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Contents
#!/usr/bin/env ruby
#This uses the map output from map_markers_to_contigs.rb
#You need a reference with the name of the contigs, containing the chromosome
#arm and a list of sequences to map. The algorithm creates a smaller reference
#file, so the search only spans across the contigs in the region. This should
#allow to use a refined mapping algorithm.
require 'bio'
require 'optparse'
$: << File.expand_path(File.dirname(__FILE__) + '/../lib')
$: << File.expand_path('.')
path= File.expand_path(File.dirname(__FILE__) + '/../lib/bioruby-polyploid-tools.rb')
require path
def log(msg)
time=Time.now.strftime("%Y-%m-%d %H:%M:%S.%L")
puts "#{time}: #{msg}"
end
markers = nil
options = {}
OptionParser.new do |opts|
opts.banner = "Usage: polymarker.rb [options]"
opts.on("-c", "--chromosome CHR", "chromosome (1A, 3B, etc)") do |o|
options[:chromosome] = o.upcase
end
opts.on("-r", "--reference FASTA", "reference with the contigs") do |o|
options[:reference] = o
end
opts.on("-m", "--map CSV", "File with the map and sequence \n Header: INDEX_90K,SNP_ID,SNP_NAME,CHR,COORDINATES_CHR,MAP_ORDER,CHR_ARM,DISTANCE_CM,SEQUENCE") do |o|
options[:map] = o
end
end.parse!
#reference="/Users/ramirezr/Documents/TGAC/references/Triticum_aestivum.IWGSP1.21.dna_rm.genome.fa"
reference = options[:reference] if options[:reference]
throw raise Exception.new(), "Reference has to be provided" unless reference
Version data entries
20 entries across 20 versions & 1 rubygems