Mercurial > repos > miller-lab > genome_diversity

annotate draw_variants.py @ 32:03c22b722882

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remove BeautifulSoup dependency
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 20 Sep 2013 13:54:23 -0400
parents a631c2f6d913
children ea52b23f1141
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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 def load_pop(file, wrapped_dict):
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10 if file == '/dev/null':
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11 pop = None
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12 else:
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13 pop = Population()
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14 pop.from_wrapped_dict(wrapped_dict)
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15 return pop
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17 def append_tags(the_list, p, p_type, val):
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18 if p is None:
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19 return
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20 for tag in p.tag_list():
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21 column, name = tag.split(':')
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22 if p_type == 'gd_genotype':
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23 column = int(column) - 2
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24 the_list.append('{0}:{1}:{2}'.format(val, column, name))
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25
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26 ################################################################################
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28 if len(sys.argv) != 11:
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29 gd_util.die('Usage')
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32 snp_file, snp_ext, snp_arg, indiv_input, annotation_input, cov_file, cov_ext, cov_arg, min_coverage, output = sys.argv[1:]
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33
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34 p_snp = load_pop(snp_file, snp_arg)
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35 p_cov = load_pop(cov_file, cov_arg)
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36
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37 if indiv_input == '/dev/null':
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38 if p_snp is not None:
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39 p_ind = p_snp
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40 elif p_cov is not None:
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41 p_ind = p_cov
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42 else:
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43 p_ind = None
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44 order_p_ind = True
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45 else:
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46 p_ind = Population()
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47 p_ind.from_population_file(indiv_input)
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48 order_p_ind = False
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49
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50 ## p ind must be from either p_snp or p_cov
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51 if p_snp is not None and p_cov is not None:
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52 if not (p_snp.is_superset(p_ind) or p_cov.is_superset(p_ind)):
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53 gd_util.die('There is an individual in the population individuals that is not in the SNP/Genotype or Coverage table')
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54 elif p_snp is not None:
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55 if not p_snp.is_superset(p_ind):
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56 gd_util.die('There is an individual in the population individuals that is not in the SNP/Genotype table')
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57 elif p_cov is not None:
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58 if not p_cov.is_superset(p_ind):
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59 gd_util.die('There is an individual in the population individuals that is not in the Coverage table')
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60
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61
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62 ################################################################################
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63
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64 prog = 'mito_draw'
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65
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66 args = [ prog ]
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67 args.append(snp_file)
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68 args.append(cov_file)
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69 args.append(annotation_input)
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70 args.append(min_coverage)
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71
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72 if order_p_ind:
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73 for column in sorted(p_ind.column_list()):
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74 individual = p_ind.individual_with_column(column)
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75 name = individual.name.split()[0]
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76 args.append('{0}:{1}:{2}'.format(0, column, name))
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77 else:
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78 append_tags(args, p_ind, 'gd_indivs', 0)
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79
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80 append_tags(args, p_snp, snp_ext, 1)
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81 append_tags(args, p_cov, cov_ext, 2)
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82
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83 with open('Ji.spec', 'w') as fh:
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84 gd_util.run_program(prog, args, stdout=fh)
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85
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86 ################################################################################
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87
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88 prog = 'varplot'
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89
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90 args = [ prog ]
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91 args.append('-w')
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92 args.append(3)
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93 args.append('-s')
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94 args.append(0.3)
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95 args.append('-g')
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96 args.append(0.2)
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97 args.append('Ji.spec')
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98
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99 with open('Ji.svg', 'w') as fh:
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100 gd_util.run_program(prog, args, stdout=fh)
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101
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102 ################################################################################
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103
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104 prog = 'convert'
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105
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106 args = [ prog ]
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107 args.append('-density')
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108 args.append(100)
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109 args.append('Ji.svg')
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110 args.append('tiff:{0}'.format(output))
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111
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112 gd_util.run_program(prog, args)
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113 sys.exit(0)