Mercurial > repos > miller-lab > genome_diversity
annotate aggregate_gd_indivs.py @ 23:66a183c44dd5
bugfix for Pathway Image tool
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Wed, 22 May 2013 15:58:18 -0400 |
parents | 95a05c1ef5d5 |
children | 91e835060ad2 |
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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 subprocess |
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5 from Population import Population |
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6 |
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7 ################################################################################ |
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8 |
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9 if len(sys.argv) < 9: |
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10 print >> sys.stderr, "Usage" |
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11 sys.exit(1) |
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12 |
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13 #input, p1_input, output, lo, hi, lo_ind, lo_ind_qual = sys.argv[1:8] |
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14 #individual_metadata = sys.argv[8:] |
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15 input, p1_input, output, = sys.argv[1:4] |
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16 individual_metadata = sys.argv[4:] |
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17 |
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18 p_total = Population() |
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19 p_total.from_tag_list(individual_metadata) |
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20 |
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21 p1 = Population() |
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22 p1.from_population_file(p1_input) |
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23 |
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24 if not p_total.is_superset(p1): |
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25 print >> sys.stderr, 'There is an individual in the population that is not in the SNP table' |
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26 sys.exit(1) |
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27 |
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28 ################################################################################ |
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29 |
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30 prog = 'aggregate' |
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31 |
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32 args = [] |
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33 args.append(prog) |
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34 args.append(input) |
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35 |
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36 columns = p1.column_list() |
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37 |
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38 for column in sorted(columns): |
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39 args.append(column) |
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40 |
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41 fh = open(output, 'w') |
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42 |
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43 #print "args:", ' '.join(args) |
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44 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr) |
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45 rc = p.wait() |
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46 fh.close() |
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47 |
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48 sys.exit(0) |
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49 |