Class: Bio::DB::Polymarker

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-polymarker_db_batch/polymarker_db_batch.rb

Instance Method Summary collapse

Constructor Details

#initialize(props) ⇒ Polymarker

Returns a new instance of Polymarker.



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 5

def initialize( props)
  @properties =Hash[*File.read(props).split(/[=\n]+/)]
  puts @properties.inspect
end

Instance Method Details

#each_running ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 25

def each_running
  query="SELECT snp_file_id, filename FROM snp_file WHERE status NOT IN ('NEW', 'DONE', 'LOADED');"
  ret = 0
  if block_given?
    ret = execute_query(query){|row| yield row }
  else
    ret = execute_query(query)
  end
  ret
end

#each_snp_in_file(file_id) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 36

def each_snp_in_file(file_id)
  query="SELECT name, chromosome, sequence FROM snp, snp_file_snp WHERE snp_file_snp.snpList_snpId = snp.snpId AND snp_file_snp.snp_file_snp_file_id = '#{file_id}';"
  ret = 0
  puts query
  if block_given?
    ret = execute_query(query){|row| yield row }
  else
    ret = execute_query(query)
  end
  ret
end

#each_to_run ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 14

def each_to_run
  query="SELECT snp_file_id, filename FROM snp_file WHERE status = 'NEW';"
  ret = 0
  if block_given?
    ret = execute_query(query){|row| yield row }
  else
    ret = execute_query(query)
  end
  ret
end

#execute_polymarker(snp_file) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 61

def execute_polymarker(snp_file)
  cmd="#{@properties['wrapper_prefix'] } polymarker.rb -m #{snp_file} -o #{snp_file}_out -c #{@properties['path_to_chromosomes']} #{@properties['wrapper_suffix'] }"
  #polymarker.rb -m 1_GWAS_SNPs.csv -o 1_test -c /Users/ramirezr/Documents/TGAC/references/Triticum_aestivum.IWGSP1.21.dna_rm.genome.fa
  execute_command(cmd)
end

#mysql_version ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 10

def mysql_version
  con.get_server_info
end

#review_running_status(file_id, filename) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 93

def review_running_status(file_id, filename)
  out_folder=@properties["execution_path"]+"/#{file_id}_#{filename}_out"
  started=File.exist?(out_folder)
  done=false
  
  if started
    lines = IO.readlines("#{out_folder}/status.txt")
  #  puts lines.inspect
    done = lines.last.split(",").include?("DONE\n") if lines.size > 1
  end
  if done 
    exons_filename="#{out_folder}/exons_genes_and_contigs.fa"
    output_primers="#{out_folder}/primers.csv"
    read_file_to_snp_file("mask_fasta", file_id, exons_filename )
    read_file_to_snp_file("polymarker_output", file_id, output_primers )
    update_status(file_id, "DONE")
  elsif started
    update_status(file_id, "RUNNING")
  end
end

#send_email(to, opts = {}) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 74

def send_email(to,opts={})
  opts[:server]      ||= 'localhost'
  opts[:from]        ||= '[email protected]'
  opts[:from_alias]  ||= 'Example Emailer'
  opts[:subject]     ||= "You need to see this"
  opts[:body]        ||= "Important stuff!"

  msg = <<END_OF_MESSAGE
From: #{opts[:from_alias]} <#{opts[:from]}>
To: <#{to}>
Subject: #{opts[:subject]}

#{opts[:body]}
END_OF_MESSAGE
  Net::SMTP.start(opts[:server]) do |smtp|
    smtp.send_message msg, opts[:from], to
  end
end

#update_status(snp_file_id, new_status) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 67

def update_status(snp_file_id, new_status)
  raise "Invalid status #{new_status}" unless ["NEW", "SUBMITTED", "RUNNING", "DONE", "ERROR"].include?(new_status)
  pst = con.prepare "UPDATE snp_file SET status = ? WHERE snp_file_id = ?"
  pst.execute new_status, snp_file_id
  con.commit
end

#write_output_file_and_execute(file_id, filename) ⇒ Object 



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# File 'lib/bio-polymarker_db_batch/polymarker_db_batch.rb', line 48

def write_output_file_and_execute(file_id, filename)
  path =@properties["execution_path"]+"/#{file_id}_#{filename}"
  puts "Writting: #{path}"
  f=File.open(path, "w")

  each_snp_in_file(file_id) do |row|
    f.puts(row.join(","))
  end
  execute_polymarker(path)
  update_status(file_id, "SUBMITTED")
  f.close
end