Mercurial > repos > miller-lab > genome_diversity

annotate draw_variants.py @ 26:91e835060ad2

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Updates to Admixture, Aggregate Individuals, and Restore Attributes to support gd_genotype
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 03 Jun 2013 12:29:29 -0400
parents 248b06e86022
children 8997f2ca8c7a
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248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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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 def run_program(prog, args, stdout_file=None, space_to_tab=False):
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8 #print "args: ", ' '.join(args)
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9 p = subprocess.Popen(args, bufsize=-1, executable=prog, stdin=None, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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10 (stdoutdata, stderrdata) = p.communicate()
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11 rc = p.returncode
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12
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13 if stdout_file is not None:
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14 with open(stdout_file, 'w') as ofh:
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15 lines = stdoutdata.split('\n')
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16 for line in lines:
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17 line = line.strip()
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18 if line:
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19 if space_to_tab:
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20 line = line.replace(' ', '\t')
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21 print >> ofh, line
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22
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23 if rc != 0:
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24 print >> sys.stderr, "FAILED: rc={0}: {1}".format(rc, ' '.join(args))
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25 print >> sys.stderr, stderrdata
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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 if len(sys.argv) < 10:
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31 print >> sys.stderr, "Usage"
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32 sys.exit(1)
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33
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34 snp_input, indel_input, coverage_input, annotation_input, indiv_input, ref_name, min_coverage, output = sys.argv[1:9]
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35 individual_metadata = sys.argv[9:]
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36
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37 p_total = Population()
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38 p_total.from_tag_list(individual_metadata)
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39
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40 p1 = Population()
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41 p1.from_population_file(indiv_input)
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42 if not p_total.is_superset(p1):
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43 print >> sys.stderr, 'There is an individual in the population individuals that is not in the SNP table'
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44 sys.exit(1)
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45
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46 ################################################################################
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47
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48 prog = 'mk_Ji'
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49
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50 args = [ prog ]
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51
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52 args.append(snp_input)
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53 args.append(indel_input)
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54 args.append(coverage_input)
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55 args.append(annotation_input)
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56 args.append(min_coverage)
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57 args.append(ref_name)
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58
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59 for tag in p1.tag_list():
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60 args.append(tag)
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61
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62 run_program(prog, args, stdout_file='mk_Ji.out')
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63
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64 ################################################################################
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65
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66 prog = 'varplot'
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67
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68 args = [ prog ]
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69 args.append('-w')
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70 args.append('3')
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71 args.append('-s')
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72 args.append('0.3')
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73 args.append('-g')
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74 args.append('0.2')
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75 args.append('mk_Ji.out')
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76
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77 run_program(prog, args, stdout_file=output)
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78 sys.exit(0)