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annotate swalign.py @ 18:e4d75f9efb90 draft

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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1 import os
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2 import ctypes
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3 import string
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4
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5 script_dir = os.path.dirname(os.path.realpath(__file__))
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6 swalign = ctypes.cdll.LoadLibrary(os.path.join(script_dir, 'libswalign.so'))
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7
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8 REVCOMP_TABLE = string.maketrans('acgtrymkbdhvACGTRYMKBDHV', 'tgcayrkmvhdbTGCAYRKMVHDB')
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9
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11 # C struct for ctypes
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12 class SeqPairC(ctypes.Structure):
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13 _fields_ = [
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14 ('a', ctypes.c_char_p),
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15 ('alen', ctypes.c_uint),
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16 ('b', ctypes.c_char_p),
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17 ('blen', ctypes.c_uint),
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18 ]
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20
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21 # C struct for ctypes
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22 class AlignC(ctypes.Structure):
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23 _fields_ = [
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24 ('seqs', ctypes.POINTER(SeqPairC)),
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25 ('start_a', ctypes.c_int),
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26 ('start_b', ctypes.c_int),
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27 ('end_a', ctypes.c_int),
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28 ('end_b', ctypes.c_int),
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29 ('matches', ctypes.c_int),
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30 ('score', ctypes.c_double),
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31 ]
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33
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34 # The Python version
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35 class Align(object):
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36 def __init__(self, align_c):
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37 self.target = align_c.seqs.contents.a
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38 self.query = align_c.seqs.contents.b
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39 # Where the first base of the target aligns on the query, in query coordinates (or 1, if <= 0).
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40 self.start_target = align_c.start_a
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41 # Where the first base of the query aligns on the target, in target coordinates (or 1, if <= 0).
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42 self.start_query = align_c.start_b
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43 # Where the last base of the target aligns on the query, in query coordinates.
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44 self.end_target = align_c.end_a
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45 # Where the last base of the query aligns on the target, in target coordinates.
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46 self.end_query = align_c.end_b
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47 self.matches = align_c.matches
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48 self.score = align_c.score
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49
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50 # Provide this common function.
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51 def __str__(self):
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52 """Print a human-readable representation of the alignment."""
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53 start_query = str(self.start_query)
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54 start_target = str(self.start_target)
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55 start_width = str(max(len(start_query), len(start_target)))
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56 line_format = '{:'+start_width+'} {} {}'
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57 output = line_format.format(start_target, self.target, self.end_target) + '\n'
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58 output += line_format.format(start_query, self.query, self.end_query)
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59 return output
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61
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62 # Initialize functions (define types).
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63 swalign.smith_waterman.restype = ctypes.POINTER(AlignC)
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64 swalign.revcomp.restype = ctypes.c_char_p
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66
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67 def smith_waterman(target, query):
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68 seq_pair = SeqPairC(target, len(target), query, len(query))
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69 align_c = swalign.smith_waterman(ctypes.pointer(seq_pair), 1).contents
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70 return Align(align_c)
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72
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73 def smith_waterman_duplex(target, query):
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74 """Smith-Waterman align query to target in both orientations and return the best.
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75 Convenience function that calls smith_waterman() twice, and returns the
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76 alignment with the highest score."""
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77 align = smith_waterman(target, query)
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78 query_rc = revcomp(query)
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79 align_rc = smith_waterman(target, query_rc)
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80 if align_rc.score > align.score:
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81 return align_rc
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82 else:
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83 return align
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84
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85
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86 def revcomp(seq):
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87 """Return the reverse complement of the input sequence.
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88 Leaves the input string unaltered."""
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89 return seq.translate(REVCOMP_TABLE)[::-1]
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90
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91
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92 def revcomp_inplace(seq):
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93 """Convert the input sequence to its reverse complement.
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94 WARNING: This will alter the input string in-place!"""
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95 swalign.revcomp(seq)