big_simon 0.2.1 → 0.2.2
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- checksums.yaml +4 -4
- data/Gemfile.lock +1 -1
- data/exe/big_simon +2 -33
- data/lib/big_simon/runners.rb +1 -1
- data/lib/big_simon/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA1:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 980c3ecda67dca9161c5b0c9f8585157a46305be
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4
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+
data.tar.gz: 26f3eee3f8758d738e8963ef514b9c555106e858
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: d4d93aeb93b23e4fb08ed1cb0a8d4b144f3ddab2d5cb521cdde25a278b779eb97431294f6f33166f16ff664cffd8bb6371194034fe4000ce1b5030c4e3641ba9
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7
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+
data.tar.gz: 5678b2858ebf3e586c8246aba357dc9b376494dd43d091acc4156421a54b6078612f5319b5a4c21bf641d8b84c9ce4eaf4f904be39c0adc180349adb561b2c67
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data/Gemfile.lock
CHANGED
data/exe/big_simon
CHANGED
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@@ -82,43 +82,19 @@ wish_outf = BigSimon::Runners.wish BigSimon::WISH, tmpdir_virus, tmpdir_host, tm
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82
82
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vhm_outf = BigSimon::Runners.vir_host_matcher BigSimon::VHM, tmpdir_virus, tmpdir_host, tmpdir
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83
83
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84
84
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# TODO separate the parser from the runner for mummer.
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85
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-
host_info_mummer = BigSimon::Runners.mummer BigSimon::MUMMER, tmpdir_virus, tmpdir_host, tmpdir, threads
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86
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-
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87
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puts "mummer"
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88
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-
pp host_info_mummer
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89
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-
puts
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85
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+
host_info_mummer = BigSimon::Runners.mummer BigSimon::MUMMER, tmpdir_virus, tmpdir_host, tmpdir, threads, all_seq_lengths
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90
86
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91
87
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# TODO separate the parser from the runner for homology
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92
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-
host_info_homology = BigSimon::Runners.homology tmpdir_virus, tmpdir_host, tmpdir, threads
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93
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-
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94
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puts "homology"
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95
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pp host_info_homology
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96
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puts
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97
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-
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88
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+
host_info_homology = BigSimon::Runners.homology tmpdir_virus, tmpdir_host, tmpdir, threads, all_seq_lengths
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98
89
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99
90
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100
91
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host_info_wish = BigSimon::Parsers.wish wish_outf
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101
92
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host_info_vhm = BigSimon::Parsers.vir_host_matcher vhm_outf
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102
93
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103
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puts "wish"
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104
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-
pp host_info_wish
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105
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puts
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106
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-
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107
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puts "vhm"
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108
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pp host_info_vhm
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109
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puts
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110
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-
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111
94
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112
95
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host_info_simple_names = BigSimon::Pipeline.collate_host_results [host_info_wish, host_info_vhm, host_info_mummer, host_info_homology], programs
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113
96
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host_info = BigSimon::Pipeline.map_taxa host_info_simple_names, name_map_virus, name_map_host
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114
97
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115
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-
puts
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116
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-
pp host_info_simple_names
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117
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-
puts
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118
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-
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119
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-
puts
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120
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-
pp host_info
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121
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puts
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122
98
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123
99
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# Just a basic all info file
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124
100
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# File.open all_predictions_fname, "w" do |f|
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@@ -137,8 +113,6 @@ end
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137
113
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138
114
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scores_files.each do |program, files|
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139
115
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files.each do |name, file|
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140
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puts "LALA 3: #{[program, name, file]} #{%w[virus host score].join}"
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141
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-
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142
116
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file.puts %w[virus host score].join "\t"
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143
117
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end
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144
118
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end
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@@ -150,8 +124,6 @@ host_info.each do |virus, h1|
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150
124
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h2[:scores].each do |program, score|
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151
125
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lines[[virus, host, program]] = [score]
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152
126
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153
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-
puts "LALA: #{[virus, host, score]}"
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154
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-
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155
127
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scores_files[program][:raw].puts [virus, host, score].join "\t"
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156
128
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end
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157
129
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@@ -159,9 +131,6 @@ host_info.each do |virus, h1|
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159
131
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h2[:scaled_scores].each do |program, score|
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160
132
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lines[[virus, host, program]] << score
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161
133
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162
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-
puts "LALA 2: #{[virus, host, score]}"
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163
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-
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164
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-
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165
134
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scores_files[program][:scaled].puts [virus, host, score].join "\t"
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166
135
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end
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167
136
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data/lib/big_simon/runners.rb
CHANGED
data/lib/big_simon/version.rb
CHANGED