Class: MiGA::MiGA

Inherits:
Object
  • Object
show all
Includes:
MiGA
Defined in:
lib/miga/common.rb,
lib/miga/version.rb

Overview

Generic class used to handle system-wide information and methods, and parent of all other MiGA::* classes.

Constant Summary collapse

@@DEBUG =

Should debugging information be reported?

false
@@DEBUG_TRACE =

Should the trace of debugging information be reported?

false

Constants included from MiGA

CITATION, VERSION, VERSION_DATE, VERSION_NAME

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.CITATION ⇒ Object

Reference of MiGA.



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# File 'lib/miga/version.rb', line 54

def self.CITATION ; CITATION ; end

.clean_fasta_file(file) ⇒ Object

Cleans a FastA file in place.



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# File 'lib/miga/common.rb', line 84

def self.clean_fasta_file(file)
  tmp_fh = nil
  begin
    if file =~ /\.gz/
      tmp_path = Tempfile.new('MiGA.gz').tap(&:close).path
      tmp_fh = Zlib::GzipWriter.open(tmp_path)
      fh = Zlib::GzipReader.open(file)
    else
      tmp_fh = Tempfile.new('MiGA')
      tmp_path = tmp_fh.path
      fh = File.open(file, 'r')
    end
    buffer = ''
    fh.each_line do |ln|
      ln.chomp!
      if ln =~ /^>\s*(\S+)(.*)/
        (id, df) = [$1, $2]
        tmp_fh.print buffer.wrap_width(80)
        buffer = ''
        tmp_fh.puts ">#{id.gsub(/[^A-Za-z0-9_\|\.]/, "_")}#{df}"
      else
        buffer << ln.gsub(/[^A-Za-z\.\-]/, '')
      end
    end
    tmp_fh.print buffer.wrap_width(80)
    tmp_fh.close
    fh.close
    FileUtils.cp(tmp_path, file)
  ensure
    begin
      tmp_fh.close unless tmp_fh.nil?
      File.unlink(tmp_path) unless tmp_path.nil?
    rescue
    end
  end
end

.DEBUG(*args) ⇒ Object

Send debug message.



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# File 'lib/miga/common.rb', line 53

def self.DEBUG(*args)
  $stderr.puts(*args) if @@DEBUG
  if @@DEBUG_TRACE
    $stderr.puts caller.map{ |v| v.gsub(/^/,'     ') }.join("\n")
  end
end

.DEBUG_OFF ⇒ Object

Turn off debugging.



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# File 'lib/miga/common.rb', line 36

def self.DEBUG_OFF() @@DEBUG=false end

.DEBUG_ON ⇒ Object

Turn on debugging.



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# File 'lib/miga/common.rb', line 32

def self.DEBUG_ON() @@DEBUG=true end

.DEBUG_TRACE_OFF ⇒ Object

Turn off debug tracing (but not debugging).



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# File 'lib/miga/common.rb', line 47

def self.DEBUG_TRACE_OFF
  @@DEBUG_TRACE=false
end

.DEBUG_TRACE_ON ⇒ Object

Turn on debug tracing (and debugging).



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# File 'lib/miga/common.rb', line 40

def self.DEBUG_TRACE_ON
  @@DEBUG_TRACE=true
  self.DEBUG_ON
end

.FULL_VERSION ⇒ Object

Complete version as string.



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# File 'lib/miga/version.rb', line 40

def self.FULL_VERSION ; VERSION.join(".") ; end

.initialized? ⇒ Boolean

Has MiGA been initialized?

Returns:

  • (Boolean) 


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# File 'lib/miga/common.rb', line 62

def self.initialized?
  File.exist?(File.expand_path('.miga_rc', ENV['MIGA_HOME'])) and
    File.exist?(File.expand_path('.miga_daemon.json', ENV['MIGA_HOME']))
end

.LONG_VERSION ⇒ Object

Complete version with nickname and date as string.



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# File 'lib/miga/version.rb', line 44

def self.LONG_VERSION
  "MiGA #{VERSION.join(".")} - #{VERSION_NAME} - #{VERSION_DATE}"
end

.root_path ⇒ Object

Root path to MiGA (as estimated from the location of the current file).



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# File 'lib/miga/common.rb', line 18

def self.root_path
  File.expand_path('../../..', __FILE__)
end

.script_path(task, opts = {}) ⇒ Object

Path to a script to be executed for task. Supported opts are:

  • :miga Path to the MiGA home to use. If not passed, the home of the library is used).

  • :project MiGA::Project object to check within plugins. If not passed, only core scripts are supported.



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# File 'lib/miga/common.rb', line 170

def self.script_path(task, opts={})
  opts[:miga] ||= root_path
  unless opts[:project].nil?
    opts[:project].plugins.each do |pl|
      if File.exist? File.expand_path("scripts/#{task}.bash", pl)
        opts[:miga] = pl
      end
    end
  end
  File.expand_path("scripts/#{task}.bash", opts[:miga])
end

.seqs_length(file, format, opts = {}) ⇒ Object

Calculates the average and standard deviation of the sequence lengths in a FastA or FastQ file (supports gzipped files). The format must be a Symbol, one of :fasta or :fastq. Additional estimations can be controlled via the opts Hash. Supported options include:

  • :n50: If true, it also returns the N50 and the median (in bp).

  • gc: If true, it also returns the G+C content (in %).



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# File 'lib/miga/common.rb', line 128

def self.seqs_length(file, format, opts={})
  fh = (file =~ /\.gz/) ? Zlib::GzipReader.open(file) : File.open(file, 'r')
  l = []
  gc = 0
  i = 0 # <- Zlib::GzipReader doesn't set $.
  fh.each_line do |ln|
    i += 1
    if (format==:fasta and ln =~ /^>/) or (format==:fastq and (i % 4)==1)
      l << 0
    elsif format==:fasta or (i % 4)==2
      l[l.size-1] += ln.chomp.size
      gc += ln.scan(/[GCgc]/).count if opts[:gc]
    end
  end
  fh.close
  
  o = { n: l.size, tot: l.inject(:+) }
  o[:avg] = o[:tot].to_f/l.size
  o[:var] = l.map{ |a| a ** 2 }.inject(:+).to_f/l.size - o[:avg]**2
  o[:sd]  = Math.sqrt o[:var]
  o[:gc]  = 100.0*gc/o[:tot] if opts[:gc]
  if opts[:n50]
    l.sort!
    thr = o[:tot]/2
    pos = 0
    l.each do |a|
      pos += a
      o[:n50] = a
      break if pos >= thr
    end
    o[:med] = o[:n].even? ?
      0.5*l[o[:n]/2-1,2].inject(:+) : l[(o[:n]-1)/2]
  end
  o
end

.tabulate(header, values) ⇒ Object

Tabulates an values, and Array of Arrays, all with the same number of entries as header. Returns an Array of String, one per line.



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# File 'lib/miga/common.rb', line 70

def self.tabulate(header, values)
  fields = [header.map(&:to_s)]
  fields << fields.first.map{ |h| h.gsub(/\S/, '-') }
  fields += values.map{ |row| row.map{ |cell| cell.nil? ? '?' : cell.to_s } }
  clen = fields.map{ |row| row.map(&:length) }.transpose.map(&:max)
  fields.map do |row|
    (0 .. clen.size-1).map do |col_n|
      col_n==0 ? row[col_n].rjust(clen[col_n]) : row[col_n].ljust(clen[col_n])
    end.join('  ')
  end
end

.VERSION ⇒ Object

Major.minor version as Float.



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# File 'lib/miga/version.rb', line 36

def self.VERSION ; VERSION[0] ; end

.VERSION_DATE ⇒ Object

Date of the current gem release.



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# File 'lib/miga/version.rb', line 50

def self.VERSION_DATE ; VERSION_DATE ; end

Instance Method Details

#result_files_exist?(base, ext) ⇒ Boolean

Check if the result files exist with base name (String) followed by the ext values (Array of String).

Returns:

  • (Boolean) 


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# File 'lib/miga/common.rb', line 185

def result_files_exist?(base, ext)
  ext = [ext] unless ext.is_a? Array
  ext.all? do |f|
    File.exist?(base + f) or File.exist?("#{base}#{f}.gz")
  end
end