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annotate specify.py @ 25:cba0d7a63b82

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workaround for gd_genotype datatype admix shift int -> float
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 29 May 2013 13:49:19 -0400
parents 248b06e86022
children 8997f2ca8c7a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
24
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
Richard Burhans <burhans@bx.psu.edu>
parents:
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1 #!/usr/bin/env python
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2
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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3 import sys
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4 import base64
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5
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6 def parse_args(args):
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7 if len(args) < 3:
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8 usage()
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9
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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10 input_file, output_file = args[1:3]
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11
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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12 individuals = []
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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13 checkboxes = []
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14 strings = []
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15
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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16 for arg in args[3:]:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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17 if ':' in arg:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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18 arg_type, arg = arg.split(':', 1)
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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19 else:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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20 print >> sys.stderr, "unknown argument:", arg
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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21 usage()
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22
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23 if arg_type == 'individual':
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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24 individuals.append(arg)
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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25 elif arg_type == 'checkbox':
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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26 checkboxes.append(arg)
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27 elif arg_type == 'string':
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28 strings.append(arg)
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29 else:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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30 print >> sys.stderr, "unknown argument:", arg
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31 usage()
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32
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33 return input_file, output_file, individuals, checkboxes, strings
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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34
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35 def usage():
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36 print >> sys.stderr, "Usage: %s <input> <output> [<individual:col:name> ...] [<checkbox:col:name> ...] [<string:base64> ...]" % (sys.argv[0])
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37 sys.exit(1)
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38
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39 def parse_individuals(individuals):
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40 ind_col2name = {}
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41 ind_name2col = {}
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42
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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43 for individual in individuals:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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44 if ':' in individual:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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45 column, name = individual.split(':', 1)
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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46 else:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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47 print >> sys.stderr, "invalid individual specification:", individual
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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48 usage()
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49
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50 try:
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51 column = int(column)
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52 except:
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53 print "individual column is not an integer:", individual
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54 usage()
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55
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56 if column not in ind_col2name:
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57 ind_col2name[column] = name
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58 else:
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59 if ind_col2name[column] != name:
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60 print "duplicate individual column:", name, column, ind_col2name[column]
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61 usage()
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62
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63 if name not in ind_name2col:
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64 ind_name2col[name] = [column]
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65 elif column not in ind_name2col[name]:
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66 ind_name2col[name].append(column)
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67
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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68 return ind_col2name, ind_name2col
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69
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70 def parse_checkboxes(checkboxes, ind_col2name):
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71 columns = []
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72
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73 for checkbox in checkboxes:
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74 if ':' in checkbox:
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75 column, name = checkbox.split(':', 1)
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76 else:
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77 print >> sys.stderr, "invalid checkbox specification:", checkbox
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78 usage()
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79
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80 try:
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81 column = int(column)
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82 except:
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83 print "checkbox column is not an integer:", checkbox
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84 usage()
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85
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86 if column not in ind_col2name:
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87 print "individual not in SNP table:", name
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88 usage()
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89
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90 if column not in columns:
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91 columns.append(column)
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92
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93 return columns
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94
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95 def parse_strings(strings, ind_col2name, ind_name2col):
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96 columns = []
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97
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98 for string in strings:
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99 try:
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100 decoded = base64.b64decode(string)
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101 except:
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102 print >> sys.stderr, "invalid base64 string:", string
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103 usage()
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104
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105 names = find_names(decoded, ind_name2col.keys())
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106 for name in names:
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107 cols = ind_name2col[name]
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108 if len(cols) == 1:
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109 col = cols[0]
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110 if col not in columns:
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111 columns.append(col)
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112 else:
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113 print >> sys.stderr, "name with multiple columns:", name
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114 usage()
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115
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116 return columns
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117
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118 def find_names(string, names):
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119 rv = []
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120 for name in names:
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121 if name in string:
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122 if name not in rv:
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123 rv.append(name)
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124 return rv
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125
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126
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127
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128
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129 input_file, output_file, individuals, checkboxes, strings = parse_args(sys.argv)
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130 ind_col2name, ind_name2col = parse_individuals(individuals)
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131 cb_cols = parse_checkboxes(checkboxes, ind_col2name)
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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132 str_cols = parse_strings(strings, ind_col2name, ind_name2col)
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133
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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134 out_cols = cb_cols
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135 for col in str_cols:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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136 if col not in out_cols:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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137 out_cols.append(col)
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138
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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139 with open(output_file, 'w') as fh:
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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140 for col in sorted(out_cols):
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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141 print >> fh, '\t'.join([str(x) for x in [col, ind_col2name[col], '']])
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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142
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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143 sys.exit(0)
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144
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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145
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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146
248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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147