Class: ListDb

Inherits:
Object
  • Object
show all
Defined in:
lib/seqtrimnext/classes/list_db.rb

Overview

List all entries in a DB, by name

list all DB names if db is ALL

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(path, db) ⇒ ListDb

Returns a new instance of ListDb.



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# 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

Class Method Details

.list_databases(path) ⇒ Object 



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# 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