# A module to validate the command line Arguments
## CREDIT: some of these methods have been adapted from SequenceServer
module GeneValidator
# TODO: If a tabular file is provided, ensure that a tabular file has the
# right number of columns
# TODO: assert_if_ruby_version_is_supported
# A module to validate the arguments passed to the Validation Class
module GVArgValidation
class << self
def validate_args(opt)
@opt = opt
assert_output_dir_does_not_exist
assert_file_present('input file', opt[:input_fasta_file])
assert_input_file_probably_fasta
assert_input_contains_single_type_sequence
assert_BLAST_output_files
assert_validations_arg
check_num_threads
Blast.validate(opt) unless @opt[:test]
Mafft.assert_mafft_installation(opt)
@opt
end
private
def assert_validations_arg
validations = %w(lenc lenr frame merge dup orf align)
if @opt[:validations]
val = @opt[:validations].collect { |v| v.strip.downcase }
validations = val unless val.include? 'all'
end
@opt[:validations] = validations
end
def check_num_threads
@opt[:num_threads] = Integer(@opt[:num_threads])
unless @opt[:num_threads] > 0
puts 'Number of threads can not be lower than 0'
end
return unless @opt[:num_threads] > 256
puts "Number of threads set at #{@opt[:num_threads]} is unusually high."
end
def assert_BLAST_output_files
return unless @opt[:blast_xml_file] || @opt[:blast_tabular_file]
if @opt[:blast_xml_file]
assert_file_present('BLAST XML file', @opt[:blast_xml_file])
elsif @opt[:blast_tabular_file]
assert_file_present('BLAST tabular file', @opt[:blast_tabular_file])
assert_tabular_options_exists
end
end
def assert_output_dir_does_not_exist
output_dir = "#{@opt[:input_fasta_file]}.html"
return unless File.exist?(output_dir)
puts "The output directory already exists for this fasta file.\n"
puts "Please remove the following directory: #{output_dir}\n"
puts "You can run the following command to remove the folder.\n"
puts "\n $ rm -r #{output_dir} \n"
exit 1
end
def assert_tabular_options_exists
return if @opt[:blast_tabular_options]
puts '*** Error: BLAST tabular options (-o) have not been set.'
puts ' Please set the "-o" option with the custom format'
puts ' used in the BLAST -outfmt argument'
exit 1
end
def assert_input_file_probably_fasta
File.open(@opt[:input_fasta_file], 'r') do |file_stream|
(file_stream.readline[0] == '>') ? true : false
end
end
def assert_file_present(desc, file, exit_code = 1)
return if file && File.exist?(File.expand_path(file))
puts "*** Error: Couldn't find the #{desc}: #{file}."
exit exit_code
end
alias_method :assert_dir_present, :assert_file_present
def assert_input_contains_single_type_sequence
fasta_content = IO.binread(@opt[:input_fasta_file])
type = BlastUtils.type_of_sequences(fasta_content)
return if type == :nucleotide || type == :protein
puts '*** Error: The input files does not contain just protein or'
puts ' nucleotide data. Please correct this and try again.'
exit 1
end
end
# Validates BLAST Installation (And BLAST databases)
class Blast
class << self
# Use a fixed minimum version of BLAST+
MINIMUM_BLAST_VERSION = '2.2.30+'
# Use the following exit codes, or 1.
EXIT_BLAST_NOT_INSTALLED = 2
EXIT_BLAST_NOT_COMPATIBLE = 3
EXIT_NO_BLAST_DATABASE = 4
def validate(opt)
@opt = opt
assert_blast_installation
assert_blast_database_provided
assert_local_blast_database_exists if @opt[:db] !~ /remote/
end
def assert_blast_installation
# Validate BLAST installation
if @opt[:blast_bin].nil?
assert_blast_installed
assert_blast_compatible
else
export_bin_dir
end
end
def assert_blast_database_provided
return unless @opt[:db].nil?
puts '*** Error: A BLAST database is required. Please pass a local or'
puts ' remote BLAST database to GeneValidator as follows:'
puts # a blank line
puts " $ genevalidator -d '~/blastdb/SwissProt' Input_File"
puts # a blank line
puts ' Or use a remote database:'
puts # a blank line
puts " $ genevalidator -d 'swissprot -remote' Input_File"
exit 1
end
def assert_local_blast_database_exists
return if system("blastdbcmd -db #{@opt[:db]} -info > /dev/null 2>&1")
puts '*** No BLAST database found at the provided path.'
puts ' Please ensure that the provided path is correct and then' \
' try again.'
exit EXIT_NO_BLAST_DATABASE
end
private
def assert_blast_installed
return if GVArgValidation.command?('blastdbcmd')
puts '*** Could not find BLAST+ binaries.'
exit EXIT_BLAST_NOT_INSTALLED
end
def assert_blast_compatible
version = `blastdbcmd -version`.split[1]
return if version >= MINIMUM_BLAST_VERSION
puts "*** Your BLAST+ version #{version} is outdated."
puts ' GeneValidator needs NCBI BLAST+ version' \
" #{MINIMUM_BLAST_VERSION} or higher."
exit EXIT_BLAST_NOT_COMPATIBLE
end
def export_bin_dir
if File.directory?(@opt[:blast_bin])
GVArgValidation.add_to_path(@opt[:blast_bin])
else
puts '*** The provided BLAST bin directory does not exist.'
puts ' Please ensure that the provided BLAST bin directory is' \
' correct and try again.'
exit EXIT_BLAST_NOT_INSTALLED
end
end
end
end
# Validates Mafft installation
class Mafft
class << self
def assert_mafft_installation(opt)
@opt = opt
if @opt[:mafft_bin].nil?
assert_mafft_installed
else
export_bin_dir
end
end
private
def assert_mafft_installed
return if GVArgValidation.command?('mafft')
puts '*** Could not find Mafft binaries.'
puts ' Ignoring error and continuing - Please note that some' \
' validations may be skipped.'
puts # a blank line
end
def export_bin_dir
if File.directory?(@opt[:mafft_bin])
GVArgValidation.add_to_path(@opt[:mafft_bin])
else
puts '*** The provided Mafft bin directory does not exist.'
puts ' Ignoring error and continuing - Please note that some' \
' validations may be skipped.'
puts # a blank line
end
end
end
end
class << self
## Checks if dir is in $PATH and if not, it adds the dir to the $PATH.
def add_to_path(bin_dir)
return if ENV['PATH'].split(':').include?(bin_dir)
ENV['PATH'] = "#{bin_dir}:#{ENV['PATH']}"
end
# Return `true` if the given command exists and is executable.
def command?(command)
system("which #{command} > /dev/null 2>&1")
end
end
end
end