Class: Genomer::Files

Inherits:
Object
  • Object
show all
Defined in:
lib/genomer/files.rb

Class Method Summary collapse

Class Method Details

.annotations_gff ⇒ Object 



43
44
45
46
47
48
 
# File 'lib/genomer/files.rb', line 43

def annotations_gff
  <<-EOF.unindent
  ##gff-version   3
  ## Add your gff3 formatted annotations to this file
  EOF
end

.gemfile ⇒ Object 



6
7
8
9
10
11
12
13
 
# File 'lib/genomer/files.rb', line 6

def gemfile
  version = Genomer::VERSION.split('.')[0..1].<<(0).join('.')
  <<-EOF.unindent
    source "https://rubygems.org"

    gem 'genomer',    '~> #{version}'
  EOF
end

.scaffold_yml ⇒ Object 



15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
 
# File 'lib/genomer/files.rb', line 15

def scaffold_yml
  <<-EOF.unindent
    # Specify your genome scaffold in YAML format here. Reference nucleotide
    # sequences in the 'sequences.fna' file using the first space delimited
    # word of each fasta header.
    #
    # Go to http://next.gs/getting-started/ to start writing genome scaffold
    # files.
    #
    # A simple one contig example is also provided below. Delete this as you
    # start writing your own scaffold.
    ---
      -
        sequence:
          source: "contig1"
  EOF
end

.sequence_fna ⇒ Object 



33
34
35
36
37
38
39
40
41
 
# File 'lib/genomer/files.rb', line 33

def sequence_fna
  <<-EOF.unindent
    ; Add your assembled contigs and scaffolds sequences to this file.
    ; These sequences can be referenced in the 'scaffold.yml' file
    ; using the first space delimited word in each fasta header.
    > contig1
    ATGC
  EOF
end