def primer_process(options, session_dir, fcdict, db, oligos):
'''Primer Process'''
#options.processor = int(options.processor)
oligo_pos = []
oligo_id_list = []
#t1 = time.time()
for oligo in oligos:
primer_seq = oligo['seq']
oligo_id_list.append(oligo['id'])
#mer = primer_seq[-options.k:]
mer = primer_seq[-options.k_value:]
mer_id = chilli.DNA2int(mer)
# p for plus strand, m for minus strand
p_pos_list, m_pos_list = get_position(options, mer_id, db)
oligo_pos.append({
'p_list' : p_pos_list,
'm_list' : m_pos_list,
})
#t2 = time.time()
#cost = t2 - t1
#print cost
product = []
binding_range = []
binding_primer = []
for i in xrange(len(oligos)):
p_list = oligo_pos[i]['p_list']
p_oligo_length = oligos[i]['size']
for k in xrange(len(oligos)):
m_list = oligo_pos[k]['m_list']
m_oligo_length = oligos[k]['size']
for j in p_list.iterkeys():
hid = str(j) # Because the database has been re-formated
try:
p_pos = p_list[j]
m_pos = m_list[j]
except:
continue
for p in p_pos:
left = get_pos_range(p, m_pos)
for pos_index in xrange(left, len(m_pos)):
f3_pos = p+1
r3_pos = m_pos[pos_index]
# The amplicon size <= p.len + m.len
if f3_pos >= r3_pos:
continue
product_size = p_oligo_length + m_pos[pos_index] - p + m_oligo_length - 1
if product_size < options.size_start:
continue
if product_size > options.size_stop:
break
p_start = p - p_oligo_length + 1
if p_start < 0:
p_start = 0
m_stop = r3_pos + m_oligo_length
if m_stop > fcdict[hid]['size']:
m_stop = fcdict[hid]['size']
binding_range.append('%s:%s-%s' % (hid, p_start, p + 1))
# Reverse: Correction for reverse
binding_range.append('%s:%s-%s' % (hid, r3_pos, m_stop))
amp = {
'hid' : hid,
'pid' : oligos[i]['id'],
'mid' : oligos[k]['id'],
'plen' : p_oligo_length,
'mlen' : m_oligo_length,
'pseq' : oligos[i]['seq'],
'mseq' : Seq.rev_com(oligos[k]['seq']),
'size' : product_size,
'f3_pos' : f3_pos,
'r3_pos' : r3_pos,
}
product.append(amp)
return product, binding_range
def primer_process(options, session_dir, fcdict, db, oligos):
'''Primer Process'''
#options.processor = int(options.processor)
oligo_pos = []
oligo_id_list = []
#t1 = time.time()
for oligo in oligos:
primer_seq = oligo['seq']
oligo_id_list.append(oligo['id'])
#mer = primer_seq[-options.k:]
mer = primer_seq[-options.k_value:]
mer_id = chilli.DNA2int(mer)
# p for plus strand, m for minus strand
p_pos_list, m_pos_list = get_position(options, mer_id, db)
oligo_pos.append({
'p_list': p_pos_list,
'm_list': m_pos_list,
})
#t2 = time.time()
#cost = t2 - t1
#print cost
product = []
binding_range = []
binding_primer = []
for i in xrange(len(oligos)):
p_list = oligo_pos[i]['p_list']
p_oligo_length = oligos[i]['size']
for k in xrange(len(oligos)):
m_list = oligo_pos[k]['m_list']
m_oligo_length = oligos[k]['size']
for j in p_list.iterkeys():
hid = str(j) # Because the database has been re-formated
try:
p_pos = p_list[j]
m_pos = m_list[j]
except:
continue
for p in p_pos:
left = get_pos_range(p, m_pos)
for pos_index in xrange(left, len(m_pos)):
f3_pos = p + 1
r3_pos = m_pos[pos_index]
# The amplicon size <= p.len + m.len
if f3_pos >= r3_pos:
continue
product_size = p_oligo_length + m_pos[
pos_index] - p + m_oligo_length - 1
if product_size < options.size_start:
continue
if product_size > options.size_stop:
break
p_start = p - p_oligo_length + 1
if p_start < 0:
p_start = 0
m_stop = r3_pos + m_oligo_length
if m_stop > fcdict[hid]['size']:
m_stop = fcdict[hid]['size']
binding_range.append('%s:%s-%s' %
(hid, p_start, p + 1))
# Reverse: Correction for reverse
binding_range.append('%s:%s-%s' %
(hid, r3_pos, m_stop))
amp = {
'hid': hid,
'pid': oligos[i]['id'],
'mid': oligos[k]['id'],
'plen': p_oligo_length,
'mlen': m_oligo_length,
'pseq': oligos[i]['seq'],
'mseq': Seq.rev_com(oligos[k]['seq']),
'size': product_size,
'f3_pos': f3_pos,
'r3_pos': r3_pos,
}
product.append(amp)
return product, binding_range
