class Sequence

Author: Almudena Bocinos Rioboo

Defines the class Sequence's attribute

Attributes

seq_comment[RW]
seq_fasta[RW]
seq_name[RW]
seq_qual[RW]
seq_rejected[RW]
seq_rejected_by_message[RW]
seq_repeated[RW]
seq_reversed[RW]

Public Class Methods

new(seq_name,seq_fasta,seq_qual, seq_comment = '') click to toggle source

storages the name and the contains from fasta sequence

# File lib/seqtrimnext/classes/sequence.rb, line 10
def initialize(seq_name,seq_fasta,seq_qual, seq_comment = '')     
    
    @seq_fasta=seq_fasta
    @seq_name=seq_name
    @seq_qual=seq_qual           
    @seq_comment = seq_comment
    
    @seq_rejected=false   
    @seq_repeated=false
    @seq_reversed=false 
    
    @seq_rejected_by_message=''
    
    @ns_present = ns_present?
    @xs_present = xs_present?
    
    
    
    # puts "INIT SEQ >>>> #{seq_name} #{seq_specie}"
    
end

Public Instance Methods

ns_present?() click to toggle source
# File lib/seqtrimnext/classes/sequence.rb, line 35
def ns_present?
  return (@seq_fasta.index('N')  != nil)
end
seq_is_long_enough(seq_min_length) click to toggle source
# File lib/seqtrimnext/classes/sequence.rb, line 43
def seq_is_long_enough(seq_min_length)
  return (@seq_fasta.length>=seq_min_length)
end
to_fasta() click to toggle source
# File lib/seqtrimnext/classes/sequence.rb, line 47
def to_fasta
              return ">"+@seq_name.to_s+"\n"+@seq_fasta  
end
to_qual() click to toggle source
# File lib/seqtrimnext/classes/sequence.rb, line 51
def to_qual
              return ">"+@seq_name.to_s+"\n"+"#{@seq_qual}"  
end
xs_present?() click to toggle source
# File lib/seqtrimnext/classes/sequence.rb, line 39
def xs_present?
  return (@seq_fasta.index('X') != nil)
end