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annotate consensus-time.py @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
parents af383638de66
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4
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1 #!/usr/bin/env python
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2 import sys
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3 import time
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4 import ctypes
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5
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6 first = None
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7 times = []
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8 for i in range(10000):
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9 py_seqs = []
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10 seq_len = 0
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11 with open(sys.argv[1]) as infile:
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12 for line in infile:
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13 if line.startswith('>'):
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14 continue
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15 seq = line.strip()
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16 if len(seq) > seq_len:
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17 seq_len = len(seq)
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18 py_seqs.append(seq)
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19
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20 seqs = (ctypes.c_char_p * len(py_seqs))()
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21 for j, seq in enumerate(py_seqs):
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22 seqs[j] = ctypes.c_char_p(seq)
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23
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24 consensus = ctypes.cdll.LoadLibrary('./consensus.so')
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25 start = time.time()
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26 consensus.get_votes(seqs, len(seqs), seq_len)
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27 elapsed = 1000 * 1000 * (time.time() - start)
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28 if i == 0:
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29 first = elapsed
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30 else:
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31 times.append(elapsed)
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32
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33 print '{:0.1f}\t{:0.1f}'.format(first, sum(times)/len(times))