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annotate make_gd_file.py @ 39:e56023008e36 default tip

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Changed revision of package_fisher_0_1_4 to be2fc454d121 Changed revision of package_matplotlib_1_2 to a03ee94316b5
author miller-lab
date Mon, 06 Jul 2015 10:32:24 -0400
parents 8997f2ca8c7a
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
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Richard Burhans <burhans@bx.psu.edu>
parents:
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1 #!/usr/bin/env python
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Richard Burhans <burhans@bx.psu.edu>
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2
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Richard Burhans <burhans@bx.psu.edu>
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3 import base64
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Richard Burhans <burhans@bx.psu.edu>
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4 import json
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Richard Burhans <burhans@bx.psu.edu>
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5 import math
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Richard Burhans <burhans@bx.psu.edu>
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6 import re
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Richard Burhans <burhans@bx.psu.edu>
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7 import sys
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Richard Burhans <burhans@bx.psu.edu>
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8
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Richard Burhans <burhans@bx.psu.edu>
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9 identifier_regex = re.compile('[0-9A-Z_a-z]+$')
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Richard Burhans <burhans@bx.psu.edu>
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10
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11 def unwrap_column_names(string):
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Richard Burhans <burhans@bx.psu.edu>
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12 column_names = []
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Richard Burhans <burhans@bx.psu.edu>
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13 string = unwrap_string(string)
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Richard Burhans <burhans@bx.psu.edu>
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14 for line in string.split('\n'):
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15 line = line.strip()
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Richard Burhans <burhans@bx.psu.edu>
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16 if is_identifier(line):
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Richard Burhans <burhans@bx.psu.edu>
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17 column_names.append(line)
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Richard Burhans <burhans@bx.psu.edu>
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18 else:
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Richard Burhans <burhans@bx.psu.edu>
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19 die('invalid column name format: {}'.format(line))
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Richard Burhans <burhans@bx.psu.edu>
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20 return column_names
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21
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22 def unwrap_string(string):
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Richard Burhans <burhans@bx.psu.edu>
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23 try:
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24 decoded = base64.b64decode(string)
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Richard Burhans <burhans@bx.psu.edu>
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25 except:
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26 die('invalid base64 string: {}'.format(string))
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27 return decoded
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28
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29 def is_identifier(string):
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30 match = identifier_regex.match(string)
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31 if match:
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32 return True
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33 else:
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34 return False
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35
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36 def read_individual_names(filename):
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Richard Burhans <burhans@bx.psu.edu>
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37 tokens = []
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Richard Burhans <burhans@bx.psu.edu>
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38 names = []
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39 with open(filename) as fh:
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40 for line in fh:
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41 line = line.rstrip('\r\n')
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42 elems = line.split()
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43
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44 columns = len(elems)
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45 if columns == 0:
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Richard Burhans <burhans@bx.psu.edu>
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46 continue
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47
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48 first_token = elems[0]
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49
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50 if columns == 1:
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51 name = first_token
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52 else:
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53 keywords = ' '.join(elems[1:])
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54 name = ' '.join([first_token, keywords])
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55
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56 if first_token not in tokens:
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57 tokens.append(first_token)
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58 names.append(name)
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59 else:
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60 die('duplicate first column entry in Names dataset: {}'.format(first_token))
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61 return names
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62
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63 def fold_line(line, maxlen, prefix):
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64 prefix_len = len(prefix)
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65
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66 lines = []
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67
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68 while len(line) > maxlen:
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69 split_points = []
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Richard Burhans <burhans@bx.psu.edu>
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70 state = 0
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71 for i in range(maxlen - prefix_len):
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72 c = line[i]
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Richard Burhans <burhans@bx.psu.edu>
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73 if state == 0:
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Richard Burhans <burhans@bx.psu.edu>
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74 if c == '"':
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Richard Burhans <burhans@bx.psu.edu>
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75 state = 1
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76 elif c in [ '{', ':', ',', '}', '[', ']' ]:
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77 split_points.append(i)
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Richard Burhans <burhans@bx.psu.edu>
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78 elif state == 1:
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Richard Burhans <burhans@bx.psu.edu>
parents:
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79 if c == '"':
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Richard Burhans <burhans@bx.psu.edu>
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80 state = 0
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Richard Burhans <burhans@bx.psu.edu>
parents:
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81 elif c == '\\':
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Richard Burhans <burhans@bx.psu.edu>
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82 state = 2
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Richard Burhans <burhans@bx.psu.edu>
parents:
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83 elif state == 2:
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Richard Burhans <burhans@bx.psu.edu>
parents:
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84 state = 1
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Richard Burhans <burhans@bx.psu.edu>
parents:
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85 idx = split_points[-1]
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Richard Burhans <burhans@bx.psu.edu>
parents:
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86 lines.append('{0}{1}'.format(prefix, line[:idx+1]))
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87 line = line[idx+1:]
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88
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parents:
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89 lines.append('{0}{1}'.format(prefix, line))
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parents:
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90
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Richard Burhans <burhans@bx.psu.edu>
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91 return lines
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Richard Burhans <burhans@bx.psu.edu>
parents:
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92
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93 def die(message):
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Richard Burhans <burhans@bx.psu.edu>
parents:
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94 print >> sys.stderr, message
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95 sys.exit(1)
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96
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97 ################################################################################
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98
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parents:
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99 type_to_columns = {
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parents:
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100 'gd_snp':4,
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parents:
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101 'gd_genotype':1
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Richard Burhans <burhans@bx.psu.edu>
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102 }
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103
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104 if len(sys.argv) != 12:
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Richard Burhans <burhans@bx.psu.edu>
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105 print >> sys.stderr, 'Usage'
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106 sys.exit(1)
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107
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108 input, scaffold_col, pos_col, ref_col, rPos_col, preamble_arg, names, species_arg, dbkey, output_type, output = sys.argv[1:12]
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parents:
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109
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110 preamble_column_names = unwrap_column_names(preamble_arg)
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Richard Burhans <burhans@bx.psu.edu>
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111 first_individual_column = len(preamble_column_names) + 1
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Richard Burhans <burhans@bx.psu.edu>
parents:
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112
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parents:
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113 individual_names = read_individual_names(names)
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parents:
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114
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115 species = unwrap_string(species_arg)
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116 if not is_identifier(species):
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117 die('invalid species format: {}'.format(species))
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parents:
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118
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119 if not output_type in type_to_columns:
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parents:
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120 die('unknown output type: {}'.format(output_type))
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121 columns_per_individual = type_to_columns[output_type]
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parents:
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122
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Richard Burhans <burhans@bx.psu.edu>
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123 jdict = {}
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parents:
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124
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parents:
diff changeset
125 column_names = preamble_column_names[:]
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
126 for i in range(1, len(individual_names) + 1):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
127 if output_type == 'gd_snp':
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
128 column_names.append('{}A'.format(i))
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
129 column_names.append('{}B'.format(i))
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
130 column_names.append('{}G'.format(i))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
131 column_names.append('{}Q'.format(i))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
132 elif output_type == 'gd_genotype':
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
133 column_names.append('{}G'.format(i))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
134 else:
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
135 die('unknown output type: {}'.format(output_type))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
136
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
137 jdict['column_names'] = column_names
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
138
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
139 individuals = []
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
140
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
141 for pos, individual in enumerate(individual_names):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
142 col = first_individual_column + pos * columns_per_individual
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
143 individuals.append([individual, col])
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
144
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
145 jdict['individuals'] = individuals
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
146
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
147 jdict['scaffold'] = int(scaffold_col)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
148 jdict['pos'] = int(pos_col)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
149 jdict['ref'] = int(ref_col)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
150 jdict['rPos'] = int(rPos_col)
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
151
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Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
152 jdict['species'] = species
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
153 jdict['dbkey'] = dbkey
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
154
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
155 json_string = json.dumps(jdict, separators=(',',':'), sort_keys=True)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
156
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
157 min_cols = len(column_names)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
158 pos_col = int(pos_col) - 1
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
159 rPos_col = int(rPos_col) - 1
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
160
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
161 def is_int(string):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
162 try:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
163 int(string)
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
164 return True
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
165 except ValueError:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
166 return False
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
167
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
168 with open(output, 'w') as ofh:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
169 lines = fold_line(json_string, 200, '#')
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
170 for line in lines:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
171 print >> ofh, line
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
172
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
173 with open(input) as fh:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
174 line_number = 0
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
175 for line in fh:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
176 line_number += 1
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
177 if line[0] == '#':
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
178 continue
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
179 line = line.rstrip('\r\n')
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
180 elems = line.split('\t')
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
181 if len(elems) < min_cols:
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
182 die('Too few columns on line {0} of input file. Expecting {1}, saw {2}.'.format(line_number, min_cols, len(elems)))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
183 if not is_int(elems[pos_col]):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
184 die('bad pos on line {0} column {1} of input file: {2}'.format(line_number, pos_col+1, elems[pos_col]))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
185 if not is_int(elems[rPos_col]):
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
186 die('bad rPos on line {0} column {1} of input file: {2}'.format(line_number, rPos_col+1, elems[rPos_col]))
8997f2ca8c7a Update to Miller Lab devshed revision bae0d3306d3b
Richard Burhans <burhans@bx.psu.edu>
parents:
diff changeset
187 print >> ofh, line