drio

class DBEvent
  attr_accessor :ref, :o_events, :sp

  def initialize(sp, events)
    @sp         = sp
    @ref        = events.split('/')[0]
    @raw_events = events
    @o_events   = Hash.new(Array.new) # Observed events

    # Iterate over each observed event

drio

#!/usr/bin/env ruby

# Generate random genomes:
#
# Creates a random genome with the number of contig you specify.
# You can pass the number of characters per line and the max size
# of the contigs.
#
class RandomGenome
  # + hr: root string for the headers

drio

#!/usr/bin/env ruby

# Basic Statistical Methods Module
# accepts: an array, the population/list
# returns: Result of running the measure (std_dev, mean, median)
#
module StatisticalTools
  def self.std_dev(population)
    n    = 0
    mean = 0.0

drio

# one 1_1 2_1 two 1_2 2_2

def foo(h1, h2)
  tmp = Hash.new {|hash, key| hash[key] = "" }
  h1.each {|k,v| tmp[k] << v }
  h2.each {|k,v| tmp[k] << " " + v }
  tmp
end

hash1 = { "one" => "1_1" , "two" => "1_2" }

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pb      # reads used: 151750
ovarian # reads used: 639290

Number of reads that map with n mismatches: (for ovarian.psl)
---------
0:500848
1:6413
2:29
3:10

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##gff-version 2
##solid-gff-version 0.2
##date 2009-03-30
##time 17:56:07
##color-code AA=0,AC=1,AG=2,AT=3,CA=1,CC=0,CG=3,CT=2,GA=2,GC=3,GG=0,GT=1,TA=3,TC=2,TG=1,TT=0
##primer-base F3=T
##max-num-mismatches 2
##max-read-length 25
##line-order fragment
##conversion unique

drio

pipeline@head0100 / $ source /opt/matlabruntime/matlab.env &&  /share/apps/corona-1.0r9.9/bin/sunspot -v
Loading matlab 2006a 64-bit
Warning: Unable to open display , MATLAB is starting without a display.
  You will not be able to display graphics on the screen.
Warning:
  MATLAB is starting without a display, using internal event queue.
  You will not be able to display graphics on the screen.

*** Applied Biosystems SOLiD Basecalling Analysis Software ***
'sunspot' version 1.0.4 (9.9, SVN 20186, 2008-06-26)

drio

module FindFiles
  def self.find(ldirs, re)
    dirs = dirs.is_a?(String) ? File.open(ldirs).readlines : ldirs
    your_files = []
    dirs.each do |d|
      Dir["#{d}/*"].each { |f| your_files << f if f =~ re }
    end
    your_files
  end
end

drio

#!/users/p-solid/local/bin/ruby19
#
# If you want to run against multiple data sets:
# ruby -e 'File.open(Dir["list*"].join).each_line{|l| puts "./create_splits.rb {File.basename(l.chomp)} #{l.chomp}"}'
#
require 'fileutils'

def run_lsf(str)
  bs = "bsub -q solid -J GBM_drio_splits '#{str}'"
  puts bs

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#!/users/p-solid/local/bin/ruby19
#
# If you want to run against multiple data sets:
# ruby -e 'File.open(Dir["list*"].join).each_line{|l| puts "./create_splits.rb {File.basename(l.chomp)} #{l.chomp}"}'
#
require 'fileutils'

def run_lsf(str)
  bs = "bsub -q solid -J GBM_drio_splits '#{str}'"
  puts bs