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annotate test.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 from __future__ import division
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3 from __future__ import print_function
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4 import sys
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5 import argparse
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6 import subprocess
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7
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8 OPT_DEFAULTS = {}
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9 USAGE = "%(prog)s [options]"
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10 DESCRIPTION = """"""
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11
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12
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13 def main(argv):
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15 parser = argparse.ArgumentParser(description=DESCRIPTION)
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16 parser.set_defaults(**OPT_DEFAULTS)
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17
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18 parser.add_argument('file1')
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19 parser.add_argument('file2')
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21 args = parser.parse_args(argv[1:])
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22
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23 """
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24 cat $fastq1 | paste - - - - \
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25 | paste - <(cat $fastq2 | paste - - - -) \
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26 | awk -f make-barcodes.awk \
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27 | sort \
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28 | align_families.py \
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29 | dunovo.py \
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30 > $sscs
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31 """
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32
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33 cmd1 = subprocess.Popen(['cat', args.file1], stdout=subprocess.PIPE)
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34 cmd2 = subprocess.Popen(['cat', args.file2], stdout=subprocess.PIPE)
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36
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37 def fail(message):
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38 sys.stderr.write(message+"\n")
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39 sys.exit(1)
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41 if __name__ == '__main__':
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42 sys.exit(main(sys.argv))