Module: Bix

Defined in:
lib/bix.rb,
lib/bix/gtf.rb,
lib/bix/blast.rb,
lib/bix/fasta.rb,
lib/bix/fastq.rb

Overview

Define it here, will get used elsewhere

Defined Under Namespace

Modules: Blast Classes: Fasta, Fastq, Gtf

Class Method Summary collapse

Class Method Details

.get_all_fastqs(io) ⇒ Object 



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# File 'lib/bix/fastq.rb', line 44

def self.get_all_fastqs(io)
  fqs = []
  while(fq = Fastq.from_io(io))
    fqs << fq
  end
  return fqs
end

.read_fastas(io) ⇒ Object 



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# File 'lib/bix/fasta.rb', line 6

def self.read_fastas(io)
  fastas = []

  fa = nil

  for line in io
    line.chomp!
    if line[0] == '>'
      fastas << fa if fa != nil

      fa = Bix::Fasta.new
      fa.header = line
      fa.seq = ""
    else
      fa.seq << line
    end

  end

  fastas << fa if fa != nil

  return fastas
end