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import re, sys, os
from libc.stdlib cimport malloc, free
from libc.stdint cimport uint8_t
from collections import defaultdict as dd
cimport cython
from cabpoa cimport *
from libc.string cimport strcpy
cdef class msa_result:
cdef int n_seq
cdef int n_cons
cdef clu_n_seq, clu_read_ids, cons_len, cons_seq, cons_cov # _cons_len:[int], _cons_seq:['']
cdef int msa_len
cdef msa_seq # _msa_seq:['']
def __cinit__(self, n_seq, n_cons, clu_n_seq, clu_read_ids, cons_len, cons_seq, cons_cov, msa_len, msa_seq):
self.n_seq = n_seq
self.n_cons = n_cons
self.clu_n_seq = clu_n_seq
self.clu_read_ids = clu_read_ids
self.cons_len = cons_len
self.cons_seq = cons_seq
self.cons_cov = cons_cov
self.msa_len = msa_len
self.msa_seq = msa_seq
@property
def n_seq(self): return self.n_seq
@property
def n_cons(self): return self.n_cons
@property
def clu_n_seq(self): return self.clu_n_seq
@property
def clu_read_ids(self): return self.clu_read_ids
@property
def cons_len(self): return self.cons_len
@property
def cons_seq(self): return self.cons_seq
@property
def cons_cov(self): return self.cons_cov
@property
def msa_len(self): return self.msa_len
@property
def msa_seq(self): return self.msa_seq
def print_msa(self):
if not self.msa_seq: return
for i, s in enumerate(self.msa_seq):
if i < self.n_seq:
print('>Seq_{}'.format(i+1))
else:
if self.n_cons > 1:
cons_id = '_{} {}'.format(i-self.n_seq+1, ','.join(list(map(str, self.clu_read_ids[i-self.n_seq]))))
else:
cons_id = ''
print('>Consensus_sequence{}'.format(cons_id))
print(s)
return
def set_seq_int_dict(m):
if m == 5: # ACGTN ==> 01234, U ==> 4
seqs = 'ACGUTN'
ints = [0, 1, 2, 3, 3, 4]
elif m == 27: # ACGTN ==> 01234, BDEFH... ==> 56789...
seqs = 'ACGTNBDEFHIJKLMOPQRSUVWXYZ*'
ints = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]
else:
raise Exception('Unexpected m: {}'.format(m))
seq2int_dict = dd(lambda: m-1)
int2seq_dict = dd(lambda: '-')
for s, i in zip(seqs, ints):
seq2int_dict[s] = i
seq2int_dict[s.lower()] = i
int2seq_dict[i] = s
return seq2int_dict, int2seq_dict
cdef class msa_aligner:
cdef abpoa_t *ab
cdef abpoa_para_t abpt
cdef seq2int_dict, int2seq_dict
cdef char* _score_mat_fn
cdef bytes _score_mat_fn_b
def __cinit__(self, aln_mode='g', is_aa=False,
match=2, mismatch=4, score_matrix=b'', gap_open1=4, gap_open2=24, gap_ext1=2, gap_ext2=1,
extra_b=10, extra_f=0.01,
cons_algrm='HB'):
self.ab = abpoa_init()
if aln_mode == 'g':
self.abpt.align_mode = ABPOA_GLOBAL_MODE
elif aln_mode == 'l':
self.abpt.align_mode = ABPOA_LOCAL_MODE
elif aln_mode == 'e':
self.abpt.align_mode = ABPOA_EXTEND_MODE
else:
raise Exception('Unknown align mode: {}'.format(aln_mode))
if is_aa:
self.abpt.m = 27
self.abpt.mat = <int*>malloc(27 * 27 * cython.sizeof(int))
else:
self.abpt.m = 5
self.abpt.mat = <int*>malloc(25 * cython.sizeof(int))
self.abpt.match = match
self.abpt.mismatch = mismatch
if score_matrix:
self.abpt.use_score_matrix = 1
_score_mat_fn_b = score_matrix.encode('utf-8')
_score_mat_fn = <char*> malloc(len(_score_mat_fn_b) + 1)
strcpy(_score_mat_fn, _score_mat_fn_b)
self.abpt.mat_fn = _score_mat_fn
self.abpt.gap_open1 = gap_open1
self.abpt.gap_open2 = gap_open2
self.abpt.gap_ext1 = gap_ext1
self.abpt.gap_ext2 = gap_ext2
self.abpt.ret_cigar = 1
self.abpt.wb = extra_b
self.abpt.wf = extra_f
self.abpt.use_qv = 0
self.abpt.end_bonus = -1 # disable end_bonus/zdrop
self.abpt.zdrop = -1
self.abpt.disable_seeding = 1
self.abpt.progressive_poa = 0
if cons_algrm.upper() == 'MF':
self.abpt.cons_algrm = ABPOA_MF
elif cons_algrm.upper() == 'HB':
self.abpt.cons_algrm = ABPOA_HB
else:
raise Exception('Unknown conseneus calling mode: {}'.format(cons_algrm))
self.seq2int_dict, self.int2seq_dict = set_seq_int_dict(self.abpt.m)
def __dealloc__(self):
free(self.abpt.mat)
abpoa_free(self.ab)
def __bool__(self):
return self.ab != NULL
def msa(self, seqs, out_cons, out_msa, max_n_cons=1, min_freq=0.25, out_pog=b'', incr_fn=b''):
cdef int seq_n = len(seqs)
cdef int exist_n = 0
cdef int tot_n = seq_n
cdef uint8_t *bseq
cdef abpoa_res_t res
cdef abpoa_cons_t abc
if out_cons: self.abpt.out_cons = 1
else: self.abpt.out_cons = 0
if out_msa: self.abpt.out_msa = 1
else: self.abpt.out_msa = 0
if max_n_cons < 1 or max_n_cons > 2:
raise Exception('Error: max number of consensus sequences should be 1 or 2.')
self.abpt.max_n_cons = max_n_cons
self.abpt.min_freq = min_freq
if out_pog:
if isinstance(out_pog, str): out_pog = bytes(out_pog, 'utf-8')
self.abpt.out_pog = out_pog
else: self.abpt.out_pog = NULL
abpoa_post_set_para(&self.abpt)
abpoa_reset(self.ab, &self.abpt, len(seqs[0]))
if incr_fn:
if isinstance(incr_fn, str):
incr_fn = bytes(incr_fn, 'utf-8')
self.abpt.incr_fn = incr_fn
abpoa_restore_graph(self.ab, &self.abpt)
exist_n = self.ab[0].abs[0].n_seq
tot_n += exist_n
else:
self.abpt.incr_fn = NULL
self.ab[0].abs[0].n_seq += seq_n
for read_i, seq in enumerate(seqs):
seq_l = len(seq)
bseq = <uint8_t*>malloc(seq_l * cython.sizeof(uint8_t))
for i in range(seq_l):
bseq[i] = self.seq2int_dict[seq[i]]
res.n_cigar = 0
abpoa_align_sequence_to_graph(self.ab, &self.abpt, bseq, seq_l, &res)
abpoa_add_graph_alignment(self.ab, &self.abpt, bseq, NULL, seq_l, NULL, res, exist_n+read_i, tot_n, 1)
free(bseq)
if res.n_cigar: free(res.graph_cigar)
if self.abpt.out_msa:
abpoa_generate_rc_msa(self.ab, &self.abpt)
elif self.abpt.out_cons:
abpoa_generate_consensus(self.ab, &self.abpt)
abc = self.ab[0].abc[0]
n_cons, clu_n_seq, clu_read_ids, cons_len, cons_seq, cons_cov, msa_len, msa_seq = 0, [], [], [], [], [], 0, []
n_cons = abc.n_cons
for i in range(n_cons):
clu_n_seq.append(abc.clu_n_seq[i])
cons_len.append(abc.cons_len[i])
clu_read_ids1, cons_seq1, cons_cov1 = [], '', []
for j in range(abc.clu_n_seq[i]):
clu_read_ids1.append(abc.clu_read_ids[i][j])
clu_read_ids.append(clu_read_ids1)
for j in range(abc.cons_len[i]):
c = abc.cons_base[i][j]
if isinstance(c, bytes): c = ord(c)
cons_seq1 += self.int2seq_dict[c]
cons_cov1.append(abc.cons_cov[i][j])
cons_seq.append(cons_seq1)
cons_cov.append(cons_cov1)
msa_len = abc.msa_len
if msa_len > 0:
for i in range(abc.n_seq + n_cons):
msa_seq1 = ''
for c in abc.msa_base[i][:msa_len]:
if isinstance(c, bytes): c = ord(c)
msa_seq1 += self.int2seq_dict[c]
msa_seq.append(msa_seq1)
if self.abpt.out_pog:
abpoa_dump_pog(self.ab, &self.abpt)
return msa_result(tot_n, n_cons, clu_n_seq, clu_read_ids, cons_len, cons_seq, cons_cov, msa_len, msa_seq)
def msa_align(self, seqs, out_cons, out_msa, max_n_cons=1, min_freq=0.25, incr_fn=b''):
cdef int seq_n = len(seqs)
cdef int exist_n = 0
cdef int tot_n = seq_n
cdef uint8_t *bseq
cdef abpoa_res_t res
cdef abpoa_cons_t abc
if out_cons: self.abpt.out_cons = 1
else: self.abpt.out_cons = 0
if out_msa: self.abpt.out_msa = 1
else: self.abpt.out_msa = 0
if max_n_cons < 1 or max_n_cons > 2:
raise Exception('Error: max number of consensus sequences should be 1 or 2.')
self.abpt.max_n_cons = max_n_cons
self.abpt.min_freq = min_freq
abpoa_post_set_para(&self.abpt)
abpoa_reset(self.ab, &self.abpt, len(seqs[0]))
if incr_fn:
if isinstance(incr_fn, str):
incr_fn = bytes(incr_fn, 'utf-8')
self.abpt.incr_fn = incr_fn
abpoa_restore_graph(self.ab, &self.abpt)
exist_n = self.ab[0].abs[0].n_seq
tot_n += exist_n
else:
self.abpt.incr_fn = NULL
self.ab[0].abs[0].n_seq += seq_n
for read_i, seq in enumerate(seqs):
seq_l = len(seq)
bseq = <uint8_t*>malloc(seq_l * cython.sizeof(uint8_t))
for i in range(seq_l):
bseq[i] = self.seq2int_dict[seq[i]]
res.n_cigar = 0
abpoa_align_sequence_to_graph(self.ab, &self.abpt, bseq, seq_l, &res)
abpoa_add_graph_alignment(self.ab, &self.abpt, bseq, NULL, seq_l, NULL, res, exist_n+read_i, tot_n, 1)
free(bseq)
if res.n_cigar: free(res.graph_cigar)
return self
def msa_add(self, new_seqs):
if isinstance(new_seqs, str):
raise TypeError('Expected a list of strings. If you want to add a single sequence, pass it as a list: ["ACGT..."]')
cdef int exist_n = 0
exist_n = self.ab[0].abs[0].n_seq
if (exist_n == 0):
raise Exception('Error: no existing sequences in the graph. Please run msa() or msa_align() first.')
cdef int seq_n = len(new_seqs)
cdef int tot_n = seq_n
cdef uint8_t *bseq
cdef abpoa_res_t res
cdef abpoa_cons_t abc
tot_n += exist_n
self.ab[0].abs[0].n_seq += seq_n
for read_i, seq in enumerate(new_seqs):
seq_l = len(seq)
bseq = <uint8_t*>malloc(seq_l * cython.sizeof(uint8_t))
for i in range(seq_l):
bseq[i] = self.seq2int_dict[seq[i]]
res.n_cigar = 0
abpoa_align_sequence_to_graph(self.ab, &self.abpt, bseq, seq_l, &res)
abpoa_add_graph_alignment(self.ab, &self.abpt, bseq, NULL, seq_l, NULL, res, exist_n+read_i, tot_n, 1)
free(bseq)
if res.n_cigar: free(res.graph_cigar)
return self
def msa_output(self):
if self.abpt.out_msa:
abpoa_generate_rc_msa(self.ab, &self.abpt)
elif self.abpt.out_cons:
abpoa_generate_consensus(self.ab, &self.abpt)
seq_n = self.ab[0].abs[0].n_seq
abc = self.ab[0].abc[0]
n_cons, clu_n_seq, clu_read_ids, cons_len, cons_seq, cons_cov, msa_len, msa_seq = 0, [], [], [], [], [], 0, []
n_cons = abc.n_cons
for i in range(n_cons):
clu_n_seq.append(abc.clu_n_seq[i])
cons_len.append(abc.cons_len[i])
clu_read_ids1, cons_seq1, cons_cov1 = [], '', []
for j in range(abc.clu_n_seq[i]):
clu_read_ids1.append(abc.clu_read_ids[i][j])
clu_read_ids.append(clu_read_ids1)
for j in range(abc.cons_len[i]):
c = abc.cons_base[i][j]
if isinstance(c, bytes): c = ord(c)
cons_seq1 += self.int2seq_dict[c]
cons_cov1.append(abc.cons_cov[i][j])
cons_seq.append(cons_seq1)
cons_cov.append(cons_cov1)
msa_len = abc.msa_len
if msa_len > 0:
for i in range(abc.n_seq + n_cons):
msa_seq1 = ''
for c in abc.msa_base[i][:msa_len]:
if isinstance(c, bytes): c = ord(c)
msa_seq1 += self.int2seq_dict[c]
msa_seq.append(msa_seq1)
return msa_result(seq_n, n_cons, clu_n_seq, clu_read_ids, cons_len, cons_seq, cons_cov, msa_len, msa_seq)
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