Sha256: 10be8fc1b1e2d9285a515b3c5e211a89da0959043d2014cd1747109983a73942
Contents?: true
Size: 1.89 KB
Versions: 2
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Stored size: 1.89 KB
Contents
#!/usr/bin/env ruby require 'optparse' require 'npsearch' require 'npsearch/arg_validator' require 'npsearch/version' opt = {} optparse = OptionParser.new do |opts| opts.banner = <<Banner * Usage: npsearch [Options] -i [Input File] * Mandatory Options: Banner opt[:input_file] = nil opts.on('-i', '--input [file]', 'Path to the input fasta file') do |f| opt[:input_file] = f end opts.separator '' opts.separator '* Optional Options:' opt[:signalp_path] = File.join(ENV['HOME'], 'signalp/signalp') opts.on('-s', '--signalp_path', String, 'The full path to the signalp script. This can be downloaded from', ' CBS. See https://www.github.com/wurmlab/NpSearch for more', ' information') do |p| opt[:signalp_path] = p end opt[:usearch_path] = File.join(ENV['HOME'], 'bin/uclust') opts.on('-u', '--usearch_path', String, 'The full path to the usearch binary. This script can be downloaded', ' from .... See https://www.github.com/wurmlab/NpSearch for more', ' information') do |p| opt[:usearch_path] = p end opt[:num_threads] = 1 opts.on('-n', '--num_threads', Integer, 'The number of threads to use when analysing the input file') do |n| opt[:num_threads] = n end opt[:orf_min_length] = 10 opts.on('-m', '--orf_min_length N', Integer, 'The minimum length of a potential neuropeptide precursor.', ' Default: 30') do |n| opt[:orf_min_length] = n end opts.on('-h', '--help', 'Display this screen') do puts opts exit end opts.on('-v', '--version', 'Shows version') do puts NpSearch::VERSION exit end end optparse.parse! # Temporary hard coding my defaults... opt[:num_threads] = 8 opt[:signalp_path] = '/Volumes/Data/data/programs/signalp-4.1/signalp' opt[:usearch_path] = '/Volumes/Data/data/programs/bin/usearch' NpSearch.init(opt) NpSearch.run
Version data entries
2 entries across 2 versions & 1 rubygems
Version | Path |
---|---|
npsearch-2.0.1 | bin/npsearch |
npsearch-2.0.0 | bin/npsearch |