Mercurial > repos > rnateam > graphprot_predict_profile

annotate graphprot_train_wrapper.py @ 5:ddcf35a868b8 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
author bgruening
date Wed, 05 Jun 2024 16:40:51 +0000
parents ace92c9a4653
children
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1 #!/usr/bin/env python3
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ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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3 import argparse as ap
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4 import os
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5 import subprocess
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6 import sys
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8 import gplib
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10 """
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12 TOOL DEPENDENCIES
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13 =================
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20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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15 GraphProt 1.1.7
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16 Best install via:
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17 https://anaconda.org/bioconda/graphprot
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18 Tested with: miniconda3, conda 4.7.12
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21 OUTPUT FILES
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22 ============
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24 data_id.model
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25 data_id.params
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26 if not --disable-cv:
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27 data_id.cv_results
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28 if not --disable-motifs:
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29 data_id.sequence_motif
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30 data_id.sequence_motif.png
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31 if --str-model:
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32 data_id.structure_motif
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33 data_id.structure_motif.png
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34 Temporary:
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35 data_id.predictions
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36 data_id.profile
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39 EXAMPLE CALLS
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40 =============
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42 python graphprot_train_wrapper.py --pos gp_data/SERBP1_positives.train.fa
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43 --neg gp_data/SERBP1_negatives.train.fa --data-id test2 --disable-cv
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44 --gp-output --opt-set-size 200 --min-train 400
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46 python graphprot_train_wrapper.py --pos gp_data/SERBP1_positives.train.fa
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47 --neg gp_data/SERBP1_negatives.train.fa --data-id test2 --disable-cv
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48 --opt-set-size 100 --min-train 200
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50 python graphprot_train_wrapper.py --pos test-data/test_positives.train.fa
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51 --neg test-data/test_negatives.train.fa --data-id gptest2 --disable-cv
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52 --opt-pos test-data/test_positives.parop.fa
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53 --opt-neg test-data/test_negatives.parop.fa
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55 python graphprot_train_wrapper.py --pos test-data/test_positives.train.fa
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56 --neg test-data/test_negatives.train.fa --data-id gptest2 --disable-cv
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57 --disable-motifs --opt-pos test-data/test_positives.parop.fa --opt-neg
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58 test-data/test_negatives.parop.fa
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61 """
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64 #######################################################################
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67 def setup_argument_parser():
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68 """Setup argparse parser."""
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69 help_description = """
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70 Galaxy wrapper script for GraphProt to train a GraphProt model on
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71 a given set of input sequences (positives and negatives .fa). By
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72 default a sequence model is trained (due to structure models
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73 being much slower to train). Also by default take a portion of
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74 the input sequences for hyperparameter optimization (HPO) prior to
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75 model training, and run a 10-fold cross validation and motif
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76 generation after model training. Thus the following output
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77 files are produced:
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78 .model model file, .params model parameter file, .png motif files
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79 (sequence, or sequence+structure), .cv_results CV results file.
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80 After model training, predict on positives to get highest whole
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81 site and profile scores found in binding sites. Take the median
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82 score out of these to store in .params file, using it later
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83 for outputting binding sites or peaks with higher confidence.
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84
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85 """
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86 # Define argument parser.
5
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87 p = ap.ArgumentParser(
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88 add_help=False,
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89 prog="graphprot_train_wrapper.py",
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90 description=help_description,
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91 formatter_class=ap.MetavarTypeHelpFormatter,
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92 )
1
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93
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94 # Argument groups.
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95 p_man = p.add_argument_group("REQUIRED ARGUMENTS")
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96 p_opt = p.add_argument_group("OPTIONAL ARGUMENTS")
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97
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98 # Required arguments.
5
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99 p_opt.add_argument("-h", "--help", action="help", help="Print help message")
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100 p_man.add_argument(
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101 "--pos",
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102 dest="in_pos_fa",
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103 type=str,
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104 required=True,
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105 help="Positive (= binding site) sequences .fa file "
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106 "for model training (option -fasta)",
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107 )
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108 p_man.add_argument(
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109 "--neg",
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110 dest="in_neg_fa",
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111 type=str,
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112 required=True,
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113 help="Negative sequences .fa file for model " "training (option -negfasta)",
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114 )
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115 p_man.add_argument(
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116 "--data-id",
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117 dest="data_id",
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118 type=str,
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119 required=True,
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120 help="Data ID (option -prefix)",
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121 )
1
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122 # Additional arguments.
5
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123 p_opt.add_argument(
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124 "--opt-set-size",
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125 dest="opt_set_size",
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126 type=int,
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127 default=500,
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128 help="Hyperparameter optimization set size (taken "
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129 "away from both --pos and --neg) (default: 500)",
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130 )
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131 p_opt.add_argument(
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132 "--opt-pos",
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133 dest="opt_pos_fa",
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134 type=str,
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135 help="Positive (= binding site) sequences .fa file "
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136 "for hyperparameter optimization (default: take "
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137 "--opt-set-size from --pos)",
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138 )
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139 p_opt.add_argument(
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140 "--opt-neg",
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141 dest="opt_neg_fa",
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142 type=str,
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143 help="Negative sequences .fa file for hyperparameter "
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144 "optimization (default: take --opt-set-size "
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145 "from --neg)",
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146 )
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147 p_opt.add_argument(
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148 "--min-train",
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149 dest="min_train",
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150 type=int,
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151 default=500,
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152 help="Minimum amount of training sites demanded " "(default: 500)",
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153 )
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154 p_opt.add_argument(
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155 "--disable-cv",
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156 dest="disable_cv",
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157 default=False,
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158 action="store_true",
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159 help="Disable cross validation step (default: false)",
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160 )
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161 p_opt.add_argument(
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162 "--disable-motifs",
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163 dest="disable_motifs",
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164 default=False,
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165 action="store_true",
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166 help="Disable motif generation step (default: false)",
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167 )
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168 p_opt.add_argument(
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169 "--gp-output",
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170 dest="gp_output",
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171 default=False,
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172 action="store_true",
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173 help="Print output produced by GraphProt " "(default: false)",
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174 )
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175 p_opt.add_argument(
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176 "--str-model",
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177 dest="train_str_model",
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178 default=False,
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179 action="store_true",
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180 help="Train a structure model (default: train " "a sequence model)",
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181 )
1
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182 return p
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183
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184
5
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185 #######################################################################
1
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186
5
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187 if __name__ == "__main__":
1
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188
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189 # Setup argparse.
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190 parser = setup_argument_parser()
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191 # Read in command line arguments.
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192 args = parser.parse_args()
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193
1
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194 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
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195 Do all sorts of sanity checking.
3
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196
1
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197 """
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198 # Check for Linux.
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199 assert "linux" in sys.platform, "please use Linux"
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200 # Check tool availability.
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201 assert gplib.is_tool("GraphProt.pl"), "GraphProt.pl not in PATH"
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202 # Check file inputs.
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203 assert os.path.exists(args.in_pos_fa), 'positives .fa file "%s" not found' % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
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204 args.in_pos_fa
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205 )
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206 assert os.path.exists(args.in_neg_fa), 'negatives .fa file "%s" not found' % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
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207 args.in_neg_fa
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208 )
1
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209 # Count .fa entries.
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210 c_pos_fa = gplib.count_fasta_headers(args.in_pos_fa)
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211 c_neg_fa = gplib.count_fasta_headers(args.in_neg_fa)
5
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212 assert c_pos_fa, 'positives .fa file "%s" no headers found' % (args.in_pos_fa)
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213 assert c_neg_fa, 'negatives .fa file "%s" no headers found' % (args.in_neg_fa)
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214 print("# positive .fa sequences: %i" % (c_pos_fa))
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215 print("# negative .fa sequences: %i" % (c_neg_fa))
1
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216 # Check additional files.
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217 if args.opt_pos_fa:
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218 assert args.opt_neg_fa, "--opt-pos but no --opt-neg given"
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219 if args.opt_neg_fa:
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220 assert args.opt_pos_fa, "--opt-neg but no --opt-pos given"
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221 # Check for lowercase only sequences, which cause GP to crash.
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222 error_mess = (
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223 "input sequences encountered containing "
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224 "only lowercase characters or lowercase characters in between "
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225 "uppercase characters. Please provide either all uppercase "
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226 "sequences or sequences containing uppercase regions surrounded "
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227 "by lowercase context regions for structure calculation (see "
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228 "viewpoint concept in original GraphProt publication "
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229 "for more details)"
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230 )
3
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231 seqs_dic = gplib.read_fasta_into_dic(args.in_pos_fa)
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232 bad_ids = gplib.check_seqs_dic_format(seqs_dic)
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233 assert not bad_ids, "%s" % (error_mess)
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234 seqs_dic = gplib.read_fasta_into_dic(args.in_neg_fa)
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235 bad_ids = gplib.check_seqs_dic_format(seqs_dic)
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236 assert not bad_ids, "%s" % (error_mess)
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237 if args.opt_pos_fa:
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238 seqs_dic = gplib.read_fasta_into_dic(args.opt_pos_fa)
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239 bad_ids = gplib.check_seqs_dic_format(seqs_dic)
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240 assert not bad_ids, "%s" % (error_mess)
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241 if args.opt_neg_fa:
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242 seqs_dic = gplib.read_fasta_into_dic(args.opt_neg_fa)
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243 bad_ids = gplib.check_seqs_dic_format(seqs_dic)
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
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244 assert not bad_ids, "%s" % (error_mess)
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245
1
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246 # If parop .fa files given.
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247 if args.opt_pos_fa and args.opt_neg_fa:
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248 c_parop_pos_fa = gplib.count_fasta_headers(args.opt_pos_fa)
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249 c_parop_neg_fa = gplib.count_fasta_headers(args.opt_neg_fa)
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250 assert c_parop_pos_fa, '--opt-pos .fa file "%s" no headers found' % (
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251 args.opt_pos_fa
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252 )
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253 assert c_parop_neg_fa, '--opt-neg .fa file "%s" no headers found' % (
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254 args.opt_neg_fa
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255 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
256 # Less than 500 for training?? You gotta be kidding.
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
257 assert c_pos_fa >= args.min_train, (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
258 "--pos for training < %i, please provide more (try at least "
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
259 "> 1000, the more the better)" % (args.min_train)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
260 )
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
261 assert c_neg_fa >= args.min_train, (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
262 "--neg for training < %i, please provide more (try at least "
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
263 "> 1000, the more the better)" % (args.min_train)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
264 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
265 # Looking closer at ratios.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
266 pos_neg_ratio = c_parop_pos_fa / c_parop_neg_fa
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
267 if pos_neg_ratio < 0.8 or pos_neg_ratio > 1.25:
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
268 assert 0, (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
269 "ratio of --opt-pos to --opt-neg < 0.8 or > 1.25 "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
270 "(ratio = %f). Try to keep ratio closer to 1 or better use "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
271 "identical numbers (keep in mind that performance measures "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
272 "such as accuracy or AUROC are not suitable for imbalanced "
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
273 " datasets!)" % (pos_neg_ratio)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
274 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
275 else:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
276 # Define some minimum amount of training sites for the sake of sanity.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
277 c_pos_train = c_pos_fa - args.opt_set_size
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
278 c_neg_train = c_neg_fa - args.opt_set_size
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
279 # Start complaining.
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
280 assert (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
281 c_pos_fa >= args.opt_set_size
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
282 ), "# positives < --opt-set-size (%i < %i)" % (c_pos_fa, args.opt_set_size)
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
283 assert (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
284 c_neg_fa >= args.opt_set_size
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
285 ), "# negatives < --opt-set-size (%i < %i)" % (c_neg_fa, args.opt_set_size)
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
286 assert (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
287 c_pos_train >= args.opt_set_size
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
288 ), "# positives remaining for training < --opt-set-size " "(%i < %i)" % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
289 c_pos_train,
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
290 args.opt_set_size,
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
291 )
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
292 assert (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
293 c_neg_train >= args.opt_set_size
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
294 ), "# negatives remaining " "for training < --opt-set-size (%i < %i)" % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
295 c_neg_train,
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
296 args.opt_set_size,
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
297 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
298 # Less than 500?? You gotta be kidding.
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
299 assert c_pos_train >= args.min_train, (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
300 "# positives remaining for training < %i, please provide more "
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
301 " (try at least > 1000, the more the better)" % (args.min_train)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
302 )
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
303 assert c_neg_train >= args.min_train, (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
304 "# negatives remaining for training < %i, please provide more "
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
305 "(try at least > 1000, the more the better)" % (args.min_train)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
306 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
307 # Looking closer at ratios.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
308 pos_neg_ratio = c_pos_train / c_neg_train
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
309 if pos_neg_ratio < 0.8 or pos_neg_ratio > 1.25:
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
310 assert 0, (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
311 "ratio of --pos to --neg < 0.8 or > 1.25 "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
312 "(ratio = %f). Try to keep ratio closer to 1 or better use "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
313 "identical numbers (keep in mind that performance measures "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
314 "such as accuracy or AUROC are not suitable for imbalanced "
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
315 "datasets!)" % (pos_neg_ratio)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
316 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
317
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
318 """
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
319 Generate parop + train .fa output files for hyperparameter
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
320 optimization + training.
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
321
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
322 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
323 # Output files for training.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
324 pos_parop_fa = args.data_id + ".positives.parop.fa"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
325 neg_parop_fa = args.data_id + ".negatives.parop.fa"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
326 pos_train_fa = args.data_id + ".positives.train.fa"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
327 neg_train_fa = args.data_id + ".negatives.train.fa"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
328
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
329 # If parop .fa files given.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
330 if args.opt_pos_fa and args.opt_neg_fa:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
331 # Just copy parop and train files.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
332 gplib.make_file_copy(args.opt_pos_fa, pos_parop_fa)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
333 gplib.make_file_copy(args.opt_neg_fa, neg_parop_fa)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
334 gplib.make_file_copy(args.in_pos_fa, pos_train_fa)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
335 gplib.make_file_copy(args.in_neg_fa, neg_train_fa)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
336 else:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
337 # Generate parop + train .fa files from input .fa files.
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
338 gplib.split_fasta_into_test_train_files(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
339 args.in_pos_fa, pos_parop_fa, pos_train_fa, test_size=args.opt_set_size
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
340 )
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
341 gplib.split_fasta_into_test_train_files(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
342 args.in_neg_fa, neg_parop_fa, neg_train_fa, test_size=args.opt_set_size
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
343 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
344
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
345 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
346 Do the hyperparameter optimization.
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
347
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
348 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
349 print("Starting hyperparameter optimization (-action ls) ... ")
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
350 check_cmd = (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
351 "GraphProt.pl -action ls -prefix "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
352 + args.data_id
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
353 + " -fasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
354 + pos_parop_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
355 + " -negfasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
356 + neg_parop_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
357 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
358 # If sequence model should be trained (default).
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
359 if not args.train_str_model:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
360 check_cmd += " -onlyseq"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
361 print(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
362 output = subprocess.getoutput(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
363 params_file = args.data_id + ".params"
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
364 assert os.path.exists(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
365 params_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
366 ), "Hyperparameter optimization output " ' .params file "%s" not found' % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
367 params_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
368 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
369 # Add model type to params file.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
370 if args.train_str_model:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
371 gplib.echo_add_to_file("model_type: structure", params_file)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
372 else:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
373 gplib.echo_add_to_file("model_type: sequence", params_file)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
374 # Get parameter string.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
375 param_string = gplib.graphprot_get_param_string(params_file)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
376
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
377 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
378 Do the model training. (Yowza!)
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
379
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
380 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
381 print("Starting model training (-action train) ... ")
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
382 check_cmd = (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
383 "GraphProt.pl -action train -prefix "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
384 + args.data_id
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
385 + " -fasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
386 + pos_train_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
387 + " -negfasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
388 + neg_train_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
389 + " "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
390 + param_string
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
391 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
392 print(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
393 output = subprocess.getoutput(check_cmd)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
394 assert output, "The following call of GraphProt.pl produced no output:\n%s" % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
395 check_cmd
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
396 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
397 if args.gp_output:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
398 print(output)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
399 model_file = args.data_id + ".model"
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
400 assert os.path.exists(model_file), 'Training output .model file "%s" not found' % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
401 model_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
402 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
403
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
404 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
405 Do the 10-fold cross validation.
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
406
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
407 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
408 if not args.disable_cv:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
409 print("Starting 10-fold cross validation (-action cv) ... ")
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
410 check_cmd = (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
411 "GraphProt.pl -action cv -prefix "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
412 + args.data_id
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
413 + " -fasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
414 + pos_train_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
415 + " -negfasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
416 + neg_train_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
417 + " "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
418 + param_string
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
419 + " -model "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
420 + model_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
421 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
422 print(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
423 output = subprocess.getoutput(check_cmd)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
424 assert output, "The following call of GraphProt.pl produced no output:\n%s" % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
425 check_cmd
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
426 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
427 if args.gp_output:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
428 print(output)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
429 cv_results_file = args.data_id + ".cv_results"
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
430 assert os.path.exists(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
431 cv_results_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
432 ), 'CV output .cv_results file "%s" not found' % (cv_results_file)
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
433
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
434 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
435 Do the motif generation.
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
436
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
437 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
438 if not args.disable_motifs:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
439 print("Starting motif generation (-action motif) ... ")
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
440 check_cmd = (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
441 "GraphProt.pl -action motif -prefix "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
442 + args.data_id
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
443 + " -fasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
444 + pos_train_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
445 + " -negfasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
446 + neg_train_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
447 + " "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
448 + param_string
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
449 + " -model "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
450 + model_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
451 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
452 print(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
453 output = subprocess.getoutput(check_cmd)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
454 assert output, "The following call of GraphProt.pl produced no output:\n%s" % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
455 check_cmd
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
456 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
457 if args.gp_output:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
458 print(output)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
459 seq_motif_file = args.data_id + ".sequence_motif"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
460 seq_motif_png_file = args.data_id + ".sequence_motif.png"
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
461 assert os.path.exists(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
462 seq_motif_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
463 ), 'Motif output .sequence_motif file "%s" not found' % (seq_motif_file)
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
464 assert os.path.exists(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
465 seq_motif_png_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
466 ), 'Motif output .sequence_motif.png file "%s" not found' % (seq_motif_png_file)
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
467 if args.train_str_model:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
468 str_motif_file = args.data_id + ".structure_motif"
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
469 str_motif_png_file = args.data_id + ".structure_motif.png"
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
470 assert os.path.exists(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
471 str_motif_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
472 ), 'Motif output .structure_motif file "%s" not found' % (str_motif_file)
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
473 assert os.path.exists(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
474 str_motif_png_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
475 ), 'Motif output .structure_motif.png file "%s" not found' % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
476 str_motif_png_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
477 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
478
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
479 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
480 Do whole site predictions on positive training set.
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
481
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
482 """
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
483 print(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
484 "Starting whole site predictions on positive training set "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
485 " (-action predict) ... "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
486 )
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
487 check_cmd = (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
488 "GraphProt.pl -action predict -prefix "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
489 + args.data_id
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
490 + " -fasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
491 + pos_train_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
492 + " "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
493 + param_string
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
494 + " -model "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
495 + model_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
496 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
497 print(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
498 output = subprocess.getoutput(check_cmd)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
499 assert output, "The following call of GraphProt.pl produced no output:\n%s" % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
500 check_cmd
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
501 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
502 if args.gp_output:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
503 print(output)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
504 ws_predictions_file = args.data_id + ".predictions"
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
505 assert os.path.exists(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
506 ws_predictions_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
507 ), 'Whole site prediction output .predictions file "%s" not found' % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
508 ws_predictions_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
509 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
510
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
511 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
512 Do profile predictions on positive training set.
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
513
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
514 """
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
515 print(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
516 "Starting profile predictions on positive training set "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
517 "-action predict_profile) ... "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
518 )
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
519 check_cmd = (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
520 "GraphProt.pl -action predict_profile -prefix "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
521 + args.data_id
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
522 + " -fasta "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
523 + pos_train_fa
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
524 + " "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
525 + param_string
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
526 + " -model "
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
527 + model_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
528 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
529 print(check_cmd)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
530 output = subprocess.getoutput(check_cmd)
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
531 assert output, "The following call of GraphProt.pl produced no output:\n%s" % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
532 check_cmd
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
533 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
534 if args.gp_output:
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
535 print(output)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
536 profile_predictions_file = args.data_id + ".profile"
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
537 assert os.path.exists(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
538 profile_predictions_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
539 ), 'Profile prediction output .profile file "%s" not found' % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
540 profile_predictions_file
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
541 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
542
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
543 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
544 Get 50 % score (median) for .predictions and .profile file.
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
545 For .profile, first extract for each site the maximum score, and then
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
546 from the list of maximum site scores get the median.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
547 For whole site .predictions, get the median from the site scores list.
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
548
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
549 """
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
550 print("Getting .profile and .predictions median scores ... ")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
551
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
552 # Whole site scores median.
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
553 ws_pred_median = gplib.graphprot_predictions_get_median(ws_predictions_file)
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
554 # Profile top site scores median.
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
555 profile_median = gplib.graphprot_profile_get_tsm(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
556 profile_predictions_file, profile_type="profile"
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
557 )
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
558 ws_pred_string = "pos_train_ws_pred_median: %f" % (ws_pred_median)
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
559 profile_string = "pos_train_profile_median: %f" % (profile_median)
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
560 gplib.echo_add_to_file(ws_pred_string, params_file)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
561 gplib.echo_add_to_file(profile_string, params_file)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
562 # Average profile top site scores median for extlr 1 to 10.
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
563 for i in range(10):
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
564 i += 1
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
565 avg_profile_median = gplib.graphprot_profile_get_tsm(
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
566 profile_predictions_file, profile_type="avg_profile", avg_profile_extlr=i
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
567 )
3
ace92c9a4653 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit efcac98677c3ea9039c1c61eaa9e58f78287ccb3"
bgruening
parents: 1
diff changeset
568
5
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
569 avg_profile_string = "pos_train_avg_profile_median_%i: %f" % (
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
570 i,
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
571 avg_profile_median,
ddcf35a868b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit ad60258f5759eaa205fec4af6143c728ea131419
bgruening
parents: 3
diff changeset
572 )
1
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
573 gplib.echo_add_to_file(avg_profile_string, params_file)
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
574
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
575 print("Script: I'm done.")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
576 print("Author: Good. Now go back to your file system directory.")
20429f4c1b95 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/graphprot commit f3fb925b83a4982e0cf9a0c11ff93ecbb8e4e6d5"
bgruening
parents:
diff changeset
577 print("Script: Ok.")