Sha256: 83b4de2e9a13c79618e920598b2cc001707a84aebb761e190dd5ff588548a0b5
Contents?: true
Size: 705 Bytes
Versions: 16
Compression:
Stored size: 705 Bytes
Contents
#!/usr/bin/env ruby
require 'scbi_fasta'
if ARGV.count!=3
puts "Usage: #{File.basename($0)} database min_size name_list"
exit
end
min_size = ARGV[1].to_i
# read keywords
keywords=File.read(ARGV[2]).split("\n")
# convert all to upcase
keywords.map { |keyword| keyword.upcase!}
# puts "Search keywords"
# keywords.each { |keyword| puts keyword}
fqr=FastaQualFile.new(ARGV[0])
all=[]
fqr.each do |n,s,c|
keywords.each do |keyword|
if s.length<=min_size
# all+=c.split(" ")
if c.upcase.index(keyword)
# puts "[#{s.length.to_s}] - #{n} - #{c}"
puts ">#{n} #{c}\n#{s}"
break
end
end
end
end
# puts all.sort.uniq.reject{|e| e=~/\d/}
fqr.close
Version data entries
16 entries across 16 versions & 1 rubygems