seqtrimnext in seqtrimnext-2.0.52

- old
+ new

@@ -1,6 +1,8 @@
 #!/usr/bin/env ruby
+# encoding: utf-8
+
 #     SeqTrimNext: Next generation sequencing preprocessor
 #     Copyright (C) <2011>
 #     Authors: Almudena Bocinos Rioboo, Diego Dario Guerrero Fernandez,
 #              Rocio Bautista Moreno, Juan Falgueras Cano & M. Gonzalo Claros
 #              email: soporte@scbi.uma.es - http://www.scbi.uma.es
@@ -55,14 +57,40 @@
 # $: << File.expand_path('~/progs/ruby/gems/scbi_drb/lib/')
 
 # $: << File.expand_path(ROOT_PATH)
 
 $: << File.expand_path('~/progs/ruby/gems/seqtrimnext/lib/')
-$: << File.expand_path('~/progs/ruby/gems/scbi_mapreduce/lib/')
+# $: << File.expand_path('~/progs/ruby/gems/scbi_mapreduce/lib/')
 
 require 'seqtrimnext'
+require 'scbi_headers'
 
+
+def put_header
+  header = ScbiHeader.new('SeqTrimNEXT',Seqtrimnext::SEQTRIM_VERSION)
+
+  header.description="SeqtrimNEXT is a customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data. It makes use of scbi_mapreduce gem to be able to run in parallel and distributed environments. It is specially suited for Roche 454 (normal and paired-end) & Ilumina datasets, although it could be easyly adapted to any other situation."
+
+  header.copyright='2011'
+
+  header.authors<< "Darío Guerrero"
+  header.authors<< "Almudena Bocinos"
+  header.authors<< "Rocío Bautista"
+  header.authors<< "Noé Fernández"
+  header.authors<< "Juan Falgueras"
+  header.authors<< "M. Gonzalo Claros"
+
+  # header.articles<< "Article one: with one description line"
+  # header.articles<< "Article two: with one description line"
+
+  # To output the header
+  puts header
+
+end
+
+put_header
+
 ############ PATHS #######################
 $SEQTRIM_PATH = ROOT_PATH
 
 if ENV['SEQTRIMNEXT_INIT'] && File.exists?(ENV['SEQTRIMNEXT_INIT'])
   $SEQTRIMNEXT_INIT=File.expand_path(ENV['SEQTRIMNEXT_INIT'])
@@ -190,11 +218,11 @@
         STDERR.puts "ERROR:Invalid workers parameter #{options[:workers]}"
         exit
       end
 
     end
-    
+
   end
 
 
 
   options[:only_workers] = false
@@ -209,17 +237,17 @@
 
   options[:use_checkpoint] = false
   opts.on( '-C', '--use_checkpoint', 'Restore at checkpoint if scbi_mapreduce_checkpoint file is available' ) do
     options[:use_checkpoint] = true
   end
-  
+
   # options[:skip_initial_stats] = false
   # opts.on( '-k', '--skip_initial_stats', 'Skip initial stats' ) do
   #   options[:skip_initial_stats] = true
   # end
-  
 
+
   options[:install_db] = nil
   opts.on( '-i', '--install_databases TYPE', 'Install base databases and reformat them if necessary') do |db_type|
     options[:install_db] = db_type
   end
 
@@ -227,24 +255,26 @@
   opts.on( '-l', '--logfile FILE', 'Write log to FILE' ) do |file|
     options[:logfile] = file
   end
 
   options[:fastq] = nil
-  opts.on( '-Q', '--fastq FILE', 'Fastq input file. Use - for <STDIN>' ) do |file|
+  opts.on( '-Q', '--fastq FILE1,FILE2',Array, 'Fastq input file. Use - for <STDIN>' ) do |file|
     options[:fastq] = file
+    puts "FILES:",file,file.class
+
   end
-  
+
   options[:format] = nil
   opts.on( '-F', '--fastq_quality_format FORMAT', 'Fastq input quality format use sanger or illumina18 for phred+33 based scores. Use illumina15 for phred+64 based scores (default is sanger) file. Use - for <STDIN>' ) do |value|
     options[:format] = value
     if !['sanger','illumina15', 'illumina18'].include?(value)
       STDERR.puts "ERROR: Invalid FASTQ format parameter #{value}"
       exit
     end
   end
-  
 
+
   options[:fasta] = nil
   opts.on( '-f', '--fasta FILE', 'Fasta input file' ) do |file|
     options[:fasta] = file
   end
 
@@ -253,11 +283,11 @@
     options[:qual] = file
   end
 
   options[:list_db] = nil
   options[:list_db_name] = 'ALL'
-  
+
   opts.on( '-L', '--list_db [DB_NAME]', 'List entries IDs in DB_NAME. Use "-L all" to view all available databases' ) do |value|
     options[:list_db] = true
     options[:list_db_name] = value if value
   end
 
@@ -279,16 +309,16 @@
 
   options[:json] = nil
   opts.on( '-j', '--json', 'Save results in json file' ) do
     options[:json] = true
   end
-  
+
   options[:skip_output] = false
   opts.on( '-K', '--no-verbose', 'Change to no verbose mode. Every sequence will not be written to output log' ) do
     options[:skip_output] = true
   end
-  
+
   options[:skip_report] = false
   opts.on( '-R', '--no-report', 'Do not generate final PDF report (gem scbi_seqtrimnext_report required if you want to generate PDF report).' ) do
     options[:skip_report] = true
   end
 
@@ -333,11 +363,11 @@
 $LOG.info("Using options: "+ options.to_json)
 
 if options[:install_db] then
   #install databases
   InstallDatabase.new(options[:install_db],$DB_PATH)
-  
+
   # reformat databases
   MakeBlastDb.new($DB_PATH)
   exit
 end
 
@@ -374,18 +404,22 @@
   end
 end
 $LOG.info "Using init file: #{$SEQTRIMNEXT_INIT}"
 $LOG.info "Using params file: #{options[:template]}"
 
-# fastq file
-if (!options[:fastq].nil? && options[:fastq]!='-' && !File.exists?(options[:fastq]))
-  $LOG.error "Input file: #{options[:fasta]} doesn't exists"
-  exit
+# check file existence
+
+if options[:fastq]
+  options[:fastq].each do |fastq_file|
+    # fastq file
+    if (!fastq_file.nil? && fastq_file!='-' && !File.exists?(File.expand_path(fastq_file)))
+      $LOG.error "Input file: #{fastq_file} doesn't exists"
+      exit
+    end
+  end
 end
 
-
-
 # fasta file
 if (!options[:fasta].nil? && !File.exists?(options[:fasta]))
   $LOG.error "Input file: #{options[:fasta]} doesn't exists"
   exit
 end
@@ -396,22 +430,20 @@
   exit
 end
 
 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"
   $LOG.info "Generating report #{cmd}"
   `#{cmd}`
 else
   skip_text='.'
-  
+
   if options[:skip_report]
     skip_text=' and remove the -R option from the command line.'
   end
-  
+
   $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