Class: Ezgff::GffDb::Annotation

Inherits:
Object
  • Object
show all
Defined in:
lib/ezgff/gffsqlitedb.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(db = nil) ⇒ Annotation

Returns a new instance of Annotation.



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# File 'lib/ezgff/gffsqlitedb.rb', line 226

def initialize(db = nil)
  @db = db
  @seqid
  @source
  @type
  @start
  @end
  @score
  @strand
  @phase
  @attributes
  @id
  @parent_id
  @gffline
end

Instance Attribute Details

#attributes ⇒ Object

Returns the value of attribute attributes.



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# File 'lib/ezgff/gffsqlitedb.rb', line 242

def attributes
  @attributes
end

#end ⇒ Object

Returns the value of attribute end.



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# File 'lib/ezgff/gffsqlitedb.rb', line 242

def end
  @end
end

#gffline ⇒ Object

Returns the value of attribute gffline.



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# File 'lib/ezgff/gffsqlitedb.rb', line 243

def gffline
  @gffline
end

#id ⇒ Object

Returns the value of attribute id.



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# File 'lib/ezgff/gffsqlitedb.rb', line 243

def id
  @id
end

#line_num ⇒ Object

Returns the value of attribute line_num.



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# File 'lib/ezgff/gffsqlitedb.rb', line 243

def line_num
  @line_num
end

#parent_id ⇒ Object

Returns the value of attribute parent_id.



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# File 'lib/ezgff/gffsqlitedb.rb', line 243

def parent_id
  @parent_id
end

#phase ⇒ Object

Returns the value of attribute phase.



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# File 'lib/ezgff/gffsqlitedb.rb', line 242

def phase
  @phase
end

#score ⇒ Object

Returns the value of attribute score.



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# File 'lib/ezgff/gffsqlitedb.rb', line 242

def score
  @score
end

#seqid ⇒ Object

Returns the value of attribute seqid.



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# File 'lib/ezgff/gffsqlitedb.rb', line 242

def seqid
  @seqid
end

#source ⇒ Object

Returns the value of attribute source.



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# File 'lib/ezgff/gffsqlitedb.rb', line 242

def source
  @source
end

#start ⇒ Object

Returns the value of attribute start.



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# File 'lib/ezgff/gffsqlitedb.rb', line 242

def start
  @start
end

#strand ⇒ Object

Returns the value of attribute strand.



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# File 'lib/ezgff/gffsqlitedb.rb', line 242

def strand
  @strand
end

#type ⇒ Object

Returns the value of attribute type.



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# File 'lib/ezgff/gffsqlitedb.rb', line 242

def type
  @type
end

Instance Method Details

#ancestors ⇒ Object 



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# File 'lib/ezgff/gffsqlitedb.rb', line 333

def ancestors
  ary = []
  sql = %Q{WITH RECURSIVE  ancestor AS (
    SELECT * FROM gff_records WHERE id=="#{id}"
    UNION ALL
    SELECT gff_records.* FROM gff_records, ancestor
    WHERE ancestor.parent = gff_records.id
    )
    SELECT * FROM ancestor;}
  res = @db.execute(sql)
  res.each do |r|
    an = Annotation.new(@db)
    an.build_from_db_record(r)
    ary << an
  end
  ary
end

#build_from_db_record(sql_result) ⇒ Object 



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# File 'lib/ezgff/gffsqlitedb.rb', line 272

def build_from_db_record(sql_result)
  ## sql_result: Array returned by @db.execute(sql)
  v = sql_result
  @seqid = v[4]
  @source  = v[5]
  @type = v[6]
  @start = v[7]
  @end = v[8]
  @score = v[9]
  @strand = v[10]
  @phase = v[11]
  @line_num = v[0]
  @gffline = v[1]
  @id = v[2]
  @parent_id = v[3]
  @attributes = JSON.parse(v[13])
end

#children ⇒ Object 



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# File 'lib/ezgff/gffsqlitedb.rb', line 303

def children
  ary = []
  sql = %Q{SELECT * FROM gff_records WHERE parent=="#{id}";}
  #      puts sql
  res = @db.execute(sql)
  res.each do |r|
    an = Annotation.new(@db)
    an.build_from_db_record(r)
    ary << an
  end
  ary
end

#dbxrefs ⇒ Object 



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# File 'lib/ezgff/gffsqlitedb.rb', line 358

def dbxrefs
  h = Hash.new
  if attributes["Dbxref"]
    attributes["Dbxref"].split(/,/).each do |x|
      m = /(.+?):/.match(x)
      key = m[1]
      val = m.post_match
      h.update({key => val})
    end
  end
  h
end

#descendants ⇒ Object 



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# File 'lib/ezgff/gffsqlitedb.rb', line 316

def descendants
  ary = []
  sql = %Q{WITH RECURSIVE r AS (
    SELECT * FROM gff_records WHERE id=="#{id}"
    UNION ALL
    SELECT gff_records.* FROM gff_records, r WHERE gff_records.parent == r.id
    )
    SELECT * FROM r}
  res = @db.execute(sql)
  res.each do |r|
    an = Annotation.new(@db)
    an.build_from_db_record(r)
    ary << an
  end
  ary
end

#length ⇒ Object 



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# File 'lib/ezgff/gffsqlitedb.rb', line 352

def length
  len = @end - @start + 1
  raise unless len > 0
  return len
end

#parent ⇒ Object 



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# File 'lib/ezgff/gffsqlitedb.rb', line 290

def parent
  if parent_id
    sql = %Q{SELECT * FROM gff_records WHERE id=="#{parent_id}";}
  #        puts sql
    res = @db.execute(sql)
    an = Annotation.new(@db)
    an.build_from_db_record(res[0])
    return an
  else
    return nil
  end
end

#to_hash ⇒ Object Also known as: to_h 



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# File 'lib/ezgff/gffsqlitedb.rb', line 249

def to_hash
  h = {
    'seqid' => seqid,
    'source' => source,
    'type' => type,
    'start' => start,
    'end' => self.end,
    'score' => score,
    'strand' => strand,
    'phase' => phase,
    'line_num' => line_num,
    'id' => id,
    'parent_id' => parent_id,
    'attributes' => attributes
  }
end

#to_json ⇒ Object 



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# File 'lib/ezgff/gffsqlitedb.rb', line 268

def to_json
  self.to_hash.to_json
end

#to_s ⇒ Object 



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# File 'lib/ezgff/gffsqlitedb.rb', line 245

def to_s
  gffline
end