Class: SequenceServer::MAKEBLASTDB

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Defined in:
lib/sequenceserver/makeblastdb.rb

Overview

Smart ‘makeblastdb` wrapper: recursively scans database directory determining which files need to be formatted or re-formatted.

Example usage:

makeblastdb = MAKEBLASTDB.new(database_dir)
makeblastdb.run # formats and re-formats databases in database_dir
makeblastdb.formatted_fastas # lists formatted databases

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(database_dir) ⇒ MAKEBLASTDB

Returns a new instance of MAKEBLASTDB.



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# File 'lib/sequenceserver/makeblastdb.rb', line 19

def initialize(database_dir)
  @database_dir = database_dir
end

Instance Attribute Details

#database_dir ⇒ Object (readonly)

Returns the value of attribute database_dir.



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# File 'lib/sequenceserver/makeblastdb.rb', line 23

def database_dir
  @database_dir
end

Instance Method Details

#any_formatted? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/sequenceserver/makeblastdb.rb', line 25

def any_formatted?
  formatted_fastas.any?
end

#any_to_format? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/sequenceserver/makeblastdb.rb', line 86

def any_to_format?
  fastas_to_format.any?
end

#any_to_format_or_reformat? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/sequenceserver/makeblastdb.rb', line 29

def any_to_format_or_reformat?
  any_to_format? || any_to_reformat?
end

#format ⇒ Object

Format any unformatted FASTA files in database directory. Returns Array of files that were formatted.



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# File 'lib/sequenceserver/makeblastdb.rb', line 46

def format
  # Make the intent clear as well as ensure the program won't crash if we
  # accidentally call format before calling scan.
  return unless any_to_format?

  fastas_to_format.select do |path, title, type|
    make_blast_database('format', path, title, type)
  end
end

#formatted_fastas ⇒ Object

Determines which FASTA files in the database directory are already formatted.



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# File 'lib/sequenceserver/makeblastdb.rb', line 70

def formatted_fastas
  return @formatted_fastas if defined?(@formatted_fastas)

  @formatted_fastas = []

  blastdbcmd.each_line do |line|
    path, *rest = line.chomp.split("\t")
    next if multipart_database_name?(path)

    rest << get_categories(path)
    @formatted_fastas << Database.new(path, *rest)
  end

  @formatted_fastas
end

#no_fastas? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/sequenceserver/makeblastdb.rb', line 33

def no_fastas?
  probably_fastas.empty?
end

#reformat ⇒ Object

Re-format databases that require reformatting. Returns Array of files that were reformatted.



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# File 'lib/sequenceserver/makeblastdb.rb', line 58

def reformat
  # Make the intent clear as well as ensure the program won't crash if
  # we accidentally call reformat before calling scan.
  return unless any_to_reformat?

  fastas_to_reformat.select do |path, title, type, non_parse_seqids|
    make_blast_database('reformat', path, title, type, non_parse_seqids)
  end
end

#run ⇒ Object

Runs makeblastdb on each file in ‘fastas_to_format` and `fastas_to_reformat`.



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# File 'lib/sequenceserver/makeblastdb.rb', line 39

def run
  format
  reformat
end