lib/cheripic/cmd.rb
#!/usr/bin/env ruby
module Cheripic
# A command line option and processing object to handle input options
#
# @!attribute [rw] options
# @return [Hash] a hash of trollop option names as keys and user or default setting as values
class Cmd
require 'trollop'
require 'pathname'
require 'ostruct'
attr_accessor :options
# creates a Cmd object using input string entry
# @param args [String]
def initialize(args)
@options = parse_arguments(args)
check_arguments
end
# method to check input command string and run appropriate
# method of the object (help or examples or parsing arguments)
# @param args [String]
def parse_arguments(args)
Trollop::with_standard_exception_handling argument_parser do
if args.empty? || args.include?('-h') || args.include?('--help')
raise Trollop::HelpNeeded
elsif args.include?('--examples')
print_examples
end
argument_parser.parse args
end
end
# trollop argument_parser for input args string and
# @return [Hash] a hash of trollop option names as keys and user or default setting as values
def argument_parser
cmds = self
Trollop::Parser.new do
version Cheripic::VERSION
banner cmds.help_message
opt :assembly, 'Assembly file in FASTA format',
:short => '-f',
:type => String
opt :input_format, 'bulk and parent alignment file format types - set either pileup or bam or vcf',
:short => '-F',
:type => String,
:default => 'pileup'
opt :mut_bulk, 'Pileup or sorted BAM file alignments from mutant/trait of interest bulk 1',
:short => '-a',
:type => String
opt :mut_bulk_vcf, 'vcf file for variants from mutant/trait of interest bulk 1',
:type => String,
:default => ''
opt :bg_bulk, 'Pileup or sorted BAM file alignments from background/wildtype bulk 2',
:short => '-b',
:type => String
opt :bg_bulk_vcf, 'vcf file for variants from background/wildtype bulk 2',
:type => String,
:default => ''
opt :output, 'custom name tag to include in the output file name',
:default => 'cheripic_results'
opt :loglevel, 'Choose any one of "info / warn / debug" level for logs generated',
:default => 'info'
opt :hmes_adjust, 'factor added to snp count of each contig to adjust for hme score calculations',
:type => Float,
:default => 0.5
opt :htlow, 'lower level for categorizing heterozygosity',
:type => Float,
:default => 0.25
opt :hthigh, 'high level for categorizing heterozygosity',
:type => Float,
:default => 0.75
opt :mindepth, 'minimum read depth at a position to consider for variant calls',
:type => Integer,
:default => 6
opt :max_d_multiple, "multiplication factor for average coverage to calculate maximum read coverage
if set zero no calculation will be made from bam file.\nsetting this value will override user set max depth",
:type => Integer,
:default => 5
opt :maxdepth, 'maximum read depth at a position to consider for variant calls
if set to zero no user max depth will be used',
:type => Integer,
:default => 0
opt :min_non_ref_count, 'minimum read depth supporting non reference base at each position',
:type => Integer,
:default => 3
opt :min_indel_count_support, 'minimum read depth supporting an indel at each position',
:type => Integer,
:default => 3
opt :ambiguous_ref_bases, 'including variant at completely ambiguous bases in the reference',
:type => String,
:default => 'false'
opt :mapping_quality, 'minimum mapping quality of read covering the position',
:short => '-q',
:type => Integer,
:default => 20
opt :base_quality, 'minimum base quality of bases covering the position',
:short => '-Q',
:type => Integer,
:default => 15
opt :noise, 'praportion of reads for a variant to conisder as noise',
:type => Float,
:default => 0.1
opt :cross_type, 'type of cross used to generated mapping population - back or out',
:type => String,
:default => 'back'
opt :use_all_contigs, 'option to select all contigs or only contigs containing variants for analysis',
:type => String,
:default => 'false'
opt :include_low_hmes, 'option to include or discard variants from contigs with
low hme-score or bfr score to list in the final output',
:type => String,
:default => 'false'
opt :polyploidy, 'Set if the data input is from polyploids',
:type => String,
:default => 'false'
opt :mut_parent, 'Pileup or sorted BAM file alignments from mutant/trait of interest parent',
:short => '-p',
:type => String,
:default => ''
opt :bg_parent, 'Pileup or sorted BAM file alignments from background/wildtype parent',
:short => '-r',
:type => String,
:default => ''
opt :repeats_file, 'repeat masker output file for the assembly ',
:short => '-R',
:type => String,
:default => ''
opt :bfr_adjust, 'factor added to hemi snp frequency of each parent to adjust for bfr calculations',
:type => Float,
:default => 0.05
opt :sel_seq_len, 'sequence length to print from either side of selected variants',
:type => Integer,
:default => 50
opt :examples, 'shows some example commands with explanation'
end
end
# help message to display from command line
def help_message
msg = <<-EOS
Cheripic v#{Cheripic::VERSION.dup}
Authors: Shyam Rallapalli and Dan MacLean
Description: Candidate mutation and closely linked marker selection for non reference genomes
Uses bulk segregant data from non-reference sequence genomes
Inputs:
1. Needs a reference fasta file of asssembly use for variant analysis
2. Pileup/Bam files for mutant (phenotype of interest) bulks and background (wildtype phenotype) bulks
3. If providing bam files, you have to include vcf files for the respective bulks
4. If polyploid species, include pileup/bam files from one or both parents
USAGE:
cheripic <options>
OPTIONS:
EOS
msg.split("\n").map{ |line| line.lstrip }.join("\n")
end
# examples to display from command line
def print_examples
msg = <<-EOS
Cheripic v#{Cheripic::VERSION.dup}
Authors: Shyam Rallapalli and Dan MacLean
EXAMPLE COMMANDS:
1. cheripic -f assembly.fa -a mutbulk.pileup -b bgbulk.pileup --output=cheripic_output
2. cheripic --assembly assembly.fa --mut-bulk mutbulk.pileup --bg-bulk bgbulk.pileup
--mut-parent mutparent.pileup --bg-parent bgparent.pileup --polyploidy true --output cheripic_results
3. cheripic --assembly assembly.fa --mut-bulk mutbulk.pileup --bg-bulk bgbulk.pileup
--mut-parent mutparent.pileup --bg-parent bgparent.pileup --polyploidy true
--no-only-frag-with-vars --no-filter-out-low-hmes --output cheripic_results
4. cheripic -h or cheripic --help
5. cheripic -v or cheripic --version
EOS
puts msg.split("\n").map{ |line| line.lstrip }.join("\n")
exit(0)
end
# calls other methods to check if command line inputs are valid
def check_arguments
convert_boolean_strings
check_output
check_log_level
check_input_entry
check_input_types
end
# convert true or false options to boolean
def convert_boolean_strings
%i{ambiguous_ref_bases use_all_contigs include_low_hmes polyploidy}.each do | symbol |
if @options.key?(symbol)
@options[symbol] = @options[symbol] == 'false' ? false : true
end
end
end
# set file given option to false if input is nil or None or ''
def check_input_entry
%i{assembly mut_bulk bg_bulk mut_bulk_vcf bg_bulk_vcf mut_parent bg_parent repeats_file}.each do | symbol |
if @options.key?(symbol)
if @options[symbol] == 'None'
param = (symbol.to_s + '_given').to_sym
@options[symbol] = ''
@options.delete(param)
end
end
end
end
# checks input files based on bulk file type
def check_input_types
inputfiles = {}
inputfiles[:required] = %i{assembly mut_bulk}
inputfiles[:optional] = %i{bg_bulk}
if @options[:input_format] == 'bam'
inputfiles[:required] << %i{mut_bulk_vcf}
inputfiles[:optional] << %i{bg_bulk_vcf}
end
if @options[:polyploidy]
inputfiles[:either] = %i{mut_parent bg_parent}
end
check_input_files(inputfiles)
end
# checks if input files are valid
def check_input_files(inputfiles)
inputfiles.each_key do | type |
inputfiles[type].flatten!
check = 0
inputfiles[type].each do | symbol |
if @options[symbol] == nil or @options[symbol] == ''
if type == :required
raise CheripicArgError.new "Options #{inputfiles}, all must be specified. Try --help for further help."
end
else
file = @options[symbol]
if symbol == :bg_bulk or symbol == :bg_bulk_vcf
if file.include? ','
@options[symbol] = []
file.split(',').each do | infile |
@options[symbol] << File.expand_path(infile)
file_exist?(symbol, infile)
end
end
else
@options[symbol] = File.expand_path(file)
file_exist?(symbol, file)
end
check = 1
end
end
if type == :either and check == 0
raise CheripicArgError.new "One of the options #{inputfiles}, must be specified. " +
'Try --help for further help.'
end
end
end
def file_exist?(symbol, file)
# checks if a given file exists
unless File.exist?(file)
raise CheripicIOError.new "#{symbol} file, #{file} does not exist!"
end
end
# checks if files with output tag name already exists
def check_output
if (@options[:output].split('') & %w{# / : * ? ' < > | & $ ,}).any?
raise CheripicArgError.new 'please choose a name tag that contains ' +
'alphanumeric characters, hyphen(-) and underscore(_) only'
end
@options[:hmes_frags] = "#{@options[:output]}_selected_hme_variants.txt"
@options[:bfr_frags] = "#{@options[:output]}_selected_bfr_variants.txt"
[@options[:hmes_frags], @options[:bfr_frags]].each do | file |
if File.exist?(file)
raise CheripicArgError.new "'#{file}' file exists " +
'please choose a different name tag to be included in the output file name'
end
end
end
# checks and sets logger level
def check_log_level
unless %w(error info warn debug).include?(@options[:loglevel])
raise CheripicArgError.new "Loglevel #{@options[:loglevel]} is not valid. " +
'It must be one of: error, info, warn, debug.'
end
logger.level = Yell::Level.new @options[:loglevel].to_sym
end
# Initializes an Implementer object using input options
# and calls run method of the Implementer to start the pipeline
# A hash of trollop option names as keys and user or default
# setting as values is passed to Implementer object
def run
@options[:hmes_frags] = File.expand_path @options[:hmes_frags]
@options[:bfr_frags] = File.expand_path @options[:bfr_frags]
analysis = Implementer.new(@options)
analysis.run
end
end # Cmd
end # Cheripic