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annotate seqtools.py @ 4:af383638de66 draft

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author nick
date Mon, 23 Nov 2015 18:44:23 -0500
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1 import os
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2 import ctypes
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3
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4 script_dir = os.path.dirname(os.path.realpath(__file__))
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5 seqtools = ctypes.cdll.LoadLibrary(os.path.join(script_dir, 'seqtoolsc.so'))
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6 seqtools.get_revcomp.restype = ctypes.c_char_p
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7 seqtools.transfer_gaps.restype = ctypes.c_char_p
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9
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10 def get_revcomp(seq):
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11 return seqtools.get_revcomp(seq)
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14 def get_diffs_frac_simple(consensus, family):
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15 c_consensus = ctypes.c_char_p(consensus)
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16 c_family = (ctypes.c_char_p * len(family))()
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17 for i, seq in enumerate(family):
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18 c_family[i] = ctypes.c_char_p(seq)
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19 seqtools.get_diffs_frac_simple.restype = ctypes.POINTER(ctypes.c_double * len(c_family))
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20 diffs = seqtools.get_diffs_frac_simple(c_consensus, c_family, len(c_family))
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21 return diffs.contents
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23
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24 def get_diffs_frac_binned(consensus, family, bins):
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25 seq_len = None
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26 c_consensus = ctypes.c_char_p(consensus)
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27 c_family = (ctypes.c_char_p * len(family))()
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28 for i, seq in enumerate(family):
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29 if seq_len:
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30 if seq_len != len(seq):
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31 return None
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32 else:
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33 seq_len = len(seq)
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34 c_family[i] = ctypes.c_char_p(seq)
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35 double_array_pointer = ctypes.POINTER(ctypes.c_double * bins)
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36 seqtools.get_diffs_frac_binned.restype = ctypes.POINTER(double_array_pointer * len(c_family))
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37 diffs_binned_c = seqtools.get_diffs_frac_binned(c_consensus, c_family, len(c_family), seq_len, bins)
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38 diffs_binned = []
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39 for diffs_c in diffs_binned_c.contents:
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40 diffs_binned.append(diffs_c.contents)
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41 return diffs_binned
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44 def transfer_gaps(aligned, seq, gap_char_in='-', gap_char_out='-'):
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45 gap_char_in_c = ctypes.c_char(gap_char_in)
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46 gap_char_out_c = ctypes.c_char(gap_char_out)
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47 return seqtools.transfer_gaps(aligned, seq, gap_char_in_c, gap_char_out_c)
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49
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50 def transfer_gaps_multi(seqs, aligned, gap_char_in='-', gap_char_out='-'):
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51 gap_char_in_c = ctypes.c_char(gap_char_in)
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52 gap_char_out_c = ctypes.c_char(gap_char_out)
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53 n_seqs = len(seqs)
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54 assert n_seqs == len(aligned), 'Error: Unequal number of gapped and ungapped sequences.'
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55 seqs_c = (ctypes.c_char_p * n_seqs)()
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56 for i, seq in enumerate(seqs):
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57 seqs_c[i] = ctypes.c_char_p(seq)
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58 aligned_c = (ctypes.c_char_p * n_seqs)()
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59 for i, seq in enumerate(aligned):
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60 aligned_c[i] = ctypes.c_char_p(seq)
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61 seqtools.transfer_gaps_multi.restype = ctypes.POINTER(ctypes.c_char_p * n_seqs)
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62 output_c = seqtools.transfer_gaps_multi(n_seqs, aligned_c, seqs_c, gap_char_in_c, gap_char_out_c)
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63 output = []
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64 for seq in output_c.contents:
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65 output.append(seq)
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66 return output