class Genomer::Files
Public Class Methods
annotations_gff()
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# 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()
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# 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()
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# 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()
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# 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