<commit_before>#!/usr/bin/ruby -w

#
# @author <NAME> <<EMAIL>riguezr at gmail dot com>
# @author <NAME>
# @license artistic license 2.0
# @update Nov-11-2014
#

require 'optparse'
require 'tmpdir'
has_build_gems = TRUE
warn <<WARN

┌──[ IMPORTANT ]──────────────────────────────────────────────┐
│ ROCker is in alpha version: undertested, and very unstable. │
│ Please don't use in production.                             │
└─────────────────────────────────────────────────────────────┘

WARN

#================================[ Options parsing ]
$o = {
   :q=>false, :r=>'R', :nucl=>false,
   :positive=>[], :negative=>[], :sbj=>[],:color=>false,
   :win=>20, :gformat=>'pdf', :width=>9, :height=>9, :minscore=>0,
   :grinder=>'grinder', :muscle=>'muscle', :blastbins=>'', :seqdepth=>3, :minovl=>0.75,
   :grindercmd=>'%1$s -reference_file "%2$s" -cf "%3$f" -base_name "%4$s"',
   :musclecmd=>'%1$s -in "%2$s" -out "%3$s" -quiet',
   :blastcmd=>'%1$s%2$s -query "%3$s" -db "%4$s" -out "%5$s" -outfmt 6 -max_target_seqs 1',
   :makedbcmd=>'%1$smakeblastdb -dbtype %2$s -in "%3$s" -out "%4$s"'
}
$t = {
   'build'   => 'Creates in silico metagenomes and training sets from reference genomes.',
   'compile' => 'Identifies the most discriminant bit-score per sequence position in a set of sequence.',
   'filter'  => 'Uses a pre-compiled set of bit-score thresholds to filter a BLAST result.',
   'plot'    => 'Generates a graphical representation of the alignment, the thresholds, and the hits.',
}
task = (ARGV.size > 0 ? ARGV.shift : '').downcase
ARGV << '-h' if ARGV.size==0
if task == 'build'
   begin
      require 'rubygems'<commit_msg>ROCker build: new grinder defaults<commit_after>#!/usr/bin/ruby -w

#
# @author <NAME> <lmrodriguezr at gmail dot com>
# @author Luis (Coto) Orellana
# @license artistic license 2.0
# @update Nov-11-2014
#

require 'optparse'
require 'tmpdir'
has_build_gems = TRUE
warn <<WARN

┌──[ IMPORTANT ]──────────────────────────────────────────────┐
│ ROCker is in alpha version: undertested, and very unstable. │
│ Please don't use in production.                             │
└─────────────────────────────────────────────────────────────┘

WARN

#================================[ Options parsing ]
$o = {
   :q=>false, :r=>'R', :nucl=>false,
   :positive=>[], :negative=>[], :sbj=>[],:color=>false,
   :win=>20, :gformat=>'pdf', :width=>9, :height=>9, :minscore=>0,
   :grinder=>'grinder', :muscle=>'muscle', :blastbins=>'', :seqdepth=>3, :minovl=>0.75,
   :grindercmd=>'%1$s -reference_file "%2$s" -cf "%3$f" -base_name "%4$s" -dc \'-~*Nn\' -md "poly4 3e-3 3.3e-8" -mr "95 5" -rd "100 uniform 5"',
   :musclecmd=>'%1$s -in "%2$s" -out "%3$s" -quiet',
   :blastcmd=>'%1$s%2$s -query "%3$s" -db "%4$s" -out "%5$s" -outfmt 6 -max_target_seqs 1',
   :makedbcmd=>'%1$smakeblastdb -dbtype %2$s -in "%3$s" -out "%4$s"'
}
$t = {
   'build'   => 'Creates in silico metagenomes and training sets from reference genomes.',
   'compile' => 'Identifies the most discriminant bit-score per sequence position in a set of sequence.',
   'filter'  => 'Uses a pre-compiled set of bit-score thresholds to filter a BLAST result.',
   'plot'    => 'Generates a graphical representation of the alignment, the thresholds, and the hits.',
}
task = (ARGV.size > 0 ? ARGV.shift : '').downcase
ARGV << '-h' if ARGV.size==0
if task == 'build'
   begin
      require 'rubygems'
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{'dir': 'git-commits-cleaned', 'id': '5170137', 'n_tokens_mistral': 1387, 'n_tokens_neox': 1243, 'n_words': 348}