pb_assembly/FALCON/falcon_kit/falcon_kit.py

__all__ = [
    'kup', 'DWA', 'falcon',
    'KmerLookup', 'KmerMatch', 'AlnRange', 'ConsensusData',
    'Alignment', 'get_alignment',
]

from ctypes import *
import os
import ext_falcon
#module_path = os.path.split(__file__)[0]


seq_coor_t = c_int
base_t = c_uint8


class KmerLookup(Structure):
    _fields_ = [("start", seq_coor_t),
                ("last", seq_coor_t),
                ("count", seq_coor_t)]


class KmerMatch(Structure):
    _fields_ = [("count", seq_coor_t),
                ("query_pos", POINTER(seq_coor_t)),
                ("target_pos", POINTER(seq_coor_t))]


class AlnRange(Structure):
    _fields_ = [("s1", seq_coor_t),
                ("e1", seq_coor_t),
                ("s2", seq_coor_t),
                ("e2", seq_coor_t),
                ("score", c_long)]


class ConsensusData(Structure):
    _fields_ = [("sequence", c_char_p),
                ("eff_cov", POINTER(c_uint))]


try:
    falcon_dll = CDLL(ext_falcon.__file__)
except OSError:
    # It seems that setup.py has changed the __file__ it attaches to an extension module.
    # I have no idea why or why, but this works around it.
    falcon_dll = CDLL(os.path.join(os.path.dirname(__file__),
                                   '..', os.path.basename(ext_falcon.__file__)))

kup = falcon_dll

kup.allocate_kmer_lookup.argtypes = [seq_coor_t]
kup.allocate_kmer_lookup.restype = POINTER(KmerLookup)
kup.init_kmer_lookup.argtypes = [POINTER(KmerLookup), seq_coor_t]
kup.free_kmer_lookup.argtypes = [POINTER(KmerLookup)]

kup.allocate_seq.argtypes = [seq_coor_t]
kup.allocate_seq.restype = POINTER(base_t)
kup.init_seq_array.argtypes = [POINTER(base_t), seq_coor_t]
kup.free_seq_array.argtypes = [POINTER(base_t)]

kup.allocate_seq_addr.argtypes = [seq_coor_t]
kup.allocate_seq_addr.restype = POINTER(seq_coor_t)
kup.free_seq_addr_array.argtypes = [POINTER(seq_coor_t)]

kup.add_sequence.argtypes = [seq_coor_t, c_uint, POINTER(c_char), seq_coor_t, POINTER(seq_coor_t),
                             POINTER(c_uint8), POINTER(KmerLookup)]
kup.mask_k_mer.argtypes = [c_long, POINTER(KmerLookup), c_long]
kup.find_kmer_pos_for_seq.argtypes = [POINTER(c_char), seq_coor_t, c_uint, POINTER(seq_coor_t),
                                      POINTER(KmerLookup)]
kup.find_kmer_pos_for_seq.restype = POINTER(KmerMatch)
kup.free_kmer_match.argtypes = [POINTER(KmerMatch)]


kup.find_best_aln_range.argtypes = [
    POINTER(KmerMatch), seq_coor_t, seq_coor_t, seq_coor_t]
kup.find_best_aln_range.restype = POINTER(AlnRange)
kup.find_best_aln_range2.argtypes = [
    POINTER(KmerMatch), seq_coor_t, seq_coor_t, seq_coor_t]
kup.find_best_aln_range2.restype = POINTER(AlnRange)
kup.free_aln_range.argtypes = [POINTER(AlnRange)]


class Alignment(Structure):
    """
    typedef struct {
        seq_coor_t aln_str_size ;
        seq_coor_t dist ;
        seq_coor_t aln_q_s;
        seq_coor_t aln_q_e;
        seq_coor_t aln_t_s;
        seq_coor_t aln_t_e;
        char * q_aln_str;
        char * t_aln_str;
    } alignment;
    """
    _fields_ = [("aln_str_size", seq_coor_t),
                ("dist", seq_coor_t),
                ("aln_q_s", seq_coor_t),
                ("aln_q_e", seq_coor_t),
                ("aln_t_s", seq_coor_t),
                ("aln_t_e", seq_coor_t),
                ("q_aln_str", c_char_p),
                ("t_aln_str", c_char_p)]


DWA = falcon_dll

DWA.align.argtypes = [POINTER(c_char), c_long, POINTER(
    c_char), c_long, c_long, c_int]
DWA.align.restype = POINTER(Alignment)
DWA.free_alignment.argtypes = [POINTER(Alignment)]


falcon = falcon_dll

falcon.generate_consensus.argtypes = [
    POINTER(c_char_p), c_uint, c_uint, c_uint, c_uint, c_uint, c_double]
falcon.generate_consensus.restype = POINTER(ConsensusData)
falcon.free_consensus_data.argtypes = [POINTER(ConsensusData)]


def get_alignment(seq1, seq0):
    K = 8
    lk_ptr = kup.allocate_kmer_lookup(1 << (K * 2))
    sa_ptr = kup.allocate_seq(len(seq0))
    sda_ptr = kup.allocate_seq_addr(len(seq0))
    kup.add_sequence(0, K, seq0, len(seq0), sda_ptr, sa_ptr, lk_ptr)

    kmer_match_ptr = kup.find_kmer_pos_for_seq(
        seq1, len(seq1), K, sda_ptr, lk_ptr)
    kmer_match = kmer_match_ptr[0]
    aln_range_ptr = kup.find_best_aln_range(kmer_match_ptr, K, K * 10, 50)
    #x,y = zip( * [ (kmer_match.query_pos[i], kmer_match.target_pos[i]) for i in range(kmer_match.count )] )
    kup.free_kmer_match(kmer_match_ptr)
    aln_range = aln_range_ptr[0]
    s1, e1, s2, e2 = aln_range.s1, aln_range.e1, aln_range.s2, aln_range.e2
    kup.free_aln_range(aln_range_ptr)

    if e1 - s1 > 500:
        #s1 = 0 if s1 < 14 else s1 - 14
        #s2 = 0 if s2 < 14 else s2 - 14
        e1 = len(seq1) if e1 >= len(seq1) - 2 * K else e1 + K * 2
        e2 = len(seq0) if e2 >= len(seq0) - 2 * K else e2 + K * 2

        alignment = DWA.align(seq1[s1:e1], e1 - s1,
                              seq0[s2:e2], e2 - s2,
                              100,
                              0)
        # print seq1[s1:e1]
        # print seq0[s2:e2]
        # if alignment[0].aln_str_size > 500:

        #aln_str1 = alignment[0].q_aln_str
        #aln_str0 = alignment[0].t_aln_str
        aln_size = alignment[0].aln_str_size
        aln_dist = alignment[0].dist
        aln_q_s = alignment[0].aln_q_s
        aln_q_e = alignment[0].aln_q_e
        aln_t_s = alignment[0].aln_t_s
        aln_t_e = alignment[0].aln_t_e

        # print "X,",alignment[0].aln_q_s, alignment[0].aln_q_e
        # print "Y,",alignment[0].aln_t_s, alignment[0].aln_t_e

        # print aln_str1
        # print aln_str0

        DWA.free_alignment(alignment)

    kup.free_seq_addr_array(sda_ptr)
    kup.free_seq_array(sa_ptr)
    kup.free_kmer_lookup(lk_ptr)
    if e1 - s1 > 500 and aln_size > 500:
        return s1, s1 + aln_q_e - aln_q_s, s2, s2 + aln_t_e - aln_t_s, aln_size, aln_dist
    else:
        return None