class Bio::SPTR
Public Instance Methods
accessions()
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SwissProt Accessions
# File lib/protk/bio_sptr_extensions.rb, line 92 def accessions return self.ac end
altnames()
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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()
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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()
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Disease
# File lib/protk/bio_sptr_extensions.rb, line 122 def disease return self.cc["DISEASE"].to_s end
domain()
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Domain
# File lib/protk/bio_sptr_extensions.rb, line 132 def domain return self.cc["DOMAIN"].to_s end
ensembl()
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Ensembl accession number
# File lib/protk/bio_sptr_extensions.rb, line 185 def ensembl return self.safely_get_drentry_for_key("Ensembl") end
ensembl_link()
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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()
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# File lib/protk/bio_sptr_extensions.rb, line 260 def feature_dump return self.ft.to_s end
function()
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Function
# File lib/protk/bio_sptr_extensions.rb, line 104 def function return self.cc["FUNCTION"].to_s end
go_entries()
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# File lib/protk/bio_sptr_extensions.rb, line 166 def go_entries return self.dr["GO"] end
go_terms()
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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()
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Intact accession number
# File lib/protk/bio_sptr_extensions.rb, line 173 def intact return self.safely_get_drentry_for_key("PRIDE") end
intact_link()
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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()
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IPI Accession number
# File lib/protk/bio_sptr_extensions.rb, line 153 def ipi return self.safely_get_drentry_for_key("IPI") end
location()
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Subcellular Location
# File lib/protk/bio_sptr_extensions.rb, line 98 def location return self.cc["SUBCELLULAR LOCATION"].to_s end
ncbi_taxon_id()
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# File lib/protk/bio_sptr_extensions.rb, line 252 def ncbi_taxon_id return self.ox["NCBI_TaxID"] end
nextbio()
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NextBIO accession number
# File lib/protk/bio_sptr_extensions.rb, line 191 def nextbio return self.safely_get_drentry_for_key("NextBio") end
nextbio_link()
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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()
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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()
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Pride accession number
# File lib/protk/bio_sptr_extensions.rb, line 179 def pride return self.safely_get_drentry_for_key("PRIDE") end
pride_link()
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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()
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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()
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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)
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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()
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# File lib/protk/bio_sptr_extensions.rb, line 248 def seq_dump return self.seq.to_s end
signalp()
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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()
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Similarity
# File lib/protk/bio_sptr_extensions.rb, line 110 def similarity return self.cc["SIMILARITY"].to_s end
species_dump()
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# File lib/protk/bio_sptr_extensions.rb, line 256 def species_dump return self.os.to_s end
subunit()
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Subunit
# File lib/protk/bio_sptr_extensions.rb, line 127 def subunit return self.cc["SUBUNIT"].to_s end
tissues()
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Tissue Specificity
# File lib/protk/bio_sptr_extensions.rb, line 116 def tissues return self.cc["TISSUE SPECIFICITY"].to_s end
uniprot_link()
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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