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annotate add_fst_column.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 8997f2ca8c7a
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1 #!/usr/bin/env python
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3 import gd_util
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4 import sys
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5 from Population import Population
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6
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7 ################################################################################
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9 if len(sys.argv) != 13:
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10 gd_util.die('Usage')
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12 input, p1_input, p2_input, input_type, data_source, min_reads, min_qual, retain, discard_fixed, biased, output, ind_arg = sys.argv[1:]
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14 p_total = Population()
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15 p_total.from_wrapped_dict(ind_arg)
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17 p1 = Population()
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18 p1.from_population_file(p1_input)
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19 if not p_total.is_superset(p1):
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20 gd_util.die('There is an individual in population 1 that is not in the SNP table')
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22 p2 = Population()
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23 p2.from_population_file(p2_input)
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24 if not p_total.is_superset(p2):
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25 gd_util.die('There is an individual in population 2 that is not in the SNP table')
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27 ################################################################################
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29 prog = 'Fst_column'
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31 args = [ prog ]
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32 args.append(input)
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33 args.append(data_source)
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34 args.append(min_reads)
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35 args.append(min_qual)
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36 args.append(retain)
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37 args.append(discard_fixed)
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38 args.append(biased)
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40 columns = p1.column_list()
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41 for column in columns:
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42 if input_type == 'gd_genotype':
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43 column = int(column) - 2
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44 args.append('{0}:1'.format(column))
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46 columns = p2.column_list()
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47 for column in columns:
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48 if input_type == 'gd_genotype':
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49 column = int(column) - 2
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50 args.append('{0}:2'.format(column))
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52 with open(output, 'w') as fh:
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53 gd_util.run_program(prog, args, stdout=fh)
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55 sys.exit(0)
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