Class Bio::GO::GeneAssociation
In: lib/bio/db/go.rb
Parent: Object

Bio::GO::GeneAssociation

$CVSROOT/go/gene-associations/gene_association.*

Data parser for the gene_association go annotation. See also the file format www.geneontology.org/doc/GO.annotation.html#file

Example

 mgi_data = File.open('gene_association.mgi').read
 mgi = Bio::GO::GeneAssociation.parser(mgi_data)

 Bio::GO::GeneAssociation.parser(mgi_data) do |entry|
   p [entry.entry_id, entry.evidence, entry.goid]
 end

Methods

goid   new   parser   to_str  

Constants

DELIMITER = "\n"   Delimiter
RS = DELIMITER   Delimiter

External Aliases

db_object_id -> entry_id

Attributes

aspect  [R]  Returns Aspect valiable.
assigned_by  [R] 
date  [R]  Returns Date variable.
db  [R]  Returns DB variable.
db_object_id  [R]  Returns Db_Object_Id variable. Alias to entry_id.
db_object_name  [R] 
db_object_symbol  [R]  Returns Db_Object_Symbol variable.
db_object_synonym  [R] 
db_object_type  [R]  Returns Db_Object_Type variable.
db_reference  [R]  Returns Db_Reference variable.
evidence  [R]  Retruns Evidence code variable.
qualifier  [R]  Returns Db_Object_Name variable.
taxon  [R]  Returns Taxon variable.
with  [R]  Returns the entry is associated with this value.

Public Class methods

new(entry)

Parsing an entry (in a line) in the gene_association flatfile.

[Source]

     # File lib/bio/db/go.rb, line 261
261:     def initialize(entry) 
262:       tmp = entry.chomp.split(/\t/)
263:       @db                = tmp[0] 
264:       @db_object_id      = tmp[1]
265:       @db_object_symbol  = tmp[2]
266:       @qualifier         = tmp[3]  # 
267:       @goid              = tmp[4]
268:       @db_reference      = tmp[5].split(/\|/)  #
269:       @evidence          = tmp[6]
270:       @with              = tmp[7].split(/\|/)  # 
271:       @aspect            = tmp[8]
272:       @db_object_name    = tmp[9]  #
273:       @db_object_synonym = tmp[10].split(/\|/) #
274:       @db_object_type    = tmp[11]
275:       @taxon             = tmp[12] # taxon:4932
276:       @date              = tmp[13] # 20010118
277:       @assigned_by       = tmp[14] 
278:     end
parser(str) {|GeneAssociation.new(line)| ...}

Retruns an Array of parsed gene_association flatfile. Block is acceptable.

[Source]

     # File lib/bio/db/go.rb, line 199
199:     def self.parser(str)
200:       if block_given?
201:         str.each(DELIMITER) {|line|
202:           next if /^!/ =~ line
203:           yield GeneAssociation.new(line)
204:         }
205:       else
206:         galist = []
207:         str.each(DELIMITER) {|line|
208:           next if /^!/ =~ line
209:           galist << GeneAssociation.new(line)
210:         }
211:         return galist
212:       end
213:     end

Public Instance methods

goid(org = nil)

Returns GO_ID in /\d{7}/ format. Giving not nil arg, returns /GO:\d{7}/ style.

[Source]

     # File lib/bio/db/go.rb, line 286
286:     def goid(org = nil)
287:       if org
288:         @goid
289:       else
290:         @goid.sub('GO:','')
291:       end
292:     end
to_str()

Bio::GO::GeneAssociation#to_str -> a line of gene_association file.

[Source]

     # File lib/bio/db/go.rb, line 295
295:     def to_str
296:       return [@db, @db_object_id, @db_object_symbol, @quialifier, @goid, 
297:               @qualifier.join("|"), @evidence, @with.join("|"), @aspect,
298:               @db_object_name, @db_object_synonym.join("|"), @db_object_type,
299:               @taxon, @date, @assigned_by].join("\t")
300:     end

[Validate]