class ListDb

List all entries in a DB, by name

list all DB names if db is ALL

Public Class Methods

list_databases(path) click to toggle source
# File lib/seqtrimnext/classes/list_db.rb, line 35
def self.list_databases(path)
  res = []
  
  if File.exists?(path)
    d=Dir.glob(File.join(path,'formatted','*.fasta'))
  
          res = d.entries.map{|e| File.basename(e)}
  end
  return res
        
        
end
new(path,db) click to toggle source
# File lib/seqtrimnext/classes/list_db.rb, line 8
def initialize(path,db)
    
                filename=File.join(path,'formatted',db)
          if File.exists?(filename)
          
                                f = File.open(filename)
                
                                f.grep(/^>(.*)$/) do |line|
                                        puts $1
                                end
                                f.close
                else
                                puts "File #{filename} doesn't exists"
                                puts ''
                                puts "Available databases:"
                                puts '-'*20
                                d=Dir.glob(File.join(path,'formatted','*.fasta'))
            d.entries.map{|e| puts File.basename(e)}

                                
#               cmd= "grep '^>' #{File.join(path,'formatted',db+'.fasta')}"
                
#               system(cmd)
          end

end