def mature_generator_v2(lines):
global map_data
# each loop should read exactly 3 lines
output_list=[]
iterator = 0
while 1:
if iterator == len(lines):
break
line_info = lines[iterator].strip()
if line_info == "":
break
line_seq = lines[iterator+1].strip()
line_db = lines[iterator+2].strip()
iterator += 3
# if no read data is matched in putative precursors, discard it
if DISCARD_NO_READ_PREC_FLAG:
no_read_prec_flag = SeqModule.check_no_read_prec(line_info, line_seq, map_data, MIN_READ_COUNT_THRESHOLD)
if no_read_prec_flag is True:
continue
# get alignment form first
output_form = SeqModule.generate_alignment_form(line_info, line_seq, line_db,
map_data, MIN_READ_COUNT_THRESHOLD)
# if mature_prime is bad, discard it
if output_form[0].split()[12] == 'bad':
continue
# check conserved sequence with blastn
# if this line_info is classified as conserved sequence, update line_info
# no need to find duplex, just mark 5p and 3p index corresponding to matched information
updated_flag = False
if ANNOTATE_FLAG == 'true' or ANNOTATE_FLAG == 'True':
output_form[0], updated_flag = SeqModule.check_conserved_seq(output_form[0], line_seq,
blastn_path, mirbase_path, ARM_EXTEND_THRESHOLD)
if updated_flag is True:
start_5p, end_5p, start_3p, end_3p = SeqModule.star_identifier_v2_conserved(output_form[0], line_seq, line_db,
MATURE_MIN_LEN, MATURE_MAX_LEN,
MAX_SERIAL_MISMATCH, MAX_MULT_MISMATCH,
MAX_SERIAL_BULGE, MAX_MULT_BULGE)
else:
start_5p, end_5p, start_3p, end_3p = SeqModule.star_identifier_v2(line_db, MATURE_MIN_LEN, MATURE_MAX_LEN,
MAX_SERIAL_MISMATCH, MAX_MULT_MISMATCH,
MAX_SERIAL_BULGE, MAX_MULT_BULGE)
if start_5p == 0 and end_5p == 0 and start_3p == 0 and end_3p == 0: # star seq not found
continue
# write putative precursor to the output file
output_form = SeqModule.generate_output_form(output_form[0], line_seq, line_db,
start_5p, start_3p, end_5p, end_3p,
map_data, MIN_READ_COUNT_THRESHOLD)
# else, do the code below
###########################################################
elif ANNOTATE_FLAG == 'false' or ANNOTATE_FLAG == 'False':
# Discard non-canonical (i.e. "hard to identify") precursor
# "Asymmetric" dot-bracket notation precursor : low accuracy, hard to identify star seq, and too many outputs
# if ")" portion is large in "left side", it's non-canonical
line_db_left = line_db[0:len(line_db)/2]
num_open = line_db_left.count("(")
num_close = line_db_left.count(")")
if float(num_close)/num_open > NON_CANONICAL_PREC_FACTOR:
continue
# find valid star sequence from putative precursors
start_5p, end_5p, start_3p, end_3p = SeqModule.star_identifier_v2(line_db, MATURE_MIN_LEN, MATURE_MAX_LEN,
MAX_SERIAL_MISMATCH, MAX_MULT_MISMATCH,
MAX_SERIAL_BULGE, MAX_MULT_BULGE)
if start_5p == 0 and end_5p == 0 and start_3p == 0 and end_3p == 0: # star seq not found
continue
# write putative precursor to the output file
output_form = SeqModule.generate_output_form(output_form[0], line_seq, line_db,
start_5p, start_3p, end_5p, end_3p,
map_data, MIN_READ_COUNT_THRESHOLD)
output_list.append(output_form)
return output_list
def mature_generator_v2(lines):
global map_data
# each loop should read exactly 3 lines
output_list = []
iterator = 0
while 1:
if iterator == len(lines):
break
line_info = lines[iterator].strip()
if line_info == "":
break
line_seq = lines[iterator + 1].strip()
line_db = lines[iterator + 2].strip()
iterator += 3
# if no read data is matched in putative precursors, discard it
if DISCARD_NO_READ_PREC_FLAG:
no_read_prec_flag = SeqModule.check_no_read_prec(
line_info, line_seq, map_data, MIN_READ_COUNT_THRESHOLD)
if no_read_prec_flag is True:
continue
# get alignment form first
output_form = SeqModule.generate_alignment_form(
line_info, line_seq, line_db, map_data, MIN_READ_COUNT_THRESHOLD)
# if mature_prime is bad, discard it
if output_form[0].split()[12] == 'bad':
continue
# check conserved sequence with blastn
# if this line_info is classified as conserved sequence, update line_info
# no need to find duplex, just mark 5p and 3p index corresponding to matched information
updated_flag = False
if ANNOTATE_FLAG == 'true' or ANNOTATE_FLAG == 'True':
output_form[0], updated_flag = SeqModule.check_conserved_seq(
output_form[0], line_seq, blastn_path, mirbase_path,
ARM_EXTEND_THRESHOLD)
if updated_flag is True:
start_5p, end_5p, start_3p, end_3p = SeqModule.star_identifier_v2_conserved(
output_form[0], line_seq, line_db, MATURE_MIN_LEN,
MATURE_MAX_LEN, MAX_SERIAL_MISMATCH, MAX_MULT_MISMATCH,
MAX_SERIAL_BULGE, MAX_MULT_BULGE)
else:
start_5p, end_5p, start_3p, end_3p = SeqModule.star_identifier_v2(
line_db, MATURE_MIN_LEN, MATURE_MAX_LEN,
MAX_SERIAL_MISMATCH, MAX_MULT_MISMATCH, MAX_SERIAL_BULGE,
MAX_MULT_BULGE)
if start_5p == 0 and end_5p == 0 and start_3p == 0 and end_3p == 0: # star seq not found
continue
# write putative precursor to the output file
output_form = SeqModule.generate_output_form(
output_form[0], line_seq, line_db, start_5p, start_3p, end_5p,
end_3p, map_data, MIN_READ_COUNT_THRESHOLD)
# else, do the code below
###########################################################
elif ANNOTATE_FLAG == 'false' or ANNOTATE_FLAG == 'False':
# Discard non-canonical (i.e. "hard to identify") precursor
# "Asymmetric" dot-bracket notation precursor : low accuracy, hard to identify star seq, and too many outputs
# if ")" portion is large in "left side", it's non-canonical
line_db_left = line_db[0:len(line_db) / 2]
num_open = line_db_left.count("(")
num_close = line_db_left.count(")")
if float(num_close) / num_open > NON_CANONICAL_PREC_FACTOR:
continue
# find valid star sequence from putative precursors
start_5p, end_5p, start_3p, end_3p = SeqModule.star_identifier_v2(
line_db, MATURE_MIN_LEN, MATURE_MAX_LEN, MAX_SERIAL_MISMATCH,
MAX_MULT_MISMATCH, MAX_SERIAL_BULGE, MAX_MULT_BULGE)
if start_5p == 0 and end_5p == 0 and start_3p == 0 and end_3p == 0: # star seq not found
continue
# write putative precursor to the output file
output_form = SeqModule.generate_output_form(
output_form[0], line_seq, line_db, start_5p, start_3p, end_5p,
end_3p, map_data, MIN_READ_COUNT_THRESHOLD)
output_list.append(output_form)
return output_list
