diff options
author | davor <vorgrimmlerdavid@gmx.de> | 2012-02-01 11:34:05 +0100 |
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committer | davor <vorgrimmlerdavid@gmx.de> | 2012-02-01 11:34:05 +0100 |
commit | 5d8d8ca06efdcb5326a0ee46bb33e85d63bfbb4a (patch) | |
tree | 3d4b21a2aaf5fe3afd180f32836acdbb160e2592 | |
parent | 61a7cad711ca8b936d802f111002fd071c1493cd (diff) |
Updated and moved scripts in new folder structure
-rw-r--r-- | 5x_cv/CV_ds_pctype_prop_algo_rseed.rb | 60 | ||||
-rw-r--r-- | 5x_cv/factors_config | 38 | ||||
-rw-r--r-- | cv/scripts/CV_ds_pctype_algo_rseed.rb | 58 | ||||
-rw-r--r-- | cv/scripts/factors_config | 17 | ||||
-rwxr-xr-x | cv/scripts/wrapper_pc_cv.sh (renamed from 5x_cv/wrapper_pc_cv.sh) | 8 |
5 files changed, 79 insertions, 102 deletions
diff --git a/5x_cv/CV_ds_pctype_prop_algo_rseed.rb b/5x_cv/CV_ds_pctype_prop_algo_rseed.rb deleted file mode 100644 index b9c55dd..0000000 --- a/5x_cv/CV_ds_pctype_prop_algo_rseed.rb +++ /dev/null @@ -1,60 +0,0 @@ -# Do a 10-fold crossvalidation -# # Author: Andreas Maunz, David Vorgrimmler -# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ...), prop(true or false), prediction_algorithm(local_mlr_prop or local_svm_regression ...) - -if ARGV.size != 5 - puts "Args: ds_name, pc_type, prop, algo, random_seed" - puts ARGV.size - exit -end - -ds_file = "datasets_nestle.yaml" -pwd=`pwd` -path = "#{pwd.chop}/#{ds_file}" -if File.exists?(path) - puts "#{ds_file} exists" -else - puts "#{ds_file} does not exist." - exit -end - -require 'rubygems' -require 'opentox-ruby' -require 'yaml' - -subjectid = nil - -ds_name = ARGV[0] # e.g. MOU -pc_type = ARGV[1] # e.g. electronic,cpsa -prop = ARGV[2] # true or false -algo = ARGV[3] # e.g. local_svm_regression, local_mlr_prop -r_seed = ARGV[4] # 1, 2, ..., 10 - -ds = YAML::load_file("datasets_nestle.yaml") -ds_uri = ds[ds_name]["dataset"] -pc_ds_uri = ds[ds_name][pc_type] - -algo_params = "pc_type=#{pc_type}"; -algo_params += ";feature_dataset_uri=#{pc_ds_uri}" -algo_params += ";propositionalized=#{prop}" -algo_params += ";prediction_algorithm=#{algo}" -puts algo_params.to_yaml - -prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first - - -# Ready -cv_args = {} -cv_args[:dataset_uri] = ds_uri -cv_args[:prediction_feature] = prediction_feature -cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:8087/algorithm/lazar" -cv_args[:algorithm_params] = algo_params -cv_args[:stratified] = false -cv_args[:random_seed] = r_seed -puts cv_args.to_yaml - -cv = OpenTox::Crossvalidation.create(cv_args).uri -puts cv - -cvr = OpenTox::CrossvalidationReport.create( cv , subjectid).uri -puts cvr diff --git a/5x_cv/factors_config b/5x_cv/factors_config deleted file mode 100644 index 604ca45..0000000 --- a/5x_cv/factors_config +++ /dev/null @@ -1,38 +0,0 @@ -#Dataset pc_type prop prediction_algorithm -MDD constitutional false local_svm_regression -MDD constitutional true local_svm_regression -MDD electronic,cpsa false local_svm_regression -MDD electronic,cpsa true local_svm_regression -MDD constitutional,electronic,cpsa false local_svm_regression -MDD constitutional,electronic,cpsa true local_svm_regression -#MDD constitutional true local_mlr_prop -#MDD electronic,cpsa true local_mlr_prop -#MDD constitutional,electronic,cpsa true local_mlr_prop -FHM2 constitutional false local_svm_regression -FHM2 constitutional true local_svm_regression -FHM2 electronic,cpsa false local_svm_regression -FHM2 electronic,cpsa true local_svm_regression -FHM2 constitutional,electronic,cpsa false local_svm_regression -FHM2 constitutional,electronic,cpsa true local_svm_regression -#MOU constitutional true local_mlr_prop -#MOU electronic,cpsa true local_mlr_prop -#MOU constitutional,electronic,cpsa true local_mlr_prop -RAT2 constitutional false local_svm_regression -RAT2 constitutional true local_svm_regression -RAT2 electronic,cpsa false local_svm_regression -RAT2 electronic,cpsa true local_svm_regression -RAT2 constitutional,electronic,cpsa false local_svm_regression -RAT2 constitutional,electronic,cpsa true local_svm_regression -#MOU constitutional true local_mlr_prop -#MOU electronic,cpsa true local_mlr_prop -#MOU constitutional,electronic,cpsa true local_mlr_prop -MOU2 constitutional false local_svm_regression -MOU2 constitutional true local_svm_regression -MOU2 electronic,cpsa false local_svm_regression -MOU2 electronic,cpsa true local_svm_regression -MOU2 constitutional,electronic,cpsa false local_svm_regression -MOU2 constitutional,electronic,cpsa true local_svm_regression -#MOU constitutional true local_mlr_prop -#MOU electronic,cpsa true local_mlr_prop -#MOU constitutional,electronic,cpsa true local_mlr_prop - diff --git a/cv/scripts/CV_ds_pctype_algo_rseed.rb b/cv/scripts/CV_ds_pctype_algo_rseed.rb new file mode 100644 index 0000000..36adb6f --- /dev/null +++ b/cv/scripts/CV_ds_pctype_algo_rseed.rb @@ -0,0 +1,58 @@ +# Do a 10-fold crossvalidation +# # Author: Andreas Maunz, David Vorgrimmler +# # @params: Dataset_name(see dataset_nestle.yaml), pc_type(electronic,cpsa or constitutional ... or nil to disable), prediction_algorithm(local_mlr_prop or local_svm_regression ...) + +if ARGV.size != 4 + puts "Args: ds_name, pc_type, algo, random_seed" + puts ARGV.size + exit +end + +ds_file = "datasets.yaml" +pwd=`pwd` +path = "#{pwd.chop}/../data/#{ds_file}" +if File.exists?(path) + puts "#{ds_file} exists" +else + puts "#{ds_file} does not exist." + exit +end + +require 'rubygems' +require 'opentox-ruby' +require 'yaml' + +subjectid = nil + +ds_name = ARGV[0] # e.g. MOU +pc_type = ARGV[1] # e.g. electronic,cpsa or nil to disable +algo = ARGV[2] # e.g. local_svm_regression, local_mlr_prop +r_seed = ARGV[3] # 1, 2, ..., 10 + +ds = YAML::load_file("../data/datasets.yaml") +ds_uri = ds[ds_name]["dataset"] +pc_ds_uri = ds[ds_name][pc_type] + +algo_params = "prediction_algorithm=#{algo}" +algo_params += ";pc_type=#{pc_type}" unless pc_type == "nil" +algo_params += ";feature_dataset_uri=#{pc_ds_uri}" unless pc_type == "nil" +puts algo_params.to_yaml + +prediction_feature = OpenTox::Dataset.find(ds_uri).features.keys.first + + +# Ready +cv_args = {} +cv_args[:dataset_uri] = ds_uri +cv_args[:prediction_feature] = prediction_feature +cv_args[:algorithm_uri] = "http://toxcreate3.in-silico.ch:80XX/algorithm/lazar" +cv_args[:algorithm_params] = algo_params +cv_args[:stratified] = false +cv_args[:random_seed] = r_seed +puts cv_args.to_yaml + +#cv = OpenTox::Crossvalidation.create(cv_args).uri +#puts cv + +#cvr = OpenTox::CrossvalidationReport.create( cv , subjectid).uri +#puts cvr diff --git a/cv/scripts/factors_config b/cv/scripts/factors_config new file mode 100644 index 0000000..83bb54c --- /dev/null +++ b/cv/scripts/factors_config @@ -0,0 +1,17 @@ +#Dataset pc_type prediction_algorithm +MDD constitutional local_svm_regression +MDD electronic,cpsa local_svm_regression +MDD topological local_svm_regression +MDD nil local_svm_regression +#FHM constitutional local_svm_regression +#FHM electronic,cpsa local_svm_regression +#FHM topological local_svm_regression +#FHM nil local_svm_regression +#RAT constitutional local_svm_regression +#RAT electronic,cpsa local_svm_regression +#RAT topological local_svm_regression +#RAT nil local_svm_regression +#MOU constitutional local_svm_regression +#MOU electronic,cpsa local_svm_regression +#MOU topological local_svm_regression +#MOU nil local_svm_regression diff --git a/5x_cv/wrapper_pc_cv.sh b/cv/scripts/wrapper_pc_cv.sh index 719885a..ed13122 100755 --- a/5x_cv/wrapper_pc_cv.sh +++ b/cv/scripts/wrapper_pc_cv.sh @@ -1,6 +1,6 @@ #!/bin/bash # Wrapper Skript for CV -# Reads factors_config, dataset_nestle.yaml and performs cv's +# Reads factors_config, ../data/datasets.yaml and performs cv's # Andreas Maunz, David Vorgrimmler, 2012 if [ $# -lt 1 ]; then @@ -10,9 +10,9 @@ fi PWD=`pwd` echo $PWD -if [ ! -f $PWD/datasets_nestle.yaml ] +if [ ! -f $PWD/../data/datasets.yaml ] then - echo "datasets_nestle.yaml does not exist." + echo "datasets.yaml does not exist." exit fi @@ -20,7 +20,7 @@ fi source $HOME/.bash_aliases otconfig THIS_DATE=`date +%Y%m%d_%H_` -CV="CV_ds_pctype_prop_algo_rseed.rb" +CV="CV_ds_pctype_algo_rseed.rb" FACTORS="$1" # Don't start when running |