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annotate offspring_heterozygosity.py @ 31:a631c2f6d913

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Update to Miller Lab devshed revision 3c4110ffacc3
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:25:27 -0400
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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 gd_util
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5
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6 from Population import Population
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7
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8 ################################################################################
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9
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10 if len(sys.argv) != 7:
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11 gd_util.die('Usage')
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12
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13 input, input_type, ind_arg, p1_input, p2_input, output = sys.argv[1:]
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14
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15 p_total = Population()
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16 p_total.from_wrapped_dict(ind_arg)
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17
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18 p1 = Population()
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19 p1.from_population_file(p1_input)
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20 if not p_total.is_superset(p1):
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21 gd_util.die('There is an individual in the first population that is not in the SNP table')
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22
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23 p2 = Population()
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24 p2.from_population_file(p2_input)
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25 if not p_total.is_superset(p2):
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26 gd_util.die('There is an individual in the second population that is not in the SNP table')
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27
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28 ################################################################################
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30 prog = 'offspring_heterozygosity'
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32 args = [ prog ]
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33 args.append(input) # a Galaxy SNP table
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34
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35 for tag in p1.tag_list():
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36 column, name = tag.split(':')
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37
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38 if input_type == 'gd_genotype':
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39 column = int(column) - 2
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41 tag = '{0}:{1}:{2}'.format(column, 0, name)
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42 args.append(tag)
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44 for tag in p2.tag_list():
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45 column, name = tag.split(':')
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47 if input_type == 'gd_genotype':
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48 column = int(column) - 2
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49
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50 tag = '{0}:{1}:{2}'.format(column, 1, name)
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51 args.append(tag)
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52
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53 with open(output, 'w') as fh:
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54 gd_util.run_program(prog, args, stdout=fh)
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55
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56 ################################################################################
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57
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58 sys.exit(0)
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59