_id].append(
contig_find_trans)
else:
print(curr_rep)
print(j)
program_stop("ecs.py-2")
for i in range(len(contig_list)):
contig_find_trans_list.append(contig_find_trans_dict[i])
fix_contigs(k)
for curr_contig_id in range(len(contig_find_trans_list)):
curr_contig_list = []
for curr_trans_info in contig_find_trans_list[curr_contig_id]:
curr_contig_list.append(curr_trans_info.tran_id)
curr_contig_list = sorted(list(set(curr_contig_list)))
ec = -1
if curr_contig_list in ec_inv_dict.values():
for (key, value) in ec_inv_dict.items():
if value == curr_contig_list:
ec = key
else:
ec = len(ec_inv_dict)
ec_inv_dict[ec] = curr_contig_list
ec_map.append(curr_contig_list)
ecs_list[curr_contig_id] = ec
contig_list[curr_contig_id].ecs_id = ec
for i in range(len(seqs)):
seq = seqs[i]
n_of_kmers_of_seq = len(seq) - k + 1
tmp_str = ""
j = 0
while j < n_of_kmers_of_seq:
curr_kmer = seq[j:j + k]
curr_kmer = str(curr_kmer)
curr_rep = kmer_rep(curr_kmer)
if curr_rep in kmer_str_dict:
curr_kmer_info = kmer_str_dict[curr_rep]
contig_include_trans = ContigIncludeTrans()
contig_include_trans.tran_id = i
contig_include_trans.pos_in_tran = j
contig_include_trans.sense_in_tran = int(((
curr_kmer == curr_rep) == curr_kmer_info.sense_in_contig))
contig_list[curr_kmer_info.contig_id].include_trans.append(
contig_include_trans)
j = j + contig_list[curr_kmer_info.contig_id].n_of_kmer
# if contig_include_trans.sense_in_tran:
# if contig_include_trans.pos_in_tran == 0:
# tmp_str = tmp_str + contig_list[curr_kmer_info.contig_id].seq
# else:
# tmp_str = tmp_str + contig_list[curr_kmer_info.contig_id].seq[k - 1]
# else:
# new_tm_str = str_pair(contig_list[curr_kmer_info.contig_id].seq)
# if contig_include_trans.pos_in_tran == 0:
# tmp_str = tmp_str + new_tm_str
# else:
# tmp_str = tmp_str + new_tm_str[k - 1]
else:
program_stop("ecs.py-3")
def load_idx(filename):
try:
fp = open(filename, 'r')
except IOError:
print(filename, "is not exist!")
program_stop("index_write_load.py")
# 1.read version
read_version = fp.readline().strip()
if read_version != kallisto_index_version:
program_stop("index_write_load.py")
# 2.read k
k = int(fp.readline().strip())
# 3.read num of trans
transcript_info.tran_num = int(fp.readline().strip())
transcript_info.tran_len = [0] * transcript_info.tran_num
for i in range(transcript_info.tran_num):
transcript_info.tran_len[i] = int(fp.readline().strip())
# 4.read kmer_str_dict and kmer_info_list
kmer_str_list_len = int(fp.readline().strip())
print("kmer_num:", kmer_str_list_len)
for i in range(kmer_str_list_len):
kmer_str_list.append("")
kmer_info_list.append("")
i = 0
while i < kmer_str_list_len:
kmer_str_list[i] = fp.readline().strip()
kmer_info = KmerInfo()
curr_kmer_info = fp.readline().strip().split(",")
kmer_info.contig_id = int(curr_kmer_info[0])
kmer_info.pos_in_contig = int(curr_kmer_info[1])
kmer_info.n_of_kmer_in_contig = int(curr_kmer_info[2])
kmer_info.sense_in_contig = int(curr_kmer_info[3])
kmer_info_list[i] = kmer_info
i = i + 1
for i in range(kmer_str_list_len):
kmer_str_dict[kmer_str_list[i]] = kmer_info_list[i]
kmer_str_list.clear()
kmer_info_list.clear()
# 5.read num of ecs
ec_map_len = int(fp.readline().strip())
print("ecs_num:", ec_map_len)
for i in range(ec_map_len):
ec_map.append([])
ec_inv_dict[i] = []
counts.append(0)
# 6.read each ecs
i = 0
while i < ec_map_len:
# 6.1 read num of each ecs
each_ecs_len = int(fp.readline().strip())
for j in range(each_ecs_len):
ec_map[i].append(0)
# 6.2 read each trans in each ecs
j = 0
while j < each_ecs_len:
ec_map[i][j] = int(fp.readline().strip())
j = j + 1
ec_inv_dict[i] = ec_map[i]
i = i + 1
# 7.read trans_names
transcript_info.tran_name = [""] * transcript_info.tran_num
for i in range(transcript_info.tran_num):
transcript_info.tran_name[i] = fp.readline().strip()
# 8.read contigs
contig_list_len = int(fp.readline().strip())
print("contig_num:", contig_list_len)
for i in range(contig_list_len):
contig_list.append(0)
ecs_list.append(0)
i = 0
while i < contig_list_len:
load_contig = Contig()
curr_contig_info = fp.readline().strip().split(",")
load_contig.id = int(curr_contig_info[0])
load_contig.n_of_kmer = int(curr_contig_info[1])
load_contig.seq = curr_contig_info[2]
# 8.1 read contig_to_trans_info
curr_contig_include_trans_len = int(fp.readline().strip())
load_contig.include_trans = [0] * curr_contig_include_trans_len
j = 0
while j < curr_contig_include_trans_len:
load_include_trans = ContigIncludeTrans()
curr_include_trans = fp.readline().strip().split(",")
load_include_trans.tran_id = int(curr_include_trans[0])
load_include_trans.pos_in_tran = int(curr_include_trans[1])
load_include_trans.sense_in_tran = int(curr_include_trans[2])
j = j + 1
i = i + 1
# 9.read ecs info
i = 0
while i < contig_list_len:
ecs_list[i] = int(fp.readline().strip())
i = i + 1
fp.close()
return k
def write_idx(filename, k):
try:
fp = open(filename, 'w')
except IOError:
print(filename, "is not exist!")
program_stop("index_write_load.py")
# 1.write version
fp.write(version + "\n")
# 2.write k
fp.write(str(k) + "\n")
# 3.write num of trans
fp.write(str(transcript_info.tran_num) + "\n")
for i in range(transcript_info.tran_num):
fp.write(str(transcript_info.tran_len[i]) + "\n")
# 4.write kmer_str_dict and kmer_info_list
for key in kmer_str_dict:
kmer_str_list.append(key)
kmer_info_list.append(kmer_str_dict[key])
i = 0
fp.write(str(len(kmer_str_list)) + "\n")
while i < len(kmer_str_list):
fp.write(kmer_str_list[i] + "\n")
fp.write(
str(kmer_info_list[i].contig_id) + "," +
str(kmer_info_list[i].pos_in_contig) + "," +
str(kmer_info_list[i].n_of_kmer_in_contig) + "," +
str(kmer_info_list[i].sense_in_contig) + "\n")
i = i + 1
# 5.write num of ecs
fp.write(str(len(ec_map)) + "\n")
# 6.write each ecs
i = 0
while i < len(ec_map):
# 6.1 write num of each ecs
fp.write(str(len(ec_map[i])) + "\n")
# 6.2 write each trans in each ecs
j = 0
while j < len(ec_map[i]):
fp.write(str(ec_map[i][j]) + "\n")
j = j + 1
i = i + 1
# 7.write trans_names
for i in range(transcript_info.tran_num):
fp.write(transcript_info.tran_name[i] + "\n")
# 8.write contigs
fp.write(str(len(contig_list)) + "\n")
i = 0
while i < len(contig_list):
fp.write(
str(contig_list[i].id) + "," + str(contig_list[i].n_of_kmer) +
"," + str(contig_list[i].seq) + "\n")
# 8.1 write contig_to_trans_info
fp.write(str(len(contig_list[i].include_trans)) + "\n")
j = 0
while j < len(contig_list[i].include_trans):
curr_include_trans = contig_list[i].include_trans[j]
fp.write(
str(curr_include_trans.tran_id) + "," +
str(curr_include_trans.pos_in_tran) + "," +
str(curr_include_trans.sense_in_tran) + "\n")
j = j + 1
i = i + 1
# 9.write ecs info
i = 0
while i < len(ecs_list):
fp.write(str(ecs_list[i]) + "\n")
i = i + 1
fp.flush()
fp.close()
def build_dbg(seqs, k):
global fw_step_kmer
tmp_kmer_map = set()
# 把序列打断,得到kmer的集合
for seq in seqs:
for i in range(len(seq) - k + 1):
curr_kmer = seq[i:i + k]
curr_kmer = str(curr_kmer)
curr_rep = kmer_rep(curr_kmer)
tmp_kmer_map.add(curr_rep)
# 给每一个kmer带上一个可以存储它信息的类
for each_kmer in tmp_kmer_map:
kmer_info = KmerInfo()
kmer_str_dict[each_kmer] = kmer_info
# 把kmer连起来,找contig
for kmer_key in kmer_str_dict:
curr_kmer = kmer_key
curr_kmer_info = kmer_str_dict[kmer_key]
if curr_kmer_info.contig_id == -1:
self_loop = 0
curr_twin = kmer_twin(curr_kmer)
fw_list = [curr_kmer]
last_kmer = curr_kmer
fw_step_kmer = curr_kmer
while fwstep(fw_step_kmer):
if fw_step_kmer == curr_kmer:
# 该if判断是否成环
self_loop = 1
break
# pass
# example(3,"ACTGAC") (5,"ACCAACCA") (5,"TCTGTCTG") (5,"AACAAACA") (5,"CACACA") (5,"ACACAC")
# print("begin:",begin,"fw:", fw, "t_kmer", self.tmp_kmer, "seqs:", self.seqs)
elif fw_step_kmer == curr_twin:
self_loop = (len(fw_list) > 1)
break
elif fw_step_kmer == kmer_twin(last_kmer):
break
fw_list.append(fw_step_kmer)
last_kmer = fw_step_kmer
fw_step_kmer = curr_twin
bw_list = []
first_kmer = curr_twin
if not self_loop:
while fwstep(fw_step_kmer):
if fw_step_kmer == curr_twin:
break
elif fw_step_kmer == curr_kmer:
break
elif fw_step_kmer == kmer_twin(first_kmer):
break
bw_list.append(fw_step_kmer)
first_kmer = fw_step_kmer
curr_kmer_list = []
for bw in reversed(bw_list):
curr_kmer_list.append(kmer_twin(bw))
for fw in fw_list:
curr_kmer_list.append(fw)
contig_list_len = len(curr_kmer_list)
curr_contig_id = len(contig_list)
contig = Contig()
contig.id = curr_contig_id
contig.n_of_kmer = contig_list_len
# 存储kmer的信息
for j in range(contig_list_len):
each_kmer = curr_kmer_list[j]
tmp_rep = kmer_rep(each_kmer)
if tmp_rep in kmer_str_dict:
kmer_str_dict[tmp_rep].contig_id = curr_contig_id
kmer_str_dict[tmp_rep].pos_in_contig = j
kmer_str_dict[
tmp_rep].n_of_kmer_in_contig = contig_list_len
if tmp_rep == each_kmer:
kmer_str_dict[tmp_rep].sense_in_contig = 1
else:
kmer_str_dict[tmp_rep].sense_in_contig = 0
else:
program_stop("contig.py")
if j == 0:
contig.seq = each_kmer
elif j > 0:
contig.seq = contig.seq + each_kmer[-1]
contig_list.append(contig)
ecs_list.append(-1)
