Sha256: f201def4ff0abf25c42f7dab0d4ba5c5029717b57dda59608947275e3d0c2450
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Size: 1.03 KB
Versions: 13
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Stored size: 1.03 KB
Contents
#!/usr/bin/env ruby
require 'optparse'
require 'ostruct'
require 'bio-maf'
require 'bio-genomic-interval'
options = OpenStruct.new
options.p = { :threads => 1 }
options.passes = 1
OptionParser.new do |opts|
opts.banner = "Usage: maf_extract_ranges_count [options] <maf> <index>"
opts.separator ""
opts.separator "Options:"
opts.on("-t", "--threads N", "Parser threads") do |n|
options.p[:threads] = n.to_i
end
opts.on("-p", "--passes N", "Number of passes") do |n|
options.passes = n.to_i
end
end.parse!(ARGV)
maf_p = ARGV.shift
index_p = ARGV.shift
parser = Bio::MAF::Parser.new(maf_p, options.p)
index = Bio::MAF::KyotoIndex.open(index_p)
def parse_interval(line)
src, r_start_s, r_end_s, _ = line.split(nil, 4)
r_start = r_start_s.to_i
r_end = r_end_s.to_i
return Bio::GenomicInterval.zero_based(src, r_start, r_end)
end
intervals = []
$stdin.each_line { |line| intervals << parse_interval(line) }
options.passes.times do
blocks = index.find(intervals, parser)
puts "TOTAL: #{blocks.count} blocks parsed."
end
Version data entries
13 entries across 13 versions & 1 rubygems