Class: Sequence

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

Overview

Author: Almudena Bocinos Rioboo

Defines the class Sequence’s attribute

Direct Known Subclasses

SequenceWithAction

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(seq_name, seq_fasta, seq_qual, seq_comment = '') ⇒ Sequence

storages the name and the contains from fasta sequence



10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
 
# 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

Instance Attribute Details

#seq_comment ⇒ Object

Returns the value of attribute seq_comment.



32
33
34
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 32

def seq_comment
  @seq_comment
end

#seq_fasta ⇒ Object

Returns the value of attribute seq_fasta.



32
33
34
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 32

def seq_fasta
  @seq_fasta
end

#seq_name ⇒ Object

Returns the value of attribute seq_name.



32
33
34
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 32

def seq_name
  @seq_name
end

#seq_qual ⇒ Object

Returns the value of attribute seq_qual.



32
33
34
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 32

def seq_qual
  @seq_qual
end

#seq_rejected ⇒ Object

Returns the value of attribute seq_rejected.



32
33
34
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 32

def seq_rejected
  @seq_rejected
end

#seq_rejected_by_message ⇒ Object

Returns the value of attribute seq_rejected_by_message.



33
34
35
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 33

def seq_rejected_by_message
  @seq_rejected_by_message
end

#seq_repeated ⇒ Object

Returns the value of attribute seq_repeated.



32
33
34
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 32

def seq_repeated
  @seq_repeated
end

#seq_reversed ⇒ Object

Returns the value of attribute seq_reversed.



32
33
34
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 32

def seq_reversed
  @seq_reversed
end

Instance Method Details

#ns_present? ⇒ Boolean

Returns:

  • (Boolean) 


35
36
37
 
# 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) ⇒ Object 



43
44
45
 
# 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 ⇒ Object 



47
48
49
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 47

def to_fasta
		return ">"+@seq_name.to_s+"\n"+@seq_fasta  
end

#to_qual ⇒ Object 



51
52
53
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 51

def to_qual
		return ">"+@seq_name.to_s+"\n"+"#{@seq_qual}"  
end

#xs_present? ⇒ Boolean

Returns:

  • (Boolean) 


39
40
41
 
# File 'lib/seqtrimnext/classes/sequence.rb', line 39

def xs_present?
  return (@seq_fasta.index('X') != nil)
end