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 = '')
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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?()
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# 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)
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# 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()
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# File lib/seqtrimnext/classes/sequence.rb, line 47 def to_fasta return ">"+@seq_name.to_s+"\n"+@seq_fasta end
to_qual()
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# File lib/seqtrimnext/classes/sequence.rb, line 51 def to_qual return ">"+@seq_name.to_s+"\n"+"#{@seq_qual}" end
xs_present?()
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# File lib/seqtrimnext/classes/sequence.rb, line 39 def xs_present? return (@seq_fasta.index('X') != nil) end