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Versions: 17
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Contents
########################################################
# Author: Almudena Bocinos Rioboo
#
# Defines the class Sequence's attribute
#
########################################################
class Sequence
#storages the name and the contains from fasta sequence
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
attr_accessor :seq_name, :seq_fasta, :seq_qual, :seq_comment , :seq_rejected, :seq_repeated , :seq_reversed
attr_accessor :seq_rejected_by_message
def ns_present?
return (@seq_fasta.index('N') != nil)
end
def xs_present?
return (@seq_fasta.index('X') != nil)
end
def seq_is_long_enough(seq_min_length)
return (@seq_fasta.length>=seq_min_length)
end
def to_fasta
return ">"+@seq_name.to_s+"\n"+@seq_fasta
end
def to_qual
return ">"+@seq_name.to_s+"\n"+"#{@seq_qual}"
end
end
Version data entries
17 entries across 17 versions & 1 rubygems