def detect_rev_seed_match(mirna_id, targetrna_id):
'''
X1_seed_match_rev
'''
mirna_seq, targetrna_seq = get_sequence(mirna_id, targetrna_id)
targetrna_seq_revcomp = utils.reverse_complement(targetrna_seq)
tmp_dict = find_mirna_subtarget_candidates(mirna_id,mirna_seq,targetrna_id,targetrna_seq_revcomp) # => list()
return run_result(tmp_dict)
def detect_seed_match(mirna_id, targetrna_id):
'''
1_Find_mirna_target_candidates
Start find_mirna_target_candidates module
'''
#seq_data
mirna_seq, targetrna_seq = get_sequence(mirna_id, targetrna_id)
targetrna_seq_revcomp = utils.reverse_complement(targetrna_seq)
#print (mirna_seq)
#print (targetrna_seq)
#print (targetrna_seq_revcomp)
#parameters - seed
mirna_start_pairing = ''
seed_length = ''
allowed_gu_wobbles = []
allowed_mismatches = []
if hasattr(seed_infor,'MIRNA_START_PAIRING'):
mirna_start_pairing = seed_infor.MIRNA_START_PAIRING
else:
print ('ERROR: MIRNA_START_PAIRING parameter does not exist in module.analysis.mirna_seed.py file')
sys.exit(1)
if hasattr(seed_infor,'SEED_LENGTH'):
seed_length = seed_infor.SEED_LENGTH
else:
print ('ERROR: SEED_LENGTH parameters do not exist in module.analysis.mirna_seed.py file')
sys.exit(1)
if hasattr(seed_infor,'ALLOWED_GU_WOBBLES'):
allowed_gu_wobbles = seed_infor.ALLOWED_GU_WOBBLES
else:
print ('ERROR: ALLOWED_GU_WOBBLES parameters do not exist in module.analysis.mirna_seed.py file')
sys.exit(1)
if hasattr(seed_infor,'ALLOWED_MISMATCHES'):
allowed_mismatches = seed_infor.ALLOWED_MISMATCHES
else:
print ('ERROR: ALLOWED_MISMATCHES parameters do not exist in module.analysis.mirna_seed.py file')
sys.exit(1)
tmp_dict = {}
#run_log("Finding seed matches and calculating motif density in targetRNA sequences...", 0)
tmp_dict = find_mirna_target_candidates(mirna_id,mirna_seq,targetrna_id,targetrna_seq_revcomp,mirna_start_pairing,seed_length,allowed_gu_wobbles,allowed_mismatches) # => list()
return run_result(tmp_dict)
def motif_occurrence(mirna_seq, targetrna_seq, tmp_dict):
two_nt_motif_prob_dict = Markov_Model(targetrna_seq)
#print (two_nt_motif_prob_dict)
motif_type_need = []
motif_type_dict = {}
motif_type_dict['p1_p8_match'] = []
motif_type_dict['p2_p8_match'] = []
motif_type_dict['p1_p7_match'] = []
motif_type_dict['p2_p7_match'] = []
motif_type_dict['p3_p8_match'] = []
for x in list(tmp_dict.keys()):
id_infor = x
targetrna_motif = tmp_dict[x][3] #NEED TO CHECK!!
motif_type = tmp_dict[x][5] #NEED TO CHECK!!
if motif_type == '8mer': #p1_p8_match, p2_p8_match, p1_p7_match, p2_p7_match, p3_p8_match
motif_type_need.append('p1_p8_match')
motif_type_dict['p1_p8_match'].append(utils.reverse_complement(targetrna_motif[0:8]))
motif_type_dict['p2_p8_match'].append(utils.reverse_complement(targetrna_motif[1:8]))
motif_type_dict['p1_p7_match'].append(utils.reverse_complement(targetrna_motif[0:7]))
motif_type_dict['p2_p7_match'].append(utils.reverse_complement(targetrna_motif[1:7]))
motif_type_dict['p3_p8_match'].append(utils.reverse_complement(targetrna_motif[2:8]))
elif motif_type == '8mer-1A': #p2_p8_match, p2_p7_match, p3_p8_match
motif_type_need.append('p2_p8_match')
motif_type_dict['p2_p8_match'].append(utils.reverse_complement(targetrna_motif[1:8]))
motif_type_dict['p2_p7_match'].append(utils.reverse_complement(targetrna_motif[1:7]))
motif_type_dict['p3_p8_match'].append(utils.reverse_complement(targetrna_motif[2:8]))
elif motif_type == '7mer-m8': #p2_p8_match, p2_p7_match, p3_p8_match
motif_type_need.append('p2_p8_match')
motif_type_dict['p2_p8_match'].append(utils.reverse_complement(targetrna_motif[1:8]))
motif_type_dict['p2_p7_match'].append(utils.reverse_complement(targetrna_motif[1:7]))
motif_type_dict['p3_p8_match'].append(utils.reverse_complement(targetrna_motif[2:8]))
elif motif_type == '7mer-m1': #p1_p7_match, p2_p7_match
motif_type_need.append('p1_p7_match')
motif_type_dict['p1_p7_match'].append(utils.reverse_complement(targetrna_motif[0:7]))
motif_type_dict['p2_p7_match'].append(utils.reverse_complement(targetrna_motif[1:7]))
elif motif_type == '7mer-1A': #p2_p7_match
motif_type_need.append('p2_p7_match')
motif_type_dict['p2_p7_match'].append(utils.reverse_complement(targetrna_motif[1:7]))
elif motif_type == '6mer-m7': #p2_p7_match
motif_type_need.append('p2_p7_match')
motif_type_dict['p2_p7_match'].append(utils.reverse_complement(targetrna_motif[1:7]))
elif motif_type == '6mer-m8': #p3_p8_match
motif_type_need.append('p3_p8_match')
motif_type_dict['p3_p8_match'].append(utils.reverse_complement(targetrna_motif[2:8]))
else:
print ('ERROR: motif_type is wrong...')
motif_type_need = utils.rm_duplicate_list(motif_type_need)
#motif_type_dict['p1_p8_match'] = utils.rm_duplicate_list(motif_type_dict['p1_p8_match'])
#motif_type_dict['p2_p8_match'] = utils.rm_duplicate_list(motif_type_dict['p2_p8_match'])
#motif_type_dict['p1_p7_match'] = utils.rm_duplicate_list(motif_type_dict['p1_p7_match'])
#motif_type_dict['p2_p7_match'] = utils.rm_duplicate_list(motif_type_dict['p2_p7_match'])
#motif_type_dict['p3_p8_match'] = utils.rm_duplicate_list(motif_type_dict['p3_p8_match'])
#print (motif_type_need)
#print (motif_type_dict['p1_p8_match'])
#print (motif_type_dict['p2_p8_match'])
#print (motif_type_dict['p1_p7_match'])
#print (motif_type_dict['p2_p7_match'])
#print (motif_type_dict['p3_p8_match'])
motif_prob_dict = {}
motif_prob_dict_each = {}
for x in motif_type_need: #each_type: p1_p8_match, p2_p8_match, p1_p7_match, p2_p7_match, p3_p8_match
test_seed = utils.rm_duplicate_list(motif_type_dict[x])
#print (test_seed) #['UGCUUGAA', 'UACUUGAA', 'UAUUUGAG', 'UAUUUGGA']
#All_existed_motifs_calc
pos_motif_number = len(motif_type_dict[x])
total_motif_number = len(targetrna_seq) - len(test_seed[0]) + 1
motif_prob, each_motif_prob_dict = calc_motif_prob(test_seed,two_nt_motif_prob_dict) #test
#print ('Motif_number: ' + str(pos_motif_number))
#print ('Total_motif: ' + str(total_motif_number))
#print ('Motif_probability: ' + str(motif_prob))
motif_binom = cumulative_binomial_distribution(pos_motif_number, total_motif_number, motif_prob)
#print ('Motif_binom_prob: ' + str(motif_binom))
motif_prob_dict[x] = [pos_motif_number, total_motif_number, motif_prob, motif_binom] #p1_p8_match => [existed_motifs, total_motifs, motif_prob, binom_prob(e.g. 0.00022)]
#Each_existed_motif_calc
existed_motif_dict = Counter(motif_type_dict[x])
#print (existed_motif_dict)
for i in existed_motif_dict.keys(): #motif => number
pos_motif_number_each = existed_motif_dict[i]
motif_prob_each = each_motif_prob_dict[i] #motif => probability
motif_binom_each = cumulative_binomial_distribution(pos_motif_number_each, total_motif_number, motif_prob_each)
#print (i)
#print ('motif_number: ' + str(pos_motif_number_each))
#print ('motif_prob_each: ' + str(motif_prob_each))
#print (motif_binom_each)
motif_prob_dict_each[i] = [pos_motif_number_each, total_motif_number, motif_prob_each, motif_binom_each]
#print (motif_prob_dict)
#print (motif_prob_dict_each)
for x in list(tmp_dict.keys()):
id_infor = x
targetrna_motif = tmp_dict[x][3] #NEED TO CHECK
motif_type = tmp_dict[x][5] #NEED TO CHECK
if motif_type == '8mer': #p1-p8 match
seed_group = 'p1_p8_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[utils.reverse_complement(targetrna_motif[0:8])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '8mer-1A': #p2_p8_match
seed_group = 'p2_p8_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[utils.reverse_complement(targetrna_motif[1:8])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '7mer-m8': #p2_p8_match
seed_group = 'p2_p8_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[utils.reverse_complement(targetrna_motif[1:8])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '7mer-m1': #p1_p7_match
seed_group = 'p1_p7_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[utils.reverse_complement(targetrna_motif[0:7])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '7mer-1A': #p2_p7_match
seed_group = 'p2_p7_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[utils.reverse_complement(targetrna_motif[1:7])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '6mer-m7': #p2_p7_match
seed_group = 'p2_p7_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[utils.reverse_complement(targetrna_motif[1:7])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '6mer-m8': #p3_p8_match
seed_group = 'p3_p8_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[utils.reverse_complement(targetrna_motif[2:8])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
else:
print ('ERROR: motif_type is wrong...')
return tmp_dict #[each_existed_motif_result], [all_existed_motif_result]
'''
motif_type_all = []
motif_type_dict = {}
for x in list(tmp_dict.keys()):
motif_targetrna_revcomp = utils.reverse_complement(str(tmp_dict[x][1]))
types = tmp_dict[x][3]
motif_type_all.append(tmp_dict[x][3]) #8-mer, 8mer-1A, 7mer-m8, 7mer-m1,
motif_type_dict[] =
print (motif_type_all)
motif_type = utils.rm_duplicate_list(motif_type_all)
print (motif_type)
seed_group = seed_grouping(motif_type)
print (seed_group)
if 'p1_p8_match' in seed_group: #8mer ||||||||
pass
elif 'p2_p8_match' in seed_group: #8mer-1A, 7mer-m8, 8mer x|||||||
pass
elif 'p1_p7_match, ' in seed_group: #7mer-m1, 8mer |||||||x
pass
elif 'p2_p7_match' in seed_group: #7mer-1A, 6mer-m7, 7mer-m1, 8mer-1A, 7mer-m8, 8mer x||||||x
pass
elif 'p3_p8_match' in seed_group: #6mer-m8, 8mer-1A, 7mer-m8, 8mer xx||||||
pass
else:
print ('ERROR: seed_group is wrong...')
'''
'''
def motif_occurrence(mirna_seq, targetrna_seq, tmp_dict):
two_nt_motif_prob_dict = Markov_Model(targetrna_seq)
#print (two_nt_motif_prob_dict)
motif_type_need = []
motif_type_dict = {}
motif_type_dict['p1_p8_match'] = []
motif_type_dict['p2_p8_match'] = []
motif_type_dict['p1_p7_match'] = []
motif_type_dict['p2_p7_match'] = []
motif_type_dict['p3_p8_match'] = []
for x in list(tmp_dict.keys()):
id_infor = x
targetrna_motif = tmp_dict[x][3] #NEED TO CHECK!!
motif_type = tmp_dict[x][5] #NEED TO CHECK!!
if motif_type == '8mer': #p1_p8_match, p2_p8_match, p1_p7_match, p2_p7_match, p3_p8_match
motif_type_need.append('p1_p8_match')
motif_type_dict['p1_p8_match'].append(
utils.reverse_complement(targetrna_motif[0:8]))
motif_type_dict['p2_p8_match'].append(
utils.reverse_complement(targetrna_motif[1:8]))
motif_type_dict['p1_p7_match'].append(
utils.reverse_complement(targetrna_motif[0:7]))
motif_type_dict['p2_p7_match'].append(
utils.reverse_complement(targetrna_motif[1:7]))
motif_type_dict['p3_p8_match'].append(
utils.reverse_complement(targetrna_motif[2:8]))
elif motif_type == '8mer-1A': #p2_p8_match, p2_p7_match, p3_p8_match
motif_type_need.append('p2_p8_match')
motif_type_dict['p2_p8_match'].append(
utils.reverse_complement(targetrna_motif[1:8]))
motif_type_dict['p2_p7_match'].append(
utils.reverse_complement(targetrna_motif[1:7]))
motif_type_dict['p3_p8_match'].append(
utils.reverse_complement(targetrna_motif[2:8]))
elif motif_type == '7mer-m8': #p2_p8_match, p2_p7_match, p3_p8_match
motif_type_need.append('p2_p8_match')
motif_type_dict['p2_p8_match'].append(
utils.reverse_complement(targetrna_motif[1:8]))
motif_type_dict['p2_p7_match'].append(
utils.reverse_complement(targetrna_motif[1:7]))
motif_type_dict['p3_p8_match'].append(
utils.reverse_complement(targetrna_motif[2:8]))
elif motif_type == '7mer-m1': #p1_p7_match, p2_p7_match
motif_type_need.append('p1_p7_match')
motif_type_dict['p1_p7_match'].append(
utils.reverse_complement(targetrna_motif[0:7]))
motif_type_dict['p2_p7_match'].append(
utils.reverse_complement(targetrna_motif[1:7]))
elif motif_type == '7mer-1A': #p2_p7_match
motif_type_need.append('p2_p7_match')
motif_type_dict['p2_p7_match'].append(
utils.reverse_complement(targetrna_motif[1:7]))
elif motif_type == '6mer-m7': #p2_p7_match
motif_type_need.append('p2_p7_match')
motif_type_dict['p2_p7_match'].append(
utils.reverse_complement(targetrna_motif[1:7]))
elif motif_type == '6mer-m8': #p3_p8_match
motif_type_need.append('p3_p8_match')
motif_type_dict['p3_p8_match'].append(
utils.reverse_complement(targetrna_motif[2:8]))
else:
print('ERROR: motif_type is wrong...')
motif_type_need = utils.rm_duplicate_list(motif_type_need)
#motif_type_dict['p1_p8_match'] = utils.rm_duplicate_list(motif_type_dict['p1_p8_match'])
#motif_type_dict['p2_p8_match'] = utils.rm_duplicate_list(motif_type_dict['p2_p8_match'])
#motif_type_dict['p1_p7_match'] = utils.rm_duplicate_list(motif_type_dict['p1_p7_match'])
#motif_type_dict['p2_p7_match'] = utils.rm_duplicate_list(motif_type_dict['p2_p7_match'])
#motif_type_dict['p3_p8_match'] = utils.rm_duplicate_list(motif_type_dict['p3_p8_match'])
#print (motif_type_need)
#print (motif_type_dict['p1_p8_match'])
#print (motif_type_dict['p2_p8_match'])
#print (motif_type_dict['p1_p7_match'])
#print (motif_type_dict['p2_p7_match'])
#print (motif_type_dict['p3_p8_match'])
motif_prob_dict = {}
motif_prob_dict_each = {}
for x in motif_type_need: #each_type: p1_p8_match, p2_p8_match, p1_p7_match, p2_p7_match, p3_p8_match
test_seed = utils.rm_duplicate_list(motif_type_dict[x])
#print (test_seed) #['UGCUUGAA', 'UACUUGAA', 'UAUUUGAG', 'UAUUUGGA']
#All_existed_motifs_calc
pos_motif_number = len(motif_type_dict[x])
total_motif_number = len(targetrna_seq) - len(test_seed[0]) + 1
motif_prob, each_motif_prob_dict = calc_motif_prob(
test_seed, two_nt_motif_prob_dict) #test
#print ('Motif_number: ' + str(pos_motif_number))
#print ('Total_motif: ' + str(total_motif_number))
#print ('Motif_probability: ' + str(motif_prob))
motif_binom = cumulative_binomial_distribution(pos_motif_number,
total_motif_number,
motif_prob)
#print ('Motif_binom_prob: ' + str(motif_binom))
motif_prob_dict[x] = [
pos_motif_number, total_motif_number, motif_prob, motif_binom
] #p1_p8_match => [existed_motifs, total_motifs, motif_prob, binom_prob(e.g. 0.00022)]
#Each_existed_motif_calc
existed_motif_dict = Counter(motif_type_dict[x])
#print (existed_motif_dict)
for i in existed_motif_dict.keys(): #motif => number
pos_motif_number_each = existed_motif_dict[i]
motif_prob_each = each_motif_prob_dict[i] #motif => probability
motif_binom_each = cumulative_binomial_distribution(
pos_motif_number_each, total_motif_number, motif_prob_each)
#print (i)
#print ('motif_number: ' + str(pos_motif_number_each))
#print ('motif_prob_each: ' + str(motif_prob_each))
#print (motif_binom_each)
motif_prob_dict_each[i] = [
pos_motif_number_each, total_motif_number, motif_prob_each,
motif_binom_each
]
#print (motif_prob_dict)
#print (motif_prob_dict_each)
for x in list(tmp_dict.keys()):
id_infor = x
targetrna_motif = tmp_dict[x][3] #NEED TO CHECK
motif_type = tmp_dict[x][5] #NEED TO CHECK
if motif_type == '8mer': #p1-p8 match
seed_group = 'p1_p8_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[
utils.reverse_complement(targetrna_motif[0:8])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '8mer-1A': #p2_p8_match
seed_group = 'p2_p8_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[
utils.reverse_complement(targetrna_motif[1:8])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '7mer-m8': #p2_p8_match
seed_group = 'p2_p8_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[
utils.reverse_complement(targetrna_motif[1:8])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '7mer-m1': #p1_p7_match
seed_group = 'p1_p7_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[
utils.reverse_complement(targetrna_motif[0:7])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '7mer-1A': #p2_p7_match
seed_group = 'p2_p7_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[
utils.reverse_complement(targetrna_motif[1:7])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '6mer-m7': #p2_p7_match
seed_group = 'p2_p7_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[
utils.reverse_complement(targetrna_motif[1:7])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
elif motif_type == '6mer-m8': #p3_p8_match
seed_group = 'p3_p8_match'
all_existed_motif_result = motif_prob_dict[seed_group]
each_existed_motif_result = motif_prob_dict_each[
utils.reverse_complement(targetrna_motif[2:8])]
tmp_dict[x].extend(each_existed_motif_result)
tmp_dict[x].extend(all_existed_motif_result)
else:
print('ERROR: motif_type is wrong...')
return tmp_dict #[each_existed_motif_result], [all_existed_motif_result]
'''
motif_type_all = []
motif_type_dict = {}
for x in list(tmp_dict.keys()):
motif_targetrna_revcomp = utils.reverse_complement(str(tmp_dict[x][1]))
types = tmp_dict[x][3]
motif_type_all.append(tmp_dict[x][3]) #8-mer, 8mer-1A, 7mer-m8, 7mer-m1,
motif_type_dict[] =
print (motif_type_all)
motif_type = utils.rm_duplicate_list(motif_type_all)
print (motif_type)
seed_group = seed_grouping(motif_type)
print (seed_group)
if 'p1_p8_match' in seed_group: #8mer ||||||||
pass
elif 'p2_p8_match' in seed_group: #8mer-1A, 7mer-m8, 8mer x|||||||
pass
elif 'p1_p7_match, ' in seed_group: #7mer-m1, 8mer |||||||x
pass
elif 'p2_p7_match' in seed_group: #7mer-1A, 6mer-m7, 7mer-m1, 8mer-1A, 7mer-m8, 8mer x||||||x
pass
elif 'p3_p8_match' in seed_group: #6mer-m8, 8mer-1A, 7mer-m8, 8mer xx||||||
pass
else:
print ('ERROR: seed_group is wrong...')
'''
'''
