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.

- Bio::GO::GeneAssociation#goid -> "001234"
- Bio::GO::GeneAssociation#goid(true) -> "GO:001234"

[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]