Class: Protein
- Inherits:
-
Object
- Object
- Protein
- Defined in:
- lib/protk/protein.rb
Instance Attribute Summary collapse
-
#group_number ⇒ Object
Returns the value of attribute group_number.
-
#group_probability ⇒ Object
Returns the value of attribute group_probability.
-
#n_indistinguishable_proteins ⇒ Object
Returns the value of attribute n_indistinguishable_proteins.
-
#peptides ⇒ Object
Returns the value of attribute peptides.
-
#percent_coverage ⇒ Object
Returns the value of attribute percent_coverage.
-
#probability ⇒ Object
Returns the value of attribute probability.
-
#protein_name ⇒ Object
Returns the value of attribute protein_name.
-
#sequence ⇒ Object
Returns the value of attribute sequence.
Class Method Summary collapse
Instance Method Summary collapse
-
#initialize ⇒ Protein
constructor
A new instance of Protein.
-
#representative_peptides ⇒ Object
Return just one peptide for each unique sequence choosing the peptide with highest probability.
Constructor Details
#initialize ⇒ Protein
Returns a new instance of Protein.
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# File 'lib/protk/protein.rb', line 52 def initialize() end |
Instance Attribute Details
#group_number ⇒ Object
Returns the value of attribute group_number.
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# File 'lib/protk/protein.rb', line 8 def group_number @group_number end |
#group_probability ⇒ Object
Returns the value of attribute group_probability.
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# File 'lib/protk/protein.rb', line 9 def group_probability @group_probability end |
#n_indistinguishable_proteins ⇒ Object
Returns the value of attribute n_indistinguishable_proteins.
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# File 'lib/protk/protein.rb', line 13 def n_indistinguishable_proteins @n_indistinguishable_proteins end |
#peptides ⇒ Object
Returns the value of attribute peptides.
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# File 'lib/protk/protein.rb', line 15 def peptides @peptides end |
#percent_coverage ⇒ Object
Returns the value of attribute percent_coverage.
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# File 'lib/protk/protein.rb', line 14 def percent_coverage @percent_coverage end |
#probability ⇒ Object
Returns the value of attribute probability.
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# File 'lib/protk/protein.rb', line 10 def probability @probability end |
#protein_name ⇒ Object
Returns the value of attribute protein_name.
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# File 'lib/protk/protein.rb', line 12 def protein_name @protein_name end |
#sequence ⇒ Object
Returns the value of attribute sequence.
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# File 'lib/protk/protein.rb', line 11 def sequence @sequence end |
Class Method Details
.from_protxml(xmlnode) ⇒ Object
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# File 'lib/protk/protein.rb', line 35 def from_protxml(xmlnode) prot=new() groupnode = xmlnode.parent prot.group_probability = groupnode['probability'].to_f prot.group_number = groupnode['group_number'].to_i prot.probability = xmlnode['probability'].to_f prot.protein_name = xmlnode['protein_name'] prot.n_indistinguishable_proteins = xmlnode['n_indistinguishable_proteins'].to_i prot.percent_coverage = xmlnode['percent_coverage'].to_f peptide_nodes = xmlnode.find('protxml:peptide','protxml:http://regis-web.systemsbiology.net/protXML') prot.peptides = peptide_nodes.collect { |e| Peptide.from_protxml(e) } prot end |
Instance Method Details
#representative_peptides ⇒ Object
Return just one peptide for each unique sequence choosing the peptide with highest probability
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# File 'lib/protk/protein.rb', line 58 def representative_peptides() best_peptides={} self.peptides.each do |peptide| seq = peptide.sequence if best_peptides[seq].nil? best_peptides[seq]=peptide else best_peptides[seq]=peptide if peptide.nsp_adjusted_probability > best_peptides[seq].nsp_adjusted_probability end end best_peptides.values end |