Class: Bio::GFFbrowser::Digest::NoCache

Inherits:
Object
  • Object
show all
Includes:
NoCacheHelpers, Parser, Gff3Sequence
Defined in:
lib/bio/db/gff/gffnocache.rb

Instance Method Summary collapse

Methods included from Parser

#each_CDS, #each_CDS_seq, #each_exon, #each_exon_seq, #each_mRNA, #each_mRNA_seq, #read_fasta, #show_unrecognized_features, #store_record, #validate_cdss, #validate_mrnas

Methods included from Helpers::Error

#error, #info, #warn

Constructor Details

#initialize(filename, options) ⇒ NoCache

Returns a new instance of NoCache.



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# File 'lib/bio/db/gff/gffnocache.rb', line 80

def initialize filename, options
  @filename = filename
  @options = options
  @iter = Bio::GFF::GFF3::FileIterator.new(@filename)
end

Instance Method Details

#each_item(list) ⇒ Object 



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# File 'lib/bio/db/gff/gffnocache.rb', line 111

def each_item list
  # p list.class
  fh = @iter.fh
  list.each do | id, io_seeklist |
    recs = []
    io_seeklist.each do | fpos |
      recs << SeekRec::fetch(fh,fpos)
    end
    seqid = recs[0].seqname
    component = find_component(recs[0])
    yield id, recs, component
  end
end

#parse ⇒ Object

parse the whole file once and store all seek locations, rather than the records themselves



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# File 'lib/bio/db/gff/gffnocache.rb', line 88

def parse
  info "---- Digest DB and store data in mRNA Hash (NoCache)"
  @count_ids          = Counter.new   # Count ids
  @count_seqnames     = Counter.new   # Count seqnames
  @componentlist      = SeekRecList.new(@iter.fh) # Store containers, like genes, contigs
  @mrnalist           = SeekLinkedRecs.new   # Store linked mRNA records
  @cdslist            = SeekLinkedRecs.new
  @exonlist           = SeekLinkedRecs.new
  @sequencelist       = {}
  @unrecognized_features = {}
  @iter.each_rec do | id, rec |
    store_record(rec)
  end
  @iter.each_sequence do | id, bioseq |
    @sequencelist[id] = bioseq.to_s
  end
  validate_mrnas 
  validate_cdss
  show_unrecognized_features
  @genelist      = @count_ids.keys 
  read_fasta
end