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1 import argparse
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2 import sys
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3 # error
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4 def stop_err( msg ):
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5 sys.stderr.write( "%s\n" % msg )
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6 sys.exit()
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7
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8 # main
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9 def main():
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10 parser = argparse.ArgumentParser() #docs.python.org/dev/library/argparse.html
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11 parser.add_argument("--input", help="Input file(s)", nargs="+")
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12 parser.add_argument("--id", help="Input file(s) id's", nargs="+")
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13 parser.add_argument("--output", help="Output file")
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14
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15 args = parser.parse_args()
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16 try:
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17 o = open(args.output, 'w')
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18 i = open(args.input[-1], 'r')
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19 separator = "\t"
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20 newline = "\n"
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21 header = "Sample"
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22 line = i.readline()
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23 o.write(line[:line.rfind(newline)] + separator + header + newline) #write the header
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24 i.close()
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25
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26 for cf,i in zip(args.input,args.id):
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27 f = open(cf, 'r')
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28 line = f.readline()
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29 line = f.readline() #skip header
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30 while line:
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31 o.write(line[:line.rfind(newline)] + separator + i + newline)
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32 line = f.readline()
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33 f.close()
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34 o.close()
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35
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36 except Exception, ex:
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37 stop_err('Error running new_column.py\n' + str(ex))
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38 sys.exit(0)
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39
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40 if __name__ == "__main__":
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41 print sys.argv
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42 main()
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