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-rw-r--r--fminer.rb115
1 files changed, 33 insertions, 82 deletions
diff --git a/fminer.rb b/fminer.rb
index 2f4cb67..190c8c1 100644
--- a/fminer.rb
+++ b/fminer.rb
@@ -302,56 +302,30 @@ post '/fminer/bbrc/?' do
]
}
feature_dataset.add_feature feature_uri, metadata
- #feature_dataset.add_feature_parameters feature_uri, feature_dataset.parameters
end
- id_arrs.each { |id_count_hash|
- id=id_count_hash.keys[0].to_i
- count=id_count_hash.values[0].to_i
- fminer_results[@@fminer.compounds[id]] || fminer_results[@@fminer.compounds[id]] = {}
- fminer_results[@@fminer.compounds[id]][feature_uri] || fminer_results[@@fminer.compounds[id]][feature_uri] = []
- if params[:nr_hits] == "true"
- fminer_results[@@fminer.compounds[id]][feature_uri] << count
- else
- fminer_results[@@fminer.compounds[id]][feature_uri] << 1
+
+ # re-format to one big hash id_arr
+ id_arr = {}; id_arrs.each { |id_count_hash| id_arr[id_count_hash.keys[0]] = id_count_hash.values[0] }
+ @@fminer.compounds.collect.each_with_index { |cmpd,id| # This collects all cmpds that have an activity
+ val = id_arr[id] ? ( params[:nr_hits] == "true" ? id_arr[id].to_i : 1 ) : 0
+ if (val != 0 or params[:complete_entries] == "true")
+ fminer_results[cmpd] || fminer_results[cmpd] = {}
+ fminer_results[cmpd][feature_uri] || fminer_results[cmpd][feature_uri] = []
+ fminer_results[cmpd][feature_uri] << val
end
}
-
- end # end of
+
+ end # end of
end # feature parsing
- # Collect compounds, in order with duplicates (owd)
- fminer_compounds_owd = @@fminer.compounds.collect
- fminer_compounds_owd.shift if fminer_compounds_owd[0].nil?
-
- # Complete fminer_results, s.t. it contains entries for any training compound
- if (params[:complete_entries] == "true")
- myhelpfeature = File.join(feature_dataset.uri,"feature","bbrc", (features.size-1).to_s)
- (fminer_compounds_owd - fminer_results.keys).each { |cmpd| # add possibly multiple entries
- fminer_results[cmpd] || fminer_results[cmpd] = {}
- fminer_results[cmpd][myhelpfeature] || fminer_results[cmpd][myhelpfeature] = []
- fminer_results[cmpd][myhelpfeature] << 0
- }
- end
-
- # Add fminer results to feature dataset along owd
- all_compounds_owd = @@fminer.training_dataset.compounds.collect { |v|
- times_in_fminer_compounds_owd = fminer_compounds_owd.count(v)
- times_in_fminer_compounds_owd == 0 ? v : Array.new(times_in_fminer_compounds_owd,v)
- }.flatten
- if (params[:complete_entries] == "true")
- all_compounds_owd.each { |compound|
- feature_dataset.add_compound(compound) # add compounds *in order*
- }
- end
-
which_row = @@fminer.training_dataset.compounds.inject({}) { |h,id| h[id]=0; h }
- unused_compounds = fminer_compounds_owd - fminer_results.keys
- (fminer_compounds_owd - unused_compounds).each { |compound|
- feature_dataset.add_compound(compound) unless (params[:complete_entries] == "true")
- fminer_results[compound].each { |feature, values|
- feature_dataset.add( compound, feature, values[which_row[compound]] )
+ @@fminer.training_dataset.compounds.each { |cmpd|
+ feature_dataset.add_compound(cmpd) # *unconditionally* add compounds *in order*
+ i = which_row[cmpd]
+ fminer_results[cmpd] && fminer_results[cmpd].each { |feature, values|
+ feature_dataset.add_data_entry( cmpd, feature, values[i] )
}
- which_row[compound] += 1
+ which_row[cmpd] += 1
}
# AM: add feature values for non-present features
# feature_dataset.complete_data_entries
@@ -515,8 +489,7 @@ post '/fminer/bbrc/sample/?' do
params[:nr_hits] == "true" ? hit_count=true: hit_count=false
matches, counts, used_compounds = lu.match_rb(@@fminer.smi,smarts,hit_count,true) # last arg: always create complete entries for sampling
- # Collect compounds, in order with duplicates (owd) and put in dataset
- used_compounds.each { |idx| feature_dataset.add_compound(@@fminer.compounds[idx]) }
+ @@fminer.training_dataset.compounds.each { |cmpd| feature_dataset.add_compound(cmpd) }
feature_dataset.add_metadata({
OT.parameters => [
@@ -539,12 +512,9 @@ post '/fminer/bbrc/sample/?' do
metadata = calc_metadata (smarts, ids, counts[smarts], nil, nil , value_map, params, smarts_p_values[smarts])
feature_uri = File.join feature_dataset.uri,"feature","last", feature_dataset.features.size.to_s
feature_dataset.add_feature feature_uri, metadata
- ids.each_with_index { |id,idx| feature_dataset.add(@@fminer.compounds[id], feature_uri, counts[smarts][idx])}
+ ids.each_with_index { |id,idx| feature_dataset.add_data_entry(@@fminer.compounds[id], feature_uri, counts[smarts][idx])}
end
- # AM: add feature values for non-present features
- # feature_dataset.complete_data_entries
-
feature_dataset.save(@subjectid)
feature_dataset.uri
end
@@ -624,30 +594,19 @@ post '/fminer/last/?' do
smarts=lu.smarts_rb(dom,'nls') # converts patterns to LAST-SMARTS using msa variant (see last-pm.maunz.de)
params[:nr_hits] == "true" ? hit_count=true : hit_count=false
params[:complete_entries] == "true" ? complete_entries=true : complete_entries=false
- matches, counts, used_compounds = lu.match_rb(@@fminer.smi,smarts,hit_count,complete_entries) # creates instantiations
-
- # Collect compounds, in order with duplicates (owd) and put in dataset
- fminer_compounds_owd = used_compounds.collect { |idx| @@fminer.compounds[idx] }
- if (complete_entries)
- all_compounds_owd = @@fminer.training_dataset.compounds.collect { |v|
- times_in_fminer_compounds_owd = fminer_compounds_owd.count(v)
- times_in_fminer_compounds_owd == 0 ? v : Array.new(times_in_fminer_compounds_owd,v)
- }.flatten
- all_compounds_owd.each { |compound| feature_dataset.add_compound(compound) }
- else
- fminer_compounds_owd.each { |compound| feature_dataset.add_compound(compound) }
- end
+ matches, counts = lu.match_rb(@@fminer.smi,smarts,hit_count,complete_entries) # creates instantiations
+ @@fminer.training_dataset.compounds.each { |cmpd| feature_dataset.add_compound(cmpd) }
matches.each do |smarts, ids|
metadata = calc_metadata (smarts, ids, counts[smarts], @@last, nil, value_map, params)
feature_uri = File.join feature_dataset.uri,"feature","last", feature_dataset.features.size.to_s
feature_dataset.add_feature feature_uri, metadata
- ids.each_with_index { |id,idx| feature_dataset.add(@@fminer.compounds[id], feature_uri, counts[smarts][idx])}
+ @@fminer.compounds.collect.each_with_index { |cmpd,id| # This collects all cmpds that have an activity
+ count_idx = matches[smarts].index(id)
+ feature_dataset.add_data_entry(cmpd, feature_uri, counts[smarts][count_idx]) if count_idx
+ }
end
- # AM: add feature values for non-present features
- # feature_dataset.complete_data_entries
-
feature_dataset.save(@subjectid)
feature_dataset.uri
end
@@ -703,25 +662,17 @@ post '/fminer/:method/match?' do
smarts = f_dataset.features.collect { |f,m| m[OT.smarts] }
params[:nr_hits] == "true" ? hit_count=true : hit_count=false
params[:complete_entries] == "true" ? complete_entries=true : complete_entries=false
- matches, counts, used_compounds = LU.new.match_rb(@@fminer.smi, smarts, hit_count, complete_entries) if smarts.size>0
-
- # Collect compounds, in order with duplicates (owd) and put in dataset
- fminer_compounds_owd = used_compounds.collect { |idx| @@fminer.compounds[idx] }
- if (complete_entries)
- all_compounds_owd = @@fminer.training_dataset.compounds.collect { |v|
- times_in_fminer_compounds_owd = fminer_compounds_owd.count(v)
- times_in_fminer_compounds_owd == 0 ? v : Array.new(times_in_fminer_compounds_owd,v)
- }.flatten
- all_compounds_owd.each { |compound| feature_dataset.add_compound(compound) }
- else
- fminer_compounds_owd.each { |compound| feature_dataset.add_compound(compound) }
- end
+ matches, counts = LU.new.match_rb(@@fminer.smi, smarts, hit_count, complete_entries) if smarts.size>0
+ @@fminer.training_dataset.compounds.each { |cmpd| feature_dataset.add_compound(cmpd) }
matches.each do |smarts, ids|
- metadata = calc_metadata (smarts, ids, counts[smarts], @@last, feature_dataset.uri, value_map, params)
- feature_uri = File.join feature_dataset.uri,"feature","bbrc","match", feature_dataset.features.size.to_s
+ metadata = calc_metadata (smarts, ids, counts[smarts], @@last, nil, value_map, params)
+ feature_uri = File.join feature_dataset.uri,"feature",params[:method], feature_dataset.features.size.to_s
feature_dataset.add_feature feature_uri, metadata
- ids.each_with_index { |id,idx| feature_dataset.add(@@fminer.compounds[id], feature_uri, counts[smarts][idx]) }
+ @@fminer.compounds.collect.each_with_index { |cmpd,id| # This collects all cmpds that have an activity
+ count_idx = matches[smarts].index(id)
+ feature_dataset.add_data_entry(cmpd, feature_uri, counts[smarts][count_idx]) if count_idx
+ }
end
feature_dataset.save @subjectid
generated by cgit v1.2.3 (git 2.25.1) at 2024-05-30 17:17:55 +0000