class Bio::SPTR

Public Instance Methods

accessions() click to toggle source

SwissProt Accessions

# File lib/protk/bio_sptr_extensions.rb, line 92
def accessions 
  return self.ac
end
altnames() click to toggle source

All alternate names

# 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() click to toggle source

The CD Antigen name

# 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() click to toggle source

Disease

# File lib/protk/bio_sptr_extensions.rb, line 122
def disease
  return self.cc["DISEASE"].to_s
end
domain() click to toggle source

Domain

# File lib/protk/bio_sptr_extensions.rb, line 132
def domain
  return self.cc["DOMAIN"].to_s
end
ensembl() click to toggle source

Ensembl accession number

# File lib/protk/bio_sptr_extensions.rb, line 185
def ensembl
  return self.safely_get_drentry_for_key("Ensembl")
end
feature_dump() click to toggle source
# File lib/protk/bio_sptr_extensions.rb, line 260
def feature_dump
  return self.ft.to_s
end
function() click to toggle source

Function

# File lib/protk/bio_sptr_extensions.rb, line 104
def function
  return self.cc["FUNCTION"].to_s    
end
go_entries() click to toggle source
# File lib/protk/bio_sptr_extensions.rb, line 166
def go_entries
  return self.dr["GO"]
end
go_terms() click to toggle source
# 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() click to toggle source

Intact accession number

# File lib/protk/bio_sptr_extensions.rb, line 173
def intact
  return self.safely_get_drentry_for_key("PRIDE")    
end
ipi() click to toggle source

IPI Accession number

# File lib/protk/bio_sptr_extensions.rb, line 153
def ipi
  return self.safely_get_drentry_for_key("IPI")
end
location() click to toggle source

Subcellular Location

# File lib/protk/bio_sptr_extensions.rb, line 98
def location
  return self.cc["SUBCELLULAR LOCATION"].to_s
end
ncbi_taxon_id() click to toggle source
# File lib/protk/bio_sptr_extensions.rb, line 252
def ncbi_taxon_id
  return self.ox["NCBI_TaxID"]
end
nextbio() click to toggle source

NextBIO accession number

# File lib/protk/bio_sptr_extensions.rb, line 191
def nextbio
  return self.safely_get_drentry_for_key("NextBio")
end
num_transmem() click to toggle source

Number of transmembrane regions

# 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() click to toggle source

Pride accession number

# File lib/protk/bio_sptr_extensions.rb, line 179
def pride
  return self.safely_get_drentry_for_key("PRIDE")
end
recname() click to toggle source

The recommended name for the Protein

# 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() click to toggle source
# File lib/protk/bio_sptr_extensions.rb, line 244
def ref_dump
  return self.ref.to_s
end
safely_get_drentry_for_key(key) click to toggle source

Helper Function to create links

# 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() click to toggle source
# File lib/protk/bio_sptr_extensions.rb, line 248
def seq_dump
  return self.seq.to_s
end
signalp() click to toggle source

Number of signal peptide features

# 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() click to toggle source

Similarity

# File lib/protk/bio_sptr_extensions.rb, line 110
def similarity
  return self.cc["SIMILARITY"].to_s    
end
species_dump() click to toggle source
# File lib/protk/bio_sptr_extensions.rb, line 256
def species_dump
  return self.os.to_s
end
subunit() click to toggle source

Subunit

# File lib/protk/bio_sptr_extensions.rb, line 127
def subunit
  return self.cc["SUBUNIT"].to_s
end
tissues() click to toggle source

Tissue Specificity

# File lib/protk/bio_sptr_extensions.rb, line 116
def tissues
  return self.cc["TISSUE SPECIFICITY"].to_s
end