Class: Bix::Gtf

Inherits:
Object
  • Object
show all
Defined in:
lib/bix/gtf.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Instance Attribute Details

#chr ⇒ Object

Returns the value of attribute chr.



5
6
7
 
# File 'lib/bix/gtf.rb', line 5

def chr
  @chr
end

#feature ⇒ Object

Returns the value of attribute feature.



5
6
7
 
# File 'lib/bix/gtf.rb', line 5

def feature
  @feature
end

#frame ⇒ Object

Returns the value of attribute frame.



5
6
7
 
# File 'lib/bix/gtf.rb', line 5

def frame
  @frame
end

#prog ⇒ Object

Returns the value of attribute prog.



5
6
7
 
# File 'lib/bix/gtf.rb', line 5

def prog
  @prog
end

#props ⇒ Object

Returns the value of attribute props.



5
6
7
 
# File 'lib/bix/gtf.rb', line 5

def props
  @props
end

#score ⇒ Object

Returns the value of attribute score.



5
6
7
 
# File 'lib/bix/gtf.rb', line 5

def score
  @score
end

#start ⇒ Object

Returns the value of attribute start.



5
6
7
 
# File 'lib/bix/gtf.rb', line 5

def start
  @start
end

#stop ⇒ Object

Returns the value of attribute stop.



5
6
7
 
# File 'lib/bix/gtf.rb', line 5

def stop
  @stop
end

#strand ⇒ Object

Returns the value of attribute strand.



5
6
7
 
# File 'lib/bix/gtf.rb', line 5

def strand
  @strand
end

Class Method Details

.get_all(io, feature_regex = //) ⇒ Object

E.g. to get all exons



42
43
44
45
46
47
48
49
50
51
52
 
# File 'lib/bix/gtf.rb', line 42

def self.get_all(io, feature_regex=//)
  gtfs = []
  for line in io
    g = Gtf.new
    g.from_line(line)
    if g.feature =~ feature_regex
      gtfs << g
    end
  end
  return gtfs
end

.get_all_by_prop(io, prop_key, feature_regex = //) ⇒ Object 



54
55
56
57
58
59
60
61
62
 
# File 'lib/bix/gtf.rb', line 54

def self.get_all_by_prop(io, prop_key, feature_regex=//)
  gtfs = get_all(io, feature_regex)
  gtfs_by_key = {}
  for g in gtfs
    gtfs_by_key[g.props[prop_key]] ||= []
    gtfs_by_key[g.props[prop_key]] << g
  end
  return gtfs_by_key
end

Instance Method Details

#from_line(line) ⇒ Object 



7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
 
# File 'lib/bix/gtf.rb', line 7

def from_line(line)
  f = line.chomp.rstrip.split("\t", -1)
  @chr = f[0]
  @prog = f[1]
  @feature = f[2]
  @start = f[3].to_i
  raise if @start < 1
  @stop = f[4].to_i
  raise if @stop < 1
  @score = f[5]
  @strand = f[6]
  raise if @strand.size > 1
  @frame = f[7]

  group = f[8]

  group.gsub!(/; /, " ") # Remove semicolons
  group.gsub!(/;$/, "") # Remove semicolons
  f = CSV::parse_line(group, :col_sep => ' ')
  raise "Unexpected number of fields in group: '#{f[7]}'" unless f.size % 2 == 0

  @props = {}
  while f.size > 0
    key = f.shift
    value = f.shift

    @props[key] = value
  end
end

#size ⇒ Object 



37
38
39
 
# File 'lib/bix/gtf.rb', line 37

def size
  return @stop - @start + 1
end

#to_s ⇒ Object 



64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
 
# File 'lib/bix/gtf.rb', line 64

def to_s
  propstr = ""
  i = 0
  for key, value in @props
    if i > 0
      propstr << " "
    end
    if value.include?(" ")
      propstr << "#{key} \"#{value}\";"
    else
      propstr << "#{key} #{value};"
    end
    i += 1
  end
  return [@chr, @prog, @feature, @start, @stop, @score, @strand, @frame, propstr].join("\t")
end