seqtrimnext 2.0.66 → 2.0.68

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: ab74e9c551c43eb30da4a881ab544c9d7754ecaa
-  data.tar.gz: acdf2c4e6d4e5d36d5fafbe1e2004178ed33b145
+  metadata.gz: 0dec16c30109eb1196eb4dcafe25b8b0f9f66bb5
+  data.tar.gz: d50c362cc94c53f04575d78d040ba86b286d488e
 SHA512:
-  metadata.gz: d60d9cb31be6eab17ff47e81e77ae3246408dee62f4061e040a9efdcfc9e6f54997e873e244a337091be391a00ca05eec2cd8d5da7b6ecdebf468b76540b5a39
-  data.tar.gz: bf2c6174ca48e5ea0d1bf9b7da3e58b01d89016674fa7050473a6dca2dc105d6156281c080e25d5906384a4587b7a51571b51ed9155043e0dee71546fff5ecb7
+  metadata.gz: ddfa27d6f631ef9197b67ae3fc936d7b42161de834023c9c5d71ec8e43f573213c27983916a717927ff4562d44a687178580c5b92659ffe5c8ce6cedea33ae2b
+  data.tar.gz: 3eb16600a5055cc3adbb4ec734ddf2011aee1a6524cc4ac9576b4577b87fbac06c3378e1c7d7bb965f8abc1aaacda18066afd62fa69888f00eb6824409d0978a

data/bin/resume_stn_stats.rb

@@ -24,11 +24,12 @@ ARGV.each do |file_path|
 
 	begin
 		res << sample_name
-		res << stats['sequences']['count']['input_count'] 
+		res << stats['sequences']['count']['input_count']
 		res << stats['sequences']['count']['output_seqs_paired'] 
 		res << stats['sequences']['count']['output_seqs'] 
 		res << stats['sequences']['count']['rejected'] 
-		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) 
+		#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) 
+		res << sprintf('%.2f',(stats['sequences']['count']['rejected'].to_f/stats['sequences']['count']['input_count'].to_f)*100)
 		
 	rescue Excepcion => e
 

data/bin/seqtrimnext

@@ -109,8 +109,8 @@ end
 
 ENV['BLASTDB']=$FORMATTED_DB_PATH
 
-OUTPUT_PATH='output_files'
-
+OUTPUT_PATH='output_files_tmp'
+DEFAULT_FINAL_OUTPUT_PATH='output_files'
 
 # TODO - COMENTAR todas las clases y metodos para que salga la descripcion cuando hagas rdoc en el terminal
 
@@ -327,6 +327,11 @@ optparse = OptionParser.new do |opts|
     options[:write_in_gzip] = true
   end
 
+  options[:final_output_path] = DEFAULT_FINAL_OUTPUT_PATH
+  opts.on( '-O', '--ouput output_files', 'Output folder. It should not exists. output_files by default') do |folder|
+    options[:final_output_path] = folder
+  end
+
   # This displays the help screen, all programs are
   # assumed to have this option.
   opts.on_tail( '-h', '--help', 'Display this screen' ) do
@@ -399,12 +404,17 @@ if (ARGV.count != 0) || (!required_options) # con esto vemos si hay argumentos,
   exit(-1)
 end
 
+if File.exists?(options[:final_output_path])
+  $LOG.error "Output folder #{options[:final_output_path]} already exists.\n Remove it if you want to launch STN again."
+  exit(-1)
+end
+
 # check for template
 if (!File.exists?(options[:template]))
   if File.exists?(File.join($SEQTRIM_PATH,'templates',options[:template]))
     options[:template] = File.join($SEQTRIM_PATH,'templates',options[:template])
   else
-    $LOG.info "Params file: #{options[:template]} doesn't exists. \n\nYou can use your own template or specify one from this list:\n============================="
+    $LOG.error "Params file: #{options[:template]} doesn't exists. \n\nYou can use your own template or specify one from this list:\n============================="
     puts Dir.glob(File.join($SEQTRIM_PATH,'templates','*.txt')).map{|t| File.basename(t)}
     exit(-1)
   end
@@ -441,7 +451,7 @@ s = Seqtrim.new(options)
 #generate report
 
 if !options[:skip_report] && system("which generate_report.rb > /dev/null ")
-  cmd="generate_report.rb output_files 2> report_generation_errors.log"
+  cmd="generate_report.rb #{OUTPUT_PATH} 2> report_generation_errors.log"
   $LOG.info "Generating report #{cmd}"
   `#{cmd}`
 else
@@ -454,4 +464,8 @@ else
   $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}"
 end
 
+if (Seqtrim.exit_status>=0) 
+  FileUtils.mv OUTPUT_PATH, options[:final_output_path]
+end
+
 exit(Seqtrim.exit_status)

data/lib/seqtrimnext/classes/em_classes/seqtrim_worker.rb

@@ -37,7 +37,7 @@ end
 
 ENV['BLASTDB']=$FORMATTED_DB_PATH
 
-OUTPUT_PATH='output_files'
+OUTPUT_PATH='output_files_tmp'
 
 puts "FORMATTED_DB_BLAST in workers: #{$FORMATTED_DB_PATH}"
 

data/lib/seqtrimnext/classes/install_database.rb

@@ -6,7 +6,7 @@ class InstallDatabase
   def initialize(type,db_path)
     
     
-    types=['core','cont_bacteria','cont_fungi','cont_mitochondrias','cont_plastids','cont_ribosome','cont_viruses']
+    types=['core','cont_bacteria','cont_fungi','cont_mitochondrias','cont_plastids','cont_ribosome','cont_viruses','adapters_illumina']
     
     if types.include?(type)
       

data/lib/seqtrimnext/version.rb

@@ -1,4 +1,4 @@
 module Seqtrimnext
-  VERSION = "2.0.66"
+  VERSION = "2.0.68"
   SEQTRIM_VERSION = VERSION
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: seqtrimnext
 version: !ruby/object:Gem::Version
-  version: 2.0.66
+  version: 2.0.68
 platform: ruby
 authors:
 - Dario Guerrero
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-05-25 00:00:00.000000000 Z
+date: 2016-12-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler