Class: Unipept::BatchIterator

Inherits:
Object
  • Object
show all
Defined in:
lib/batch_iterator.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(batch_size) ⇒ BatchIterator 



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# File 'lib/batch_iterator.rb', line 7

def initialize(batch_size)
  @batch_size = batch_size
end

Instance Attribute Details

#batch_size ⇒ Object (readonly)

Returns the value of attribute batch_size.



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# File 'lib/batch_iterator.rb', line 5

def batch_size
  @batch_size
end

Instance Method Details

#csv_taxa2tree?(line) ⇒ Boolean 



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# File 'lib/batch_iterator.rb', line 39

def csv_taxa2tree?(line)
  line.include? 'taxon_id'
end

#fasta?(line) ⇒ Boolean

Checks if the geven line is a fasta header.



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# File 'lib/batch_iterator.rb', line 35

def fasta?(line)
  line.start_with? '>'
end

#iterate(lines, &block) ⇒ Object

Splits the input lines into slices, based on the batch_size of the current command. Executes the given block for each of the batches.

Supports both normal input and input in the fasta format.



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# File 'lib/batch_iterator.rb', line 19

def iterate(lines, &block)
  first_line = lines.next rescue return
  if fasta? first_line
    fasta_iterator(first_line, lines, &block)
  elsif csv_taxa2tree? first_line
    csv_taxa_iterator(first_line, lines, &block)
  else
    normal_iterator(first_line, lines, &block)
  end
end