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annotate inbreeding_and_kinship.py @ 36:51cd0307fb70

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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
parents a631c2f6d913
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1 #!/usr/bin/env python
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3 import sys
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4 import gd_util
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6 ################################################################################
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8 if len(sys.argv) != 6:
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9 gd_util.die('Usage')
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11 ped_input, ind_input, computed_value, output, kinship_input = sys.argv[1:]
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13 ################################################################################
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15 prog = 'inbreed'
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17 args = [ prog ]
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18 args.append(ped_input) # pedigree
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19 args.append(ind_input) # specified individuals (e.g.,,potential breeding population)
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20 args.append(kinship_input) # kinships of founders
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21 args.append(computed_value) # 0 = inbreedng coefficients, 1 = kinships, 2 = mean kinships
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23 with open(output, 'w') as fh:
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24 gd_util.run_program(prog, args, stdout=fh)
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26 ################################################################################
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28 sys.exit(0)
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