Class: CagnutBwa::SampOneFastq

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Defined in:
lib/cagnut_bwa/functions/samp_one_fastq.rb

Instance Method Summary collapse

Instance Method Details

#bwa_samp_one_fastq(script_name) ⇒ Object 



73
74
75
76
77
78
79
80
81
 
# File 'lib/cagnut_bwa/functions/samp_one_fastq.rb', line 73

def bwa_samp_one_fastq script_name
  file = File.join jobs_dir, "#{@order}_#{script_name}.sh"
  path = File.expand_path "../templates/#{script_name}.sh", __FILE__
  template = Tilt.new path
  File.open(file, 'w') do |f|
    f.puts template.render Object.new, job_params(script_name)
  end
  File.chmod(0700, file)
end

#fetch_filename(file) ⇒ Object 



20
21
22
23
24
25
26
27
 
# File 'lib/cagnut_bwa/functions/samp_one_fastq.rb', line 20

def fetch_filename file
  filename = File.basename(file)
  if filename.match '_R1_'
    filename.gsub '_R1_', '_R2_'
  elsif filename.match '_1_'
    filename.gsub '_1_', '_2_'
  end
end

#generate_script ⇒ Object 



45
46
47
48
49
 
# File 'lib/cagnut_bwa/functions/samp_one_fastq.rb', line 45

def generate_script
  script_name = data_type == 'ONEFASTQ' ? 'bwa_samp_one_fastq' : 'bwa_samse_one_fastq'
  bwa_samp_one_fastq script_name
  script_name
end

#initizaline(opts = {}) ⇒ Object 



9
10
11
12
13
14
15
16
17
18
 
# File 'lib/cagnut_bwa/functions/samp_one_fastq.rb', line 9

def initizaline opts = {}
  @order = sprintf '%02i', opts[:order]
  @job_name = "#{prefix_name}_#{sample_name}_Samp"
  @seq = opts[:input].nil? ? "#{seqs_path}" : opts[:input]
  abort('Cant recognized sequence files') if @seq.nil?
  @sai = "#{opts[:dirs][:input]}/#{File.basename(@seq).gsub('.gz', '').gsub('.txt','.sai')}"
  @seq2 = @seq.match('_1_') ? "#{File.expand_path(fetch_filename(@seq), File.dirname(@seq))}" : ''
  @sai2 = @sai.match('_1_') ? "#{opts[:dirs][:input]}/#{fetch_filename(@sai)}" : ''
  @output = "#{opts[:dirs][:output]}/#{sample_name}_sequence.aligned.sam.gz"
end

#job_params(script_name) ⇒ Object 



83
84
85
86
87
88
89
90
91
92
93
 
# File 'lib/cagnut_bwa/functions/samp_one_fastq.rb', line 83

def job_params script_name
  {
    jobs_dir: jobs_dir,
    script_name: script_name,
    output: @output,
    seq: @seq,
    seq2: @seq2,
    samp_options: (data_type == 'ONEFASTQ' ? 'samp_one_fastq_options' : 'samse_one_fastq_options'),
    run_local: ::Cagnut::JobManage.run_local
  }
end

#queuing_options(previous_job_id = nil) ⇒ Object 



36
37
38
39
40
41
42
43
 
# File 'lib/cagnut_bwa/functions/samp_one_fastq.rb', line 36

def queuing_options previous_job_id = nil
  {
    previous_job_id: previous_job_id,
    adjust_memory: ['h_vmem=5G'],
    parallel_env: ['30'],
    tools: ['bwa', 'samp']
  }
end

#run(previous_job_id = nil) ⇒ Object 



29
30
31
32
33
34
 
# File 'lib/cagnut_bwa/functions/samp_one_fastq.rb', line 29

def run previous_job_id = nil
  puts "Submitting bwaSampOneFastq #{sample_name} RG_STR= #{rg_str}"
  script_name = generate_script
  ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
  [@job_name, @output]
end

#samp_one_fastq_options ⇒ Object 



51
52
53
54
55
56
57
58
59
60
61
 
# File 'lib/cagnut_bwa/functions/samp_one_fastq.rb', line 51

def samp_one_fastq_options
  array = samp_params.dup
  array.insert 1, 'sampe'
  array << "-r \"#{rg_str}\""
  array << "#{ref_fasta}"
  array << "#{@sai}"
  array << "#{@sai2}"
  array << "#{@seq}"
  array << "#{@seq2} | gzip > #{@output}"
  array.uniq.compact
end

#samse_one_fastq_options ⇒ Object 



63
64
65
66
67
68
69
70
71
 
# File 'lib/cagnut_bwa/functions/samp_one_fastq.rb', line 63

def samse_one_fastq_options
  array = samp_params.dup
  array.insert 1, 'sampe'
  array << "-r \"#{rg_str}\""
  array << "#{ref_fasta}"
  array << "#{@sai}"
  array << "#{@seq} | gzip > #{@output}"
  array.uniq.compact
end