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1 import sys
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2 # error
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3 def stop_err( msg ):
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4 sys.stderr.write( "%s\n" % msg )
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5 sys.exit()
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6
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7 # main
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8 def main():
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9 args = sys.argv[1:-2]
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10
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11 try:
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12 o = open(sys.argv[-1], 'w')
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13 i = open(args[1], 'r')
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14 separator = "\t"
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15 newline = "\n"
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16 line = i.readline()
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17 #write the header
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18 o.write(line[:line.rfind(newline)] + separator + "Sample" + separator + "Replicate" + newline)
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19 i.close()
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20
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21 current = 1
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22 sampleID = args[0]
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23 count = 1
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24
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25 while True:
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26 print str(o)
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27 f = open(args[current], 'r')
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28 line = f.readline()
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29 line = f.readline()
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30 while line:
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31 o.write(line[:line.rfind(newline)] + separator + sampleID + separator + str(count) + newline)
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32 line = f.readline()
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33 f.close()
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34
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35 if current >= (len(args) - 1):
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36 break
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37 if args[current + 1].find("/") is -1:
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38 sampleID = args[current + 1]
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39 current += 1
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40 count = 1
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41 else:
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42 count += 1
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43 current += 1
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44 o.close()
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45
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46 except Exception, ex:
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47 stop_err('Error running new_column.py\n' + str(ex))
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48 sys.exit(0)
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49
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50 if __name__ == "__main__":
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51 print sys.argv
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52 main()
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