hocomoco12 data

Author: VorontsovIE

app/controllers/macroape/scans_controller.rb

@@ -14,7 +14,7 @@ def query_matrix_examples
   helper_method :query_matrix_examples
 
   def default_params
-    common_options = { collection: :hocomoco_11_human,
+    common_options = { collection: :hocomoco_12_core,
       background: BackgroundForm.uniform,
       query: DataModelForm.new(
         effective_count: 100, pseudocount: :log,

app/controllers/perfectosape/scans_controller.rb

@@ -14,7 +14,7 @@ def default_params
     EOS
 
     { snp_list_text: test_snps,
-      collection: :hocomoco_11_human,
+      collection: :hocomoco_12_core,
       pvalue_cutoff: 0.0005,
       fold_change_cutoff: 4
     }

app/helpers/application_helper.rb

@@ -54,13 +54,15 @@ def collection_motif_image(collection_name, motif, orientation)
   end
 
   def motif_info(collection_name, motif)
-    if [:hocomoco_11_human, :hocomoco_11_mouse].include?(collection_name)
+    if [:hocomoco_12_core, :hocomoco_12_rsnp, :hocomoco_12_invivo, :hocomoco_12_invitro].include?(collection_name)
+      motif_url = "https://hocomoco12.autosome.org/motif/#{motif}"
+    elsif [:hocomoco_11_human, :hocomoco_11_mouse].include?(collection_name)
       motif_url = "https://hocomoco11.autosome.org/motif/#{motif}"
     elsif [:hocomoco_10_human, :hocomoco_10_mouse].include?(collection_name)
       motif_url = "https://hocomoco10.autosome.org/motif/#{motif}"
     elsif collection_name == :hocomoco # v9
       infos = /^(?<model_base>.+)_(?<model_type>f1|f2|do|si)$/.match(motif)
-      motif_url = "http://autosome.org/HOCOMOCO/modelDetails.php?tf=#{infos[:model_base]}&model=#{infos[:model_type]}"
+      motif_url = "https://autosome.org/HOCOMOCO/modelDetails.php?tf=#{infos[:model_base]}&model=#{infos[:model_type]}"
     else
       motif_url = nil
     end
@@ -82,10 +84,28 @@ def uniprot_mapping
     end
   end
 
+  def annotation_by_h12_collection(collection_name)
+    @cache_annotation_by_collection ||= {}
+    @cache_annotation_by_collection[collection_name] ||= begin
+      collection_suffix = collection_name.split('_').last.upcase
+      annotation_fn = Rails.root.join("public/motif_collection/H12#{collection_suffix}_annotation.jsonl")
+      File.readlines(annotation_fn).map{|l|
+        JSON.parse(l)
+      }.group_by{|d|
+        d['name']
+      }.transform_values{|grp|
+        raise unless grp.size == 1
+        grp.first
+      }
+    end
+  end
+
   def uniprot_links(collection_name, motif)
     if [:hocomoco_11_human, :hocomoco_11_mouse, :hocomoco_10_human, :hocomoco_10_mouse].include?(collection_name)
       uniprot_name = motif[/^(?<uniprot>.+_HUMAN|.+_MOUSE)\..*/, :uniprot]
       return uniprot_link("#{uniprot_name}", uniprot_name)
+    elsif [:hocomoco_12_core, :hocomoco_12_rsnp, :hocomoco_12_invivo, :hocomoco_12_invitro].include?(collection_name)
+      uniprot_name = annotation_by_h12_collection(collection_name)[motif][:uniprot_id_human]
     end
     motif_id = motif.split.first # names in uniprot mapping aren't complete names but just first parts (e.g. `MA0512.1` for `MA0512.1 Rxra`)
     uniprot_names = uniprot_mapping[collection_name.to_sym][motif_id]

app/inputs/motif_collection_selector_input.rb

@@ -1,4 +1,7 @@
 class MotifCollectionSelectorInput < SelectorFromEnumInput
-  variants [:hocomoco_11_human, :hocomoco_11_mouse, :jaspar, :selex, :swissregulon, :homer]
+  variants [
+    :hocomoco_12_core, :hocomoco_12_rsnp, :hocomoco_12_invivo, :hocomoco_12_invitro,
+    :hocomoco_11_human, :hocomoco_11_mouse, :jaspar, :selex, :swissregulon, :homer
+  ]
   i18n_scope 'enumerize.collection'
 end

app/validators/motif_collection_validator.rb

@@ -1,5 +1,8 @@
 class MotifCollectionValidator < ActiveModel::Validations::InclusionValidator
-  VARIANTS = [:hocomoco_11_human, :hocomoco_11_mouse, :jaspar, :selex, :swissregulon, :homer]
+  VARIANTS = [
+    :hocomoco_12_core, :hocomoco_12_rsnp, :hocomoco_12_invivo, :hocomoco_12_invitro,
+    :hocomoco_11_human, :hocomoco_11_mouse, :jaspar, :selex, :swissregulon, :homer
+  ]
   def delimiter
     VARIANTS
   end

config/locales/en.yml

@@ -68,6 +68,10 @@ en:
       hocomoco_10_mouse: 'HOCOMOCO-10 (mouse)'
       hocomoco_11_human: 'HOCOMOCO-11 (human)'
       hocomoco_11_mouse: 'HOCOMOCO-11 (mouse)'
+      hocomoco_12_core: 'HOCOMOCO-12 (H12CORE)'
+      hocomoco_12_rsnp: 'HOCOMOCO-12 (H12RSNP)'
+      hocomoco_12_invivo: 'HOCOMOCO-12 (H12INVIVO)'
+      hocomoco_12_invitro: 'HOCOMOCO-12 (H12INVITRO)'
       jaspar: 'JASPAR'
       selex: 'HT-SELEX'
       swissregulon: 'SwissRegulon'
@@ -145,23 +149,23 @@ en:
         collection: |
           Collection of transcription factor binding site models (motifs).
           Available collections:
-          <a href="http://hocomoco.autosome.org/">HOCOMOCO</a>,
-          <a href="http://jaspar.genereg.net/">JASPAR</a>,
-          <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877582/">HT-SELEX</a>,
-          <a href="http://swissregulon.unibas.ch/fcgi/sr">SwissRegulon</a>,
-          and <a href="http://homer.salk.edu/homer/motif/motifDatabase.html">HOMER</a>.
+          <a href="https://hocomoco.autosome.org/">HOCOMOCO</a>,
+          <a href="https://jaspar.uio.no/">JASPAR</a>,
+          <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877582/">HT-SELEX</a>,
+          <a href="https://swissregulon.unibas.ch/">SwissRegulon</a>,
+          and <a href="http://homer.ucsd.edu/homer/motif/motifDatabase.html">HOMER</a>.
         pvalue_cutoff: "P-value cutoff to treat a DNA subsequence as a TF binding site."
         fold_change_cutoff: "Minimal P-value fold change."
     Macroape:
       ScanForm:
         collection: |
           Collection of transcription factor binding site motifs to scan.
           Available collections:
-          <a href="http://autosome.org/HOCOMOCO/">HOCOMOCO</a>,
-          <a href="http://jaspar.genereg.net/">JASPAR</a>,
-          <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877582/">HT-SELEX</a>,
-          <a href="http://swissregulon.unibas.ch/fcgi/sr">SwissRegulon</a>,
-          and <a href="http://homer.salk.edu/homer/motif/motifDatabase.html">HOMER</a>.
+          <a href="https://hocomoco.autosome.org/">HOCOMOCO</a>,
+          <a href="https://jaspar.uio.no/">JASPAR</a>,
+          <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2877582/">HT-SELEX</a>,
+          <a href="https://swissregulon.unibas.ch/">SwissRegulon</a>,
+          and <a href="http://homer.ucsd.edu/homer/motif/motifDatabase.html">HOMER</a>.
         pvalue: 'P-value level to select the motif thresholds.'
         pvalue_boundary: 'Upper boundary (default) means that the obtained P-value is greater than or equal to the requested P-value.'
         similarity_cutoff: 'Minimal similarity to report.'