Module: Bix

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

.read_frq(io_or_fn) ⇒ Object

Reads a frq file, producing a list of hashes with the keys :chr, :snp, :a1, :a2, :maf, :nchrobs



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# File 'lib/bix/plink.rb', line 69

def self.read_frq(io_or_fn)
  io = io_or_fn.instance_of?(String) ? File.new(io_or_fn) : io
  io.gets # header
  res = []
  for line in io
    f = line.chomp.split
    h = {}
    h[:chr] = f[0]
    h[:snp] = f[1]
    h[:a1] = f[2]
    h[:a2] = f[3]
    h[:maf] = f[4].to_f
    h[:nchrobs] = f[5].to_i

    res << h
  end

  return res
end

.read_tfam(io_or_fn) ⇒ Object

Reads a tfam file, extracting a list of the individual names



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# File 'lib/bix/plink.rb', line 5

def self.read_tfam(io_or_fn)
  io = io_or_fn.instance_of?(String) ? File.new(io_or_fn) : io

  inds = []

  for line in io
    line.chomp!
    next if line[0] == '#'
    f = line.split(/\t| /)
    inds << f[1]
  end

  return inds
end

.read_tped(io_or_fn, ind_list = nil, as_array = false) ⇒ Object

Reads a tped file. Produces a hash of ind_name => [haplotype 1, haplotype 2]. ind_list specifies ind_names, if nil, ind names are just 0,1,2… as_array indicates whether haps will be output as strings or arrays



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# File 'lib/bix/plink.rb', line 23

def self.read_tped(io_or_fn, ind_list=nil, as_array=false)
  io = io_or_fn.instance_of?(String) ? File.new(io_or_fn) : io

  ind_map = nil

  for line in io
    line.chomp!
    next if line[0] == '#'
    f = line.split(/ |\t/)

    if !ind_map
      ind_map = {}
      # Initialize ind_map first
      if ind_list
        for i in 0...ind_list.size
          ind_map[ind_list[i]] = i
        end
      else
        ((f.size-4)/2).times do |ind_idx|
          ind_map[ind_idx] = ind_idx
        end
      end

      # Initialize haps object
      haps = {} # name => [hap1_vec, hap2_vec]
      for name, ind_idx in ind_map
        if as_array
          haps[name] = [[], []]
        else
          haps[name] = ["", ""]
        end
      end
    end


    for name, ind_idx in ind_map
      haps[name][0] << f[4 + 2 * ind_idx + 0]
      haps[name][1] << f[4 + 2 * ind_idx + 1]
    end
  end

  return haps
end