Class: EupathDBGFF

Inherits:
JgiGenesGff show all
Defined in:
lib/eupathdb_gff.rb

Overview

Unlike JGI genes files, ApiDB files have several differences:

- genes on the reverse strand appear in order of their exons, and so
  the exons are not all in the correct order with respect to the underlying
  sequence.

Instance Attribute Summary collapse

Instance Method Summary collapse

Methods inherited from JgiGenesGff

#distance_iterator

Constructor Details

#initialize(path) ⇒ EupathDBGFF

Returns a new instance of EupathDBGFF.



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# File 'lib/eupathdb_gff.rb', line 14

def initialize(path)
  @file = File.open path, 'r'
  @next_gff = read_record
  @features_to_ignore = [
    'rRNA',
    'tRNA',
    'snRNA',
    'transcript',
    'ncRNA',
  ]
end

Instance Attribute Details

#features_to_ignore ⇒ Object

Returns the value of attribute features_to_ignore.



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# File 'lib/eupathdb_gff.rb', line 12

def features_to_ignore
  @features_to_ignore
end

Instance Method Details

#ignore_line?(cur) ⇒ Boolean

ignore this line when parsing the file

Returns:

  • (Boolean) 


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# File 'lib/eupathdb_gff.rb', line 117

def ignore_line?(cur)
  return ['supercontig', 'introgressed_chromosome_region'].include?(cur.feature)
end

#ignore_record?(record) ⇒ Boolean

Certain things I don’t want uploaded, like apicoplast genome, etc.

Returns:

  • (Boolean) 


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# File 'lib/eupathdb_gff.rb', line 122

def ignore_record?(record)
  if !record or !record.seqname or
      @features_to_ignore.include?(record.feature) or 
      record.seqname.match(/^apidb\|NC\_/) or
      record.seqname.match(/^apidb\|API_IRAB/) or
      record.seqname.match(/^apidb\|M76611/) or
      record.seqname.match(/^apidb\|X95276/) #or
#        record.seqname.match(/^apidb\|Pf/)
    return true
  else
    return false
  end
end

#next_gene ⇒ Object 



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# File 'lib/eupathdb_gff.rb', line 26

def next_gene
  cur = @next_gff

  if !cur
    return nil
  end
  
  # Ignore the supercontigs at the start of the file
  while ignore_line?(cur) or ignore_record?(cur)
    @next_gff = read_record
    cur = @next_gff
    if !cur
      return nil
    end
  end
  
  if cur.feature != 'gene'
    raise Exception, "Badly parsed apidb line: #{cur}. Expected gene first."
  end
  
  # save line so can set these values later,
  # i
  gene_line = cur
    
    
  # First mRNA
  cur = read_record
  
  if cur.feature != 'mRNA'
    # skip rRNA type genes because they are not relevant
    if ignore_record?(cur)
      # skip forward to the next gene
      while cur.feature != 'gene'
        cur = read_record
        return nil if cur.nil? # we have reached the end on an ignored gene
      end
      @next_gff = cur
      if cur
        return next_gene
      else
        return nil
      end
    else
      raise Exception, "Badly parsed apidb line: #{cur}. Expected mRNA next."
    end
  end
  
  # Setup the gene in itself
  gene = setup_gene_from_first_line gene_line
  
  # setup stuff from mRNA line
  ids = cur.attributes['Ontology_term']
  if ids
    gene.go_identifiers = ids.split ','
  end
  
  # Next CDS
  cur = read_record
  if cur.feature != 'CDS'
    raise Exception, "Badly parsed apidb line: #{cur}. Expected CDS next."
  end
  gene.cds = []
  while cur.feature == 'CDS'
    f = Bio::Location.new
    f.from = cur.start
    f.to = cur.end
    gene.cds.push f
      
    cur = read_record
  end
    
  #next exons
  if cur.feature != 'exon'
    raise Exception, "Badly parsed apidb line: #{cur}. Expected exon next."
  end
  gene.exons = []
  while cur and cur.feature == 'exon'
    f = Bio::Location.new
    f.from = cur.start
    f.to = cur.end
    gene.exons.push f
      
    cur = read_record
  end
    
  @next_gff = cur

  return gene
end