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annotate utils/subsample.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 from __future__ import division
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3 import sys
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4 import random
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5 import argparse
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6
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7 OPT_DEFAULTS = {'fraction':0.1, 'seed':1}
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8 USAGE = "%(prog)s [options]"
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9 DESCRIPTION = """"""
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10
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11 def main(argv):
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12
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13 parser = argparse.ArgumentParser(description=DESCRIPTION)
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14 parser.set_defaults(**OPT_DEFAULTS)
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15
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16 parser.add_argument('infile', metavar='read-families.tsv', nargs='?',
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17 help='The input reads, sorted into families.')
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18 parser.add_argument('-f', '--fraction', type=float,
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19 help='Fraction of families to output. Default: %(default)s')
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20 parser.add_argument('-s', '--seed', type=int,
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21 help='Random number generator seed. Default: %(default)s')
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22
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23 args = parser.parse_args(argv[1:])
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24
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25 random.seed(args.seed)
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26
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27 if args.infile:
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28 infile = open(args.infile)
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29 else:
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30 infile = sys.stdin
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31
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32 family = []
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33 last_barcode = None
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34 for line in infile:
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35 fields = line.rstrip('\r\n').split('\t')
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36 if not fields:
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37 continue
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38 barcode = fields[0]
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39 if barcode != last_barcode:
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40 if random.random() <= args.fraction:
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41 sys.stdout.write(''.join(family))
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42 family = []
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43 family.append(line)
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44 last_barcode = barcode
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45
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46 if infile is not sys.stdin:
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47 infile.close()
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49
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50 def fail(message):
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51 sys.stderr.write(message+"\n")
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52 sys.exit(1)
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53
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54 if __name__ == '__main__':
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55 sys.exit(main(sys.argv))