Class: MbraveTagsCreator

Inherits:
Object
  • Object
show all
Extended by:
StaticMethods
Defined in:
lib/mbrave_tags_creator.rb

Overview

Class to support creation of tag groups, tag layout templates and generation of the mbrave.yml config needed by limber to be able to generate the mbrave UMI file at the end of the bioscan process. rubocop:disable Metrics/ClassLength

Defined Under Namespace

Modules: StaticMethods

Constant Summary collapse

YAML_FILENAME = 
'mbrave.yml'
TAG_IDENTIFIER = 
'Bioscan'

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from StaticMethods

create_tag_plates, process_create_tag_groups, process_create_tag_plates, text_code_for_tag_layout

Constructor Details

#initialize(params) ⇒ MbraveTagsCreator

Returns a new instance of MbraveTagsCreator.



18
19
20
21
22
23
24
25
26
27
 
# File 'lib/mbrave_tags_creator.rb', line 18

def initialize(params)
  @forward_filename = params[:forward_filename]
  @reverse_filename = params[:reverse_filename]
  @tag_identifier = params[:tag_identifier]
  @version = params[:version]
  @yaml_filename = params[:yaml_filename]
  @forward_group = nil
  @reverse_groups = []
  @yaml_contents = {}
end

Instance Attribute Details

#forward_filename ⇒ Object (readonly)

Returns the value of attribute forward_filename.



10
11
12
 
# File 'lib/mbrave_tags_creator.rb', line 10

def forward_filename
  @forward_filename
end

#forward_group ⇒ Object (readonly)

Returns the value of attribute forward_group.



10
11
12
 
# File 'lib/mbrave_tags_creator.rb', line 10

def forward_group
  @forward_group
end

#reverse_filename ⇒ Object (readonly)

Returns the value of attribute reverse_filename.



10
11
12
 
# File 'lib/mbrave_tags_creator.rb', line 10

def reverse_filename
  @reverse_filename
end

#reverse_groups ⇒ Object (readonly)

Returns the value of attribute reverse_groups.



10
11
12
 
# File 'lib/mbrave_tags_creator.rb', line 10

def reverse_groups
  @reverse_groups
end

#tag_identifier ⇒ Object (readonly)

Returns the value of attribute tag_identifier.



10
11
12
 
# File 'lib/mbrave_tags_creator.rb', line 10

def tag_identifier
  @tag_identifier
end

#version ⇒ Object (readonly)

Returns the value of attribute version.



10
11
12
 
# File 'lib/mbrave_tags_creator.rb', line 10

def version
  @version
end

#yaml_filename ⇒ Object (readonly)

Returns the value of attribute yaml_filename.



10
11
12
 
# File 'lib/mbrave_tags_creator.rb', line 10

def yaml_filename
  @yaml_filename
end

Class Method Details

.log_line ⇒ Object 



34
35
36
37
38
39
 
# File 'lib/mbrave_tags_creator.rb', line 34

def self.log_line
  # We want to enforce that logs go to STDOUT while printing the barcodes
  # rubocop:disable Rails/Output
  puts yield
  # rubocop:enable Rails/Output
end

Instance Method Details

#create_1_tag_group_forward ⇒ Object

rubocop:disable Metrics/AbcSize rubocop:disable Metrics/MethodLength



54
55
56
57
58
59
60
61
62
63
64
65
66
 
# File 'lib/mbrave_tags_creator.rb', line 54

def create_1_tag_group_forward
  tags = []
  mbrave_tags = []
  log_line { "Creating forward_tags from: #{forward_filename}" }
  CSV.foreach(forward_filename, headers: true) do |row|
    tag = Tag.new(map_id: row['Forward Index Number'], oligo: row['F index sequence'])
    tags.push(tag)
    mbrave_tags.push(row['Forward Oligo Label'])
  end
  log_line { " - #{forward_tag_group_name}" }
  @forward_group = _create_tag_group(forward_tag_group_name, tags)
  _add_to_yaml(yaml_filename, forward_tag_group_name, mbrave_tags, version, 1)
end

#create_24_tag_groups_reverse ⇒ Object 



68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
 
# File 'lib/mbrave_tags_creator.rb', line 68

def create_24_tag_groups_reverse
  tags = []
  mbrave_tags = []
  group = 1
  log_line { "Creating reverse tags from: #{reverse_filename}" }
  CSV.foreach(reverse_filename, headers: true) do |row|
    _validate_reverse_row(row)
    map_id = row['Reverse Index Number'].to_i
    pos = ((map_id - 1) % 4) + 1
    tag = Tag.new(map_id: pos, oligo: row['R index sequence'])
    tags.push(tag)
    mbrave_tags.push(row['Reverse Oligo Label'])

    if pos == 4
      log_line { " - #{reverse_tag_group_name(group)}" }
      @reverse_groups.push(_create_tag_group(reverse_tag_group_name(group), tags))
      _add_to_yaml(yaml_filename, reverse_tag_group_name(group), mbrave_tags, version, group)
      group += 1
      tags = []
      mbrave_tags = []
    end
  end
end

#create_tag_layout_templates ⇒ Object

rubocop:enable Metrics/AbcSize rubocop:enable Metrics/MethodLength



95
96
97
98
99
100
101
102
103
104
105
106
107
108
 
# File 'lib/mbrave_tags_creator.rb', line 95

def create_tag_layout_templates
  log_line { 'Creating tag layout templates:' }
  @reverse_groups.each_with_index do |reverse_group, index|
    log_line { " - #{tag_layout_template_name(index)}" }
    TagLayoutTemplate.create(
      name: tag_layout_template_name(index),
      tag_group: @forward_group,
      tag2_group: reverse_group,
      direction_algorithm: 'TagLayout::InColumnsThenColumns',
      walking_algorithm: 'TagLayout::Quadrants',
      enabled: true
    )
  end
end

#forward_tag_group_name ⇒ Object 



114
115
116
 
# File 'lib/mbrave_tags_creator.rb', line 114

def forward_tag_group_name
  "#{tag_identifier}_forward_96_#{version}"
end

#log_line ⇒ Object 



29
30
31
32
 
# File 'lib/mbrave_tags_creator.rb', line 29

def log_line(&)
  # We want to enforce that logs go to STDOUT while printing the barcodes
  self.class.log_line(&)
end

#reverse_tag_group_name(group) ⇒ Object 



118
119
120
 
# File 'lib/mbrave_tags_creator.rb', line 118

def reverse_tag_group_name(group)
  "#{tag_identifier}_reverse_4_#{group}_#{version}"
end

#tag_layout_template_name(group) ⇒ Object 



110
111
112
 
# File 'lib/mbrave_tags_creator.rb', line 110

def tag_layout_template_name(group)
  "#{tag_identifier}_384_template_#{group + 1}_#{version}"
end

#write_yaml(yaml_filename) ⇒ Object 



41
42
43
44
45
46
47
48
49
50
 
# File 'lib/mbrave_tags_creator.rb', line 41

def write_yaml(yaml_filename)
  log_line { "Generating file #{yaml_filename}" }
  new_contents = {}
  new_contents['development'] = @yaml_contents
  new_contents['test'] = @yaml_contents
  new_contents['staging'] = @yaml_contents
  new_contents['training'] = @yaml_contents
  new_contents['production'] = @yaml_contents
  File.write(yaml_filename, new_contents.to_yaml)
end