require 'zlib'
namespace '001' do
@number = 1
desc 'Clears yeast sequence data'
task :clear_sequence_data do
Gene.delete_all
end
desc 'Load yeast DNA sequence data'
task :load_sequence_data => :clear_sequence_data do
file_gz = PROJECT_ROOT + '/data/yeast_protein_genes.fasta.gz'
Zlib::GzipReader.open(file_gz) do |file|
Bio::FlatFile.auto(file).each {|entry| Gene.create_from_flatfile entry }
end
end
desc 'Clears sequence alignment data'
task :clear_alignment_data do
Alignment.delete_all
end
desc 'Loads the sequence alignment data'
task :load_alignment_data => ['clear_alignment_data'] do
file_gz = PROJECT_ROOT + '/data/yeast_alignments.txt.gz'
Zlib::GzipReader.open(file_gz) do |file|
entry = nil
file.each_line do |line|
if line =~ /\d+\s\d+/
Alignment.create_from_alignment(entry.strip) if entry
entry = ''
end
entry += line
end
end
end
desc 'Clears all data, and repeats milestone 001 analysis'
task :analysis_rebuild => [
'load_sequence_data',
'load_alignment_data'
]
desc 'Rebuilds website files'
task :www_rebuild do
file = File.dirname(__FILE__) + '/description.markdown.erb'
Stage.create_from_markdown_erb(@number,file)
end
end
