From: "Ken L." <lists@...>
Date: 2012-09-06T01:33:02+09:00
Subject: Newbie needs help

Hi everyone,

I'm new to Ruby and am encountering a problem with an error message that
I don't quite understand.  I am hoping someone more experienced can
explain where I have gone wrong. Any help would be much appreciated.

When I do not specify parameters, I get no errors:

 ruby ~/Ruby_code/Align_against_reference.rb "temp.fastq"
"temp.alignment"
.........................done
Run options:

# Running tests:

......

Finished tests in 0.007649s, 784.4163 tests/s, 6144.5941 assertions/s.

6 tests, 47 assertions, 0 failures, 0 errors, 0 skips


But when I specify which lines of the file to process, I get the
following:

ruby ~/Ruby_code/Align_against_reference.rb "temp.fastq"
"temp.alignment" 0 40
..........done
/home/lok2/bin/ruby/lib/ruby/1.9.1/test/unit.rb:167:in `block in
non_options': file not found: 0 (ArgumentError)
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/test/unit.rb:146:in
`map!'
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/test/unit.rb:146:in
`non_options'
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/test/unit.rb:207:in
`non_options'
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/test/unit.rb:52:in
`process_args'
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/minitest/unit.rb:891:in
`_run'
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/minitest/unit.rb:884:in
`run'
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/test/unit.rb:21:in `run'
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/test/unit.rb:326:in
`block (2 levels) in autorun'
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/test/unit.rb:27:in
`run_once'
        from /home/lok2/bin/ruby/lib/ruby/1.9.1/test/unit.rb:325:in
`block in autorun'



My script:

require("/home/lok2/Ruby_code/SeqRead.rb")

start = ARGV[2].to_i
stop = ARGV[3].to_i == 0 ? :eof : ARGV[3].to_i

fastq = FastxReader.new
fastq.readSingleEnd(ARGV[0], start, stop)

pL = DNA.new("TGC CGG AGT CAG CGT") # 5' -> 3' left primer
pR = DNA.new("AGT CAG AGT CGC CAC") # 5' -> 3' right primer

sm = {
  'AA' => 1, 'AG' => 0, 'AC' => 0, 'AT' => 0,
  'GA' => 0, 'GG' => 1, 'GC' => 0, 'GT' => 0,
  'CA' => 0, 'CG' => 0, 'CC' => 1, 'CT' => 0,
  'TA' => 0, 'TG' => 0, 'TC' => 0, 'TT' => 1
}

insert =
DNA.new("CTGTTCTCCCTACATCAAATGTCTATCCCCGCACCAAGTGGAGATTCCATGAGGATGAGG")

def align(reference, test, similarity_matrix, gapPenality=0)
  aln = NW.new(reference, test, similarity_matrix, gapPenality)
  if (aln.score == reference.length)
    return aln
  else
    aln2 = NW.new(reference, test.rev_comp.reverse, similarity_matrix,
gapPenality)
  end
  temp =(aln.score > aln2.score) ? aln : aln2
  return(temp)
end


temp = File.open(ARGV[1], "w")
alignments = fastq.reads.each do |read|
  temp.puts ">" + read.readName
  temp.puts "Sequence:"
  temp.puts read.dna_seq
  aln=align(insert, read.stripPrimers(pL, pR), sm, 0)
  print "."
  temp.puts "Alignment:"
  temp.puts aln.display
  temp.puts "Errors:"
  temp.puts aln.errors
  temp.puts "\n"
end

Here are the relevant parts from SeqRead.rb

class FastxReader

  attr_reader :reads, :type

  def initialize(type=:fastq)
    @type = type
    @reads = []
  end

  def readSingleEnd (fastx_file, startline=0, endline=:eof)
    file = File.open(fastx_file, "r")
    endline=File.foreach(fastx_file).inject(0){|c, l| c+1} if endline ==
:eof
    (0...startline).each {|x| file.readline}
    while file.lineno < endline && !file.eof? do
      @reads << readRecord(file, @type)
    end
    file.close
  end

  def readPairedEnd (fastx_file_1, fastx_file_2)
    fileA = File.open(fastx_file_1)
    fileB = File.open(fastx_file_2)
    while !fileA.eof? && !fileB.eof? do
      readA = readRecord(fileA, @type)
      readB = readRecord(fileB, @type)
      @reads << PairedEndRead.new(readA, readB)
    end
    fileA.close
    fileB.close
  end

  def readRecord(fastxFile, fileType=:fastq)
    record = []
    if fileType == :fastq
      4.times {|x| record << fastxFile.gets.strip}
      SeqRead.new(record[1], record[3], record[0].split("
").first).stripPrimer("N")
    elsif filetype == :fasta
      2.times {|x| record << fastxFile.gets.strip}
      SeqRead.new(record[1], record[0]).stripPrimer("N")
    else
      throw ArgumentError
    end
  end


end

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