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annotate consensus.py @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #!/usr/bin/env python
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2 import os
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3 import sys
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4 import ctypes
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5 import argparse
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6
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7 script_dir = os.path.dirname(os.path.realpath(__file__))
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8 consensus = ctypes.cdll.LoadLibrary(os.path.join(script_dir, 'libconsensus.so'))
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9 consensus.get_consensus.restype = ctypes.c_char_p
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10 consensus.get_consensus_duplex.restype = ctypes.c_char_p
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11 consensus.build_consensus_duplex_simple.restype = ctypes.c_char_p
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12
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13 ARG_DEFAULTS = {'alignment':sys.stdin}
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14 DESCRIPTION = "Get the consensus of a set of aligned sequences."
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15
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16
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17 def make_argparser():
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18 parser = argparse.ArgumentParser(description=DESCRIPTION)
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19 parser.set_defaults(**ARG_DEFAULTS)
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20 parser.add_argument('alignment', type=argparse.FileType('r'),
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21 help='The aligned sequences, in FASTA format (but no multi-line sequences).')
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22 return parser
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23
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24
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25 def main(argv):
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26 parser = make_argparser()
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27 args = parser.parse_args(argv[1:])
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28 sequences = []
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29 line_num = 0
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30 for line in args.alignment:
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31 line_num += 1
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32 if line_num % 2 == 0:
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33 sequences.append(line.rstrip('\r\n'))
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34 cons = get_consensus(sequences)
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35 print(cons)
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36
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37
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38 # N.B.: The quality scores must be aligned with their accompanying sequences.
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39 def get_consensus(align, quals=[], cons_thres=-1.0, qual_thres=' ', gapped=False):
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40 cons_thres_c = ctypes.c_double(cons_thres)
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41 qual_thres_c = ctypes.c_char(qual_thres)
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42 n_seqs = len(align)
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43 if gapped:
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44 gapped_c = 1
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45 else:
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46 gapped_c = 0
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47 assert not quals or len(quals) == n_seqs, 'Different number of sequences and quals.'
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48 seq_len = None
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49 for seq in (align + quals):
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50 if seq_len is None:
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51 seq_len = len(seq)
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52 else:
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53 assert seq_len == len(seq), ('All sequences in the alignment must be the same length: '
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54 '{}bp != {}bp.\nAlignment:\n{}'.format(seq_len, len(seq),
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55 '\n'.join(align)))
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56 align_c = (ctypes.c_char_p * n_seqs)()
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57 for i, seq in enumerate(align):
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58 align_c[i] = ctypes.c_char_p(seq)
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59 quals_c = (ctypes.c_char_p * n_seqs)()
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60 for i, qual in enumerate(quals):
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61 quals_c[i] = ctypes.c_char_p(qual)
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62 if not quals:
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63 quals_c = 0
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64 return consensus.get_consensus(align_c, quals_c, n_seqs, seq_len, cons_thres_c, qual_thres_c,
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65 gapped_c)
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66
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67
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68 # N.B.: The quality scores must be aligned with their accompanying sequences.
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69 def get_consensus_duplex(align1, align2, quals1=[], quals2=[], cons_thres=-1.0, qual_thres=' ',
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70 method='iupac'):
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71 assert method in ('iupac', 'freq')
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72 cons_thres_c = ctypes.c_double(cons_thres)
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73 qual_thres_c = ctypes.c_char(qual_thres)
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74 n_seqs1 = len(align1)
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75 n_seqs2 = len(align2)
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76 assert (not quals1 and not quals2) or (quals1 and quals2)
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77 assert not quals1 or len(quals1) == n_seqs1
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78 assert not quals2 or len(quals2) == n_seqs2
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79 seq_len = None
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80 for seq in (align1 + align2 + quals1 + quals2):
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81 if seq_len is None:
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82 seq_len = len(seq)
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83 else:
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84 assert seq_len == len(seq), 'All sequences in the alignment must be the same length.'
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85 align1_c = (ctypes.c_char_p * n_seqs1)()
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86 for i, seq in enumerate(align1):
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87 align1_c[i] = ctypes.c_char_p(seq)
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88 align2_c = (ctypes.c_char_p * n_seqs1)()
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89 for i, seq in enumerate(align2):
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90 align2_c[i] = ctypes.c_char_p(seq)
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91 quals1_c = (ctypes.c_char_p * n_seqs1)()
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92 for i, seq in enumerate(quals1):
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93 quals1_c[i] = ctypes.c_char_p(seq)
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94 quals2_c = (ctypes.c_char_p * n_seqs1)()
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95 for i, seq in enumerate(quals2):
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96 quals2_c[i] = ctypes.c_char_p(seq)
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97 if not quals1:
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98 quals1_c = 0
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99 if not quals2:
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100 quals2_c = 0
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101 return consensus.get_consensus_duplex(align1_c, align2_c, quals1_c, quals2_c, n_seqs1, n_seqs2,
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102 seq_len, cons_thres_c, qual_thres_c, method)
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103
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104
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105 def build_consensus_duplex_simple(cons1, cons2, gapped=False):
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106 assert len(cons1) == len(cons2)
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107 cons1_c = ctypes.c_char_p(cons1)
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108 cons2_c = ctypes.c_char_p(cons2)
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109 if gapped:
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110 gapped_c = 1
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111 else:
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112 gapped_c = 0
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113 return consensus.build_consensus_duplex_simple(cons1_c, cons2_c, gapped_c)
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114
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115
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116 if __name__ == '__main__':
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117 sys.exit(main(sys.argv))