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1 #!/usr/bin/env python
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2
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3 import sys
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4 import argparse
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5
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6 def main():
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7
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8 VERSION = 0.1
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9
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10 parser = argparse.ArgumentParser(description="Calculates the means of rows of a numeric tab delimited table.")
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11 parser.add_argument("-i", "--infile", help="Input tab delimted numeric file")
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12 parser.add_argument("-o", "--outfile", help="Output list of means")
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13 parser.add_argument("-s", "--skip", default=0, help="Number of header rows to skip", type=int)
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14 parser.add_argument("--version", action='store_true')
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15
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16 args = parser.parse_args()
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17
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18 if args.version:
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19 print("means_by_row.py version: %.1f" % VERSION)
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20 return
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21
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22 infile = str(args.infile)
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23 outfile = str(args.outfile)
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24 skip = int(args.skip)
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25
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26 lines = open( infile, 'r').readlines()
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27
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28 averages = []
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29 linenum = 0
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30
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31 for line in lines:
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32 if int(skip) > 0:
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33 skip -= 1
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34 continue
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35 line.rstrip()
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36 sum = 0.0
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37 count = 0.0
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38 units = line.split('\t')
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39 for unit in units:
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40 try:
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41 unit = float(unit)
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42 sum += unit
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43 count += 1
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44 except:
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45 print("WARNING: Non numeric found at line %f.1" % linenum)
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46 continue
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47 avg = 0
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48 if count > 0:
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49 avg = sum/count
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50 averages.append(avg)
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51 linenum += 1
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52
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53 fout = open(outfile, 'w')
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54 fout.write("Sample_Average\n")
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55
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56 for avg in averages:
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57 fout.write(str('%.3f' % avg)+ '\n')
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58
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59 return
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60
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61 if __name__ == "__main__": main()
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