Class: Bio::SPTR

Inherits:
EMBLDB
  • Object
show all
Defined in:
lib/protk/bio_sptr_extensions.rb

Instance Method Summary collapse

Instance Method Details

#accessions ⇒ Object

SwissProt Accessions



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# File 'lib/protk/bio_sptr_extensions.rb', line 92

def accessions 
  return self.ac
end

#altnames ⇒ Object

All alternate names



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# File 'lib/protk/bio_sptr_extensions.rb', line 68

def altnames
  altnames=""
  
  pname_field=self.de
  entries=pname_field.split(";")
  entries.each do |entry|
    m=entry.match(/\s*(.*?):\s*(.*?)=(.*)/)
    if ( m!=nil)
      if ( (m[1]=="AltName") && (m[2]!="CD_antigen") )
        altnames << "#{m[3]}; "
        
      end
    end
  end
  
  if ( altnames!="") # Get ride of extraneous "; "
    altnames.chop!.chop!
  end
  
  return altnames
end

#cd ⇒ Object

The CD Antigen name



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# File 'lib/protk/bio_sptr_extensions.rb', line 51

def cd
  pname_field=self.de
  entries=pname_field.split(";")
  entries.each do |entry|
    m=entry.match(/\s*(.*?):\s*(.*?)=(.*)/)
    if ( m!=nil)
      if ( (m[1]=="AltName") && (m[2]=="CD_antigen") )
        return m[3]
      end
    end
  end
  
  return ""
end

#disease ⇒ Object

Disease



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# File 'lib/protk/bio_sptr_extensions.rb', line 122

def disease
  return self.cc["DISEASE"].to_s
end

#domain ⇒ Object

Domain



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# File 'lib/protk/bio_sptr_extensions.rb', line 132

def domain
  return self.cc["DOMAIN"].to_s
end

#ensembl ⇒ Object

Ensembl accession number



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# File 'lib/protk/bio_sptr_extensions.rb', line 185

def ensembl
  return self.safely_get_drentry_for_key("Ensembl")
end

#ensembl_link ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 211

def ensembl_link
  return "http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;t=#{self.ensembl}"
end

#feature_dump ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 260

def feature_dump
  return self.ft.to_s
end

#function ⇒ Object

Function



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# File 'lib/protk/bio_sptr_extensions.rb', line 104

def function
  return self.cc["FUNCTION"].to_s    
end

#go_entries ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 166

def go_entries
  return self.dr["GO"]
end

#go_terms ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 157

def go_terms
  terms = self.dr["GO"]
  if terms
    return terms.collect { |e| e[0] }
  else
    return nil
  end
end

#intact ⇒ Object

Intact accession number



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# File 'lib/protk/bio_sptr_extensions.rb', line 173

def intact
  return self.safely_get_drentry_for_key("PRIDE")    
end

#intact_link ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 203

def intact_link
  return "http://www.ebi.ac.uk/intact/pages/interactions/interactions.xhtml?query=#{self.intact}*"
end

#ipi ⇒ Object

IPI Accession number



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# File 'lib/protk/bio_sptr_extensions.rb', line 153

def ipi
  return self.safely_get_drentry_for_key("IPI")
end

#location ⇒ Object

Subcellular Location



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# File 'lib/protk/bio_sptr_extensions.rb', line 98

def location
  return self.cc["SUBCELLULAR LOCATION"].to_s
end

#ncbi_taxon_id ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 252

def ncbi_taxon_id
  return self.ox["NCBI_TaxID"]
end

#nextbio ⇒ Object

NextBIO accession number



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# File 'lib/protk/bio_sptr_extensions.rb', line 191

def nextbio
  return self.safely_get_drentry_for_key("NextBio")
end

#nextbio_link ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 199

def nextbio_link
  return "http://www.nextbio.com/b/home/home.nb?id=#{self.nextbio}&type=feature"
end

#num_transmem ⇒ Object

Number of transmembrane regions



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# File 'lib/protk/bio_sptr_extensions.rb', line 217

def num_transmem
  begin
    if ( self.ft["TRANSMEM"]==nil)
      return 0.to_s
    else
      return self.ft["TRANSMEM"].length.to_s
    end
  rescue
    p "Warning: Unable to parse feature table for entry #{self.accession}"
  end
end

#pride ⇒ Object

Pride accession number



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# File 'lib/protk/bio_sptr_extensions.rb', line 179

def pride
  return self.safely_get_drentry_for_key("PRIDE")
end

#pride_link ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 207

def pride_link
  return "http://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=#{self.pride}"
end

#recname ⇒ Object

The recommended name for the Protein



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# File 'lib/protk/bio_sptr_extensions.rb', line 35

def recname
  pname_field=self.de
  entries=pname_field.split(";")
  entries.each do |entry|
    m=entry.match(/\s*(.*?):\s*(.*?)=(.*)/)
    if ( m!=nil)
      if ( m[1]=="RecName")
        return m[3]
      end
    end
  end   
  return ""
end

#ref_dump ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 244

def ref_dump
  return self.ref.to_s
end

#safely_get_drentry_for_key(key) ⇒ Object

Helper Function to create links



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# File 'lib/protk/bio_sptr_extensions.rb', line 143

def safely_get_drentry_for_key(key)
  if ( self.dr[key]==nil)
    return ""
  end

  return dr[key][0][0]
end

#seq_dump ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 248

def seq_dump
  return self.seq.to_s
end

#signalp ⇒ Object

Number of signal peptide features



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# File 'lib/protk/bio_sptr_extensions.rb', line 232

def signalp
  begin
    if ( self.ft["SIGNAL"]==nil)
      return 0.to_s
    else
      return self.ft["SIGNAL"].length.to_s
    end
  rescue
    p "Warning: Unable to parse feature table for entry #{self.accession}"      
  end
end

#similarity ⇒ Object

Similarity



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# File 'lib/protk/bio_sptr_extensions.rb', line 110

def similarity
  return self.cc["SIMILARITY"].to_s    
end

#species_dump ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 256

def species_dump
  return self.os.to_s
end

#subunit ⇒ Object

Subunit



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# File 'lib/protk/bio_sptr_extensions.rb', line 127

def subunit
  return self.cc["SUBUNIT"].to_s
end

#tissues ⇒ Object

Tissue Specificity



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# File 'lib/protk/bio_sptr_extensions.rb', line 116

def tissues
  return self.cc["TISSUE SPECIFICITY"].to_s
end

#uniprot_link ⇒ Object 



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# File 'lib/protk/bio_sptr_extensions.rb', line 195

def uniprot_link
  return "http://www.uniprot.org/uniprot/#{self.accession}.html"
end