Class: FastaProcessor

Inherits:
FastaUtils::FastaReader
  • Object
show all
Defined in:
lib/seqtrimnext/utils/fasta2xml.rb

Overview

Define a subclass to override events

Instance Method Summary collapse

Instance Method Details

#on_begin_process ⇒ Object

override begin processing



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# File 'lib/seqtrimnext/utils/fasta2xml.rb', line 43

def on_begin_process()
    
  # print XML header
  puts "<?xml version=\"1.0\"?>\n<trace_volume>\n";
  
end

#on_end_process ⇒ Object

override end processing



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# File 'lib/seqtrimnext/utils/fasta2xml.rb', line 59

def on_end_process()

  #print foot
  puts "</trace_volume>\n";
  
end

#on_process_sequence(seq_name, seq_fasta) ⇒ Object

override sequence processing



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# File 'lib/seqtrimnext/utils/fasta2xml.rb', line 51

def on_process_sequence(seq_name,seq_fasta)
  
  # prints the xml tags
  puts "<trace>\n\t<trace_name>#{seq_name}</trace_name>\n\t<clip_vector_left>1</clip_vector_left>\n\t<clip_vector_right>#{seq_fasta.length.to_s}</clip_vector_right>\n</trace>\n";
  
end