class ActionLowQuality
Author: Almudena Bocinos Rioboo
Defines the main methods that are necessary to execute PluginActionLowHighSize
Inherit: Plugin
Public Class Methods
new(start_pos,end_pos)
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Calls superclass method
SeqtrimAction::new
# File lib/seqtrimnext/actions/action_low_quality.rb, line 12 def initialize(start_pos,end_pos) super(start_pos,end_pos) # esto es cut=false porque al principio el plugin lowqual estaba al inicio del pipeline y habia que dejar # la secuencia larga para que se encontrasen los contaminantes y vectores # Tambien esta por si un linker tiene baja calidad que pueda encontrarlo @cut =false end
Public Instance Methods
apply_decoration(char)
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def apply_to(seq)
# seq.seq_fasta = seq.seq_fasta.slice(start_pos,end_pos) $LOG.debug " Applying #{self.class} to #{seq.seq_name} . This sequence will be ignored due to low quality " #delete sequence if it was created
end
# File lib/seqtrimnext/actions/action_low_quality.rb, line 30 def apply_decoration(char) return char.downcase.on_white end