seqtrimnext 2.0.66 → 2.0.68
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checksums.yaml
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@@ -1,7 +1,7 @@
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---
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0dec16c30109eb1196eb4dcafe25b8b0f9f66bb5
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data.tar.gz: d50c362cc94c53f04575d78d040ba86b286d488e
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SHA512:
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metadata.gz:
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metadata.gz: ddfa27d6f631ef9197b67ae3fc936d7b42161de834023c9c5d71ec8e43f573213c27983916a717927ff4562d44a687178580c5b92659ffe5c8ce6cedea33ae2b
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data.tar.gz: 3eb16600a5055cc3adbb4ec734ddf2011aee1a6524cc4ac9576b4577b87fbac06c3378e1c7d7bb965f8abc1aaacda18066afd62fa69888f00eb6824409d0978a
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data/bin/resume_stn_stats.rb
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@@ -24,11 +24,12 @@ ARGV.each do |file_path|
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begin
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res << sample_name
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res << stats['sequences']['count']['input_count']
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res << stats['sequences']['count']['input_count']
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res << stats['sequences']['count']['output_seqs_paired']
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res << stats['sequences']['count']['output_seqs']
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res << stats['sequences']['count']['rejected']
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res << sprintf('%.2f',(stats['sequences']['count']['rejected'].to_f/(stats['sequences']['count']['output_seqs_paired'].to_i+stats['sequences']['count']['output_seqs'].to_i).to_f)*100)
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#res << sprintf('%.2f',(stats['sequences']['count']['rejected'].to_f/(stats['sequences']['count']['output_seqs_paired'].to_i+stats['sequences']['count']['output_seqs'].to_i).to_f)*100)
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res << sprintf('%.2f',(stats['sequences']['count']['rejected'].to_f/stats['sequences']['count']['input_count'].to_f)*100)
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rescue Excepcion => e
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data/bin/seqtrimnext
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@@ -109,8 +109,8 @@ end
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ENV['BLASTDB']=$FORMATTED_DB_PATH
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OUTPUT_PATH='
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-
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OUTPUT_PATH='output_files_tmp'
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DEFAULT_FINAL_OUTPUT_PATH='output_files'
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# TODO - COMENTAR todas las clases y metodos para que salga la descripcion cuando hagas rdoc en el terminal
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@@ -327,6 +327,11 @@ optparse = OptionParser.new do |opts|
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options[:write_in_gzip] = true
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end
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options[:final_output_path] = DEFAULT_FINAL_OUTPUT_PATH
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opts.on( '-O', '--ouput output_files', 'Output folder. It should not exists. output_files by default') do |folder|
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options[:final_output_path] = folder
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end
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# This displays the help screen, all programs are
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# assumed to have this option.
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opts.on_tail( '-h', '--help', 'Display this screen' ) do
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@@ -399,12 +404,17 @@ if (ARGV.count != 0) || (!required_options) # con esto vemos si hay argumentos,
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exit(-1)
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end
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if File.exists?(options[:final_output_path])
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$LOG.error "Output folder #{options[:final_output_path]} already exists.\n Remove it if you want to launch STN again."
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exit(-1)
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end
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# check for template
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if (!File.exists?(options[:template]))
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if File.exists?(File.join($SEQTRIM_PATH,'templates',options[:template]))
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options[:template] = File.join($SEQTRIM_PATH,'templates',options[:template])
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else
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$LOG.
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$LOG.error "Params file: #{options[:template]} doesn't exists. \n\nYou can use your own template or specify one from this list:\n============================="
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puts Dir.glob(File.join($SEQTRIM_PATH,'templates','*.txt')).map{|t| File.basename(t)}
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exit(-1)
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end
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@@ -441,7 +451,7 @@ s = Seqtrim.new(options)
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#generate report
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if !options[:skip_report] && system("which generate_report.rb > /dev/null ")
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cmd="generate_report.rb
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cmd="generate_report.rb #{OUTPUT_PATH} 2> report_generation_errors.log"
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$LOG.info "Generating report #{cmd}"
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`#{cmd}`
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else
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@@ -454,4 +464,8 @@ else
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$LOG.info "If you want a detailed report in PDF format, be sure you have installed the optional seqtrimnext_report gem (gem install seqtrimnext_report)#{skip_text}"
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end
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if (Seqtrim.exit_status>=0)
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FileUtils.mv OUTPUT_PATH, options[:final_output_path]
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end
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exit(Seqtrim.exit_status)
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@@ -6,7 +6,7 @@ class InstallDatabase
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def initialize(type,db_path)
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types=['core','cont_bacteria','cont_fungi','cont_mitochondrias','cont_plastids','cont_ribosome','cont_viruses']
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types=['core','cont_bacteria','cont_fungi','cont_mitochondrias','cont_plastids','cont_ribosome','cont_viruses','adapters_illumina']
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if types.include?(type)
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data/lib/seqtrimnext/version.rb
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metadata
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@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: seqtrimnext
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version: !ruby/object:Gem::Version
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version: 2.0.
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version: 2.0.68
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platform: ruby
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authors:
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- Dario Guerrero
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@@ -9,7 +9,7 @@ authors:
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autorequire:
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bindir: bin
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cert_chain: []
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-
date: 2016-
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date: 2016-12-14 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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