seqtrimnext 2.0.59 → 2.0.60

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: a3858c7d16c231f2bd9a8a20a79e71793fa4a26b
+  data.tar.gz: 8737fb4a873639ccf4784fa0b0f4add4778df20f
+SHA512:
+  metadata.gz: 8885fc85c63703652371ecc1a4bc67670de700b8151ba0cf3e3e706904b979a4eeb777b289c2553b229832a556887572c0c8760978f7f6306b099a085a850ab1
+  data.tar.gz: a9c3c18e94a240720afd44840ba297259ec888c28381ec4855eec68b38dba3387b76df33c5211b2a91f9fec5d23e03645b792ae4fa71e8c82ea36dfc965e2e1e

data/.gitignore

@@ -0,0 +1,14 @@
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log

data/Gemfile

@@ -0,0 +1,4 @@
+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in seqtrimnext.gemspec
+gemspec

data/LICENSE.txt

@@ -0,0 +1,22 @@
+Copyright (c) 2015 dariogf
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/Rakefile

@@ -1,39 +1,8 @@
-require 'rubygems'
-gem 'hoe', '>= 2.1.0'
-require 'hoe'
-require 'fileutils'
-require './lib/seqtrimnext'
-
-Hoe.plugin :newgem
-# Hoe.plugin :website
-# Hoe.plugin :cucumberfeatures
-
-# Generate all the Rake tasks
-# Run 'rake -T' to see list of generated tasks (from gem root directory)
-$hoe = Hoe.spec 'seqtrimnext' do
-  self.developer 'Dario Guerrero & Almudena Bocinos', 'dariogf@gmail.com & alkoke@gmail.com'
-  self.post_install_message = 'PostInstall.txt' # TODO remove if post-install message not required
-  self.rubyforge_name       = self.name # TODO this is default value
-  # self.extra_deps         = ['narray','gnuplot','term-ansicolor','xml-simple','scbi_blast','scbi_drb','scbi_fasta','scbi_fastq','scbi_plot','scbi_math']
-  
-  self.extra_deps = []
-  self.extra_deps << ['narray','>=0']
-  self.extra_deps << ['gnuplot','>=0']
-  self.extra_deps << ['term-ansicolor','>=1.0.5']
-  self.extra_deps << ['xml-simple','>=1.0.12']
-  self.extra_deps << ['scbi_blast','>=0.0.34']
-  self.extra_deps << ['scbi_mapreduce','>=0.0.38']
-  self.extra_deps << ['scbi_fasta','>=0.1.7']
-  self.extra_deps << ['scbi_fastq','>=0.0.18']
-  self.extra_deps << ['scbi_plot','>=0.0.6']
-  self.extra_deps << ['scbi_math','>=0.0.1']
-  self.extra_deps << ['scbi_headers','>=0.0.2']
-
-end
-
-require 'newgem/tasks'
-Dir['tasks/**/*.rake'].each { |t| load t }
-
-# TODO - want other tests/tasks run by default? Add them to the list
-# remove_task :default
-# task :default => [:spec, :features, :redocs]
+require "bundler/gem_tasks"
+
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs << 'test'
+  t.pattern = "test/*_test.rb"
+end

data/bin/seqtrimnext

@@ -119,7 +119,7 @@ require 'install_requirements'
 
 ins = InstallRequirements.new
 if (!ins.check_install_requirements)
-  exit
+  exit(-1)
 end
 
 require "logger"
@@ -378,7 +378,7 @@ end
 
 if !File.exists?($FORMATTED_DB_PATH)
   STDERR.puts "Database path not found: #{$FORMATTED_DB_PATH}. \n\n\nInstall databases to this path or set your BLASTDB environment variable (eg.: export BLASTDB=new_path)"
-  exit
+  exit(-1)
 end
 
 
@@ -395,7 +395,7 @@ if (ARGV.count != 0) || (!required_options) # con esto vemos si hay argumentos,
   puts "You must provide all required options"
   puts ""
   puts optparse.help
-  exit
+  exit(-1)
 end
 
 # check for template
@@ -405,7 +405,7 @@ if (!File.exists?(options[:template]))
   else
     $LOG.info "Params file: #{options[:template]} doesn't exists. \n\nYou can use your own template or specify one from this list:\n============================="
     puts Dir.glob(File.join($SEQTRIM_PATH,'templates','*.txt')).map{|t| File.basename(t)}
-    exit
+    exit(-1)
   end
 end
 $LOG.info "Using init file: #{$SEQTRIMNEXT_INIT}"
@@ -418,7 +418,7 @@ if options[:fastq]
     # 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
+      exit(-1)
     end
   end
 end
@@ -426,13 +426,13 @@ end
 # fasta file
 if (!options[:fasta].nil? && !File.exists?(options[:fasta]))
   $LOG.error "Input file: #{options[:fasta]} doesn't exists"
-  exit
+  exit(-1)
 end
 
 # qual file
 if ((!options[:qual].nil?)&&(!File.exists?(options[:qual])))
   $LOG.error "Input file: #{options[:qual]} doesn't exists"
-  exit
+  exit(-1)
 end
 
 s = Seqtrim.new(options)

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

@@ -19,7 +19,7 @@
 #
 # $: << File.expand_path(ROOT_PATH)
 
-$: << File.expand_path('~/progs/ruby/gems/seqtrimnext/lib/')
+# $: << File.expand_path('~/progs/ruby/gems/seqtrimnext/lib/')
 # $: << File.expand_path('~/progs/ruby/gems/scbi_mapreduce/lib')
 
 require 'seqtrimnext'

data/lib/seqtrimnext/classes/extract_stats.rb

@@ -196,7 +196,7 @@ class ExtractStats
 
     # sequence min size, is taken directly from params file
     # max sequence limit is calculated here 
-    if (@sequence_lengths_stats.variance_coefficient<=10) or (@params.get_param('accept_very_long_sequences')=='true')
+    if (@sequence_lengths_stats.variance_coefficient<=10) or (@params.get_param('accept_very_long_sequences').to_s=='true')
 
       # high size limit is calculated with stats
       @params.set_param('max_sequence_size_raw',(@sequence_lengths_stats.max+10).to_i)

data/lib/seqtrimnext/classes/seqtrim.rb

@@ -262,7 +262,7 @@ class Seqtrim
     end
 
     # Extract global stats
-    if params.get_param('generate_initial_stats')=='true'
+    if params.get_param('generate_initial_stats').to_s=='true'
       $LOG.info "Calculatings stats"
       ExtractStats.new(sequence_readers,params)
     else
@@ -273,7 +273,7 @@ class Seqtrim
     # save used params to file
     params.save_file(File.join(OUTPUT_PATH,'used_params.txt'))
     
-    piro_on = (params.get_param('next_generation_sequences')=='true')
+    piro_on = (params.get_param('next_generation_sequences').to_s=='true')
 
       params.load_mids(params.get_param('mids_db'))
       params.load_ab_adapters(params.get_param('adapters_ab_db'))
@@ -281,7 +281,7 @@ class Seqtrim
       params.load_linkers(params.get_param('linkers_db'))
       
       #execute cd-hit
-      if params.get_param('remove_clonality')=='true'
+      if params.get_param('remove_clonality').to_s=='true'
         cmd=get_custom_cdhit(cd_hit_input_file,params)
         if cmd.empty?
           cmd=get_cd_hit_cmd(cd_hit_input_file,workers,$SEQTRIMNEXT_INIT)

data/lib/seqtrimnext/plugins/plugin_contaminants.rb

@@ -154,7 +154,7 @@ class PluginContaminants < Plugin
 
 
 
-    if ((not actions.empty? ) && (reject=='true'))
+    if ((not actions.empty? ) && (reject.to_s=='true'))
       #reject sequence
       # puts "SEQ_REJECTED= TRUE >>> "
       seq.seq_rejected=true

data/lib/seqtrimnext/plugins/plugin_indeterminations.rb

@@ -100,7 +100,7 @@ class PluginIndeterminations < Plugin
 		      a.right_action=true
 		      actions.push a
 		  
-          if @params.get_param('middle_indetermination_rejects')=='true'
+          if @params.get_param('middle_indetermination_rejects').to_s=='true'
 		        seq.seq_rejected=true 
             seq.seq_rejected_by_message='Indeterminations in middle of sequence'
           end

data/lib/seqtrimnext/plugins/plugin_low_quality.rb

@@ -119,7 +119,7 @@ class PluginLowQuality < Plugin
 
      if ((self.class.to_s=='PluginLowQuality') && seq.seq_qual.nil? ) 
        $LOG.debug " Quality File haven't been provided. It's impossible to execute " + self.class.to_s     
-     elsif ((seq.seq_qual.size>0) && (@params.get_param('use_qual')=='true'))
+     elsif ((seq.seq_qual.size>0) && (@params.get_param('use_qual').to_s=='true'))
           
           $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: checking low quality of the sequence"
           

data/lib/seqtrimnext/plugins/plugin_vectors.rb

@@ -101,7 +101,7 @@ class PluginVectors < Plugin
       # puts " near #{near_to_extrem(v,seq,min_vector_size)} #{vector_size}>=#{min_vector_size}"
       #c.q_end+seq.insert_start+max_to_end)>=seq.seq_fasta_orig.size-1)  #if ab adapter is very near to the end of original sequence  
       
-      piro_on=@params.get_param('next_generation_sequences')
+      piro_on=@params.get_param('next_generation_sequences').to_s
       
       if (((piro_on=='true')  && (!seq.range_inside_action_type?(v.q_beg,v.q_end,ActionLinker)) && (!seq.range_inside_action_type?(v.q_beg,v.q_end,ActionMultipleLinker)))    ||   # if vectors DB not is contained inside detected linkers
            (piro_on=='false'))
@@ -110,7 +110,7 @@ class PluginVectors < Plugin
          if !near_to_extrem(v,seq,min_vector_size)
        		type = 'ActionUnexpectedVector'
 
-          if @params.get_param('middle_vector_rejects')=='true'
+          if @params.get_param('middle_vector_rejects').to_s=='true'
     			  seq.seq_rejected=true
   				  seq.seq_rejected_by_message='unexpected vector'
           end

data/lib/seqtrimnext/plugins_old/plugin_adapters_old.rb

@@ -0,0 +1,156 @@
+require "plugin"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute PluginAdapters                                                     
+# Inherit: Plugin
+########################################################
+
+class PluginAdaptersOld < Plugin
+  
+  def get_type_adapter(p_start,p_end,seq)
+       #if q_beg is nearer the left, add adapter action by the left,
+       #if q_end esta is nearer the right , add adapter action by  the right
+       #NOTE: If the adapter is very near from left and rigth,
+       #then the sequence isn't valid, because almost sequence is adapter.
+       
+       
+       v1= p_end.to_i
+       v2= p_start.to_i   
+       
+        # puts " startadapter #{v2} endadapter #{v1} insert_start #{seq.insert_start}  insert_end #{seq.insert_end}"
+       
+        # puts " #{v2+seq.insert_start} <? #{seq.seq_fasta.length - v1 - 1 + seq.seq_fasta_orig.length - seq.insert_end-1}"
+       if (v2+seq.insert_start  < (seq.seq_fasta.length - v1 - 1+ seq.seq_fasta_orig.length - seq.insert_end-1)) #IF THE NEAREST ONE IS THE LEFT
+         type = "ActionLeftAdapter"          
+         
+       else
+          type = "ActionRightAdapter"
+         
+       end
+       return type
+  end 
+  
+  
+  def cut_by_right(adapter,seq)
+    
+    left_size = adapter.q_beg-seq.insert_start+1
+    right_size = seq.insert_end-adapter.q_end+1
+    left_size=0 if (left_size<0)
+    right_size=0 if (right_size<0) 
+    
+    return (left_size>(right_size/2).to_i)
+    
+  end
+ 
+ def do_blasts(seqs)
+    # find MIDS  with less results than max_target_seqs value 
+    blast=BatchBlast.new("-db #{@params.get_param('adapters_db')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_adapters')} -perc_identity #{@params.get_param('blast_percent_adapters')}")  
+    $LOG.debug('BLAST:'+blast.get_blast_cmd)
+
+    fastas=[]
+    
+    seqs.each do |seq|
+     fastas.push ">"+seq.seq_name
+     fastas.push seq.seq_fasta
+    end
+    
+    # fastas=fastas.join("\n")
+    
+    blast_table_results = blast.do_blast(fastas)
+    
+    # puts blast_table_results.inspect
+   
+    return blast_table_results
+ end
+ 
+ 
+ def exec_seq(seq,blast_query)
+   if blast_query.query_id != seq.seq_name
+     raise "Blast and seq names does not match, blast:#{blast_query.query_id} sn:#{seq.seq_name}"
+   end
+   
+    $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for adapters into the sequence" 
+  
+        
+    # blast=BatchBlast.new("-db #{File.join($FORMATTED_DB_PATH,'adapters.fasta')}",'blastn'," -task blastn-short -evalue #{@params.get_param('blast_evalue_adapters')} -perc_identity #{@params.get_param('blast_percent_adapters')}")  
+    
+    # blast with only one sequence, no with many sequences from a database
+    #---------------------------------------------------------------------
+    
+    # blast_table_results = blast.do_blast(seq.seq_fasta)             #rise seq to adapterss  executing over blast
+    
+    #blast_table_results = BlastTableResult.new(res) 
+    
+    # blast_table_results.inspect         
+    
+    adapters=[]
+    # blast_table_results.querys.each do |query|     # first round to save adapters without overlap
+      merge_hits(blast_query,adapters)
+    # end
+
+    begin 
+      adapters2=adapters                            # second round to save adapters without overlap
+      adapters = []
+      merge_hits(adapters2,adapters)
+    end until (adapters2.count == adapters.count) 
+
+    actions=[] 
+    adapter_size=0
+    # @stats['adapter_size']={}
+    adapters.each do |ad|                           # adds the correspondent action to the sequence  
+       
+       type = get_type_adapter(ad.q_beg,ad.q_end,seq)
+       a = seq.new_action(ad.q_beg,ad.q_end,type) 
+       # puts " state left_action #{a.left_action} right_action #{a.right_action}"
+         
+
+       adapter_size=ad.q_end-ad.q_beg+1 
+       
+       if cut_by_right(ad,seq)
+        
+        # puts "action right end1 #{seq.insert_end}"
+        
+        a.right_action=true    #mark rigth action to get the left insert
+      else 
+          
+        # puts " cut1 by left #{seq.insert_start} ad #{ad.q_beg+seq.insert_start} #{ad.q_end+seq.insert_start}"
+                 
+        a.left_action = true   #mark left action to get the right insert        
+        
+      end 
+      
+      a.message = ad.subject_id 
+      a.reversed = ad.reversed 
+      actions.push a 
+      
+      # @stats[:adapter_size]={adapter_size => 1} 
+      add_stats('adapter_size',adapter_size)  
+        
+    end 
+    seq.add_actions(actions)
+    #    
+  end
+
+  #Returns an array with the errors due to parameters are missing 
+  def self.check_params(params)
+    errors=[]
+    
+    comment='Blast E-value used as cut-off when searching for adapters or primers'
+    default_value = 1e-6
+		params.check_param(errors,'blast_evalue_adapters','Float',default_value,comment)
+		
+		comment='Minimum required identity (%) for a reliable adapter'
+		default_value = 95
+		params.check_param(errors,'blast_percent_adapters','Integer',default_value,comment)
+    
+    comment='Path for adapter database'
+		default_value = File.join($FORMATTED_DB_PATH,'adapters.fasta')
+		params.check_param(errors,'adapters_db','DB',default_value,comment)		
+    
+    return errors
+  end
+  
+  
+end