seqtrimnext 2.0.49 → 2.0.50

data/History.txt

@@ -1,3 +1,7 @@
+=== 2.0.50 2012-06-13
+
+Added classification plugin
+
 === 2.0.49 2012-05-24
 
 Updated gem dependencies

data/Manifest.txt

@@ -24,6 +24,7 @@ History.txt
 lib/seqtrimnext/actions/action_ab_adapter.rb
 lib/seqtrimnext/actions/action_ab_far_adapter.rb
 lib/seqtrimnext/actions/action_ab_left_adapter.rb
+lib/seqtrimnext/actions/action_classify.rb
 lib/seqtrimnext/actions/action_empty_insert.rb
 lib/seqtrimnext/actions/action_ignore_repeated.rb
 lib/seqtrimnext/actions/action_indetermination.rb
@@ -77,6 +78,7 @@ lib/seqtrimnext/plugins/plugin_adapters.rb
 lib/seqtrimnext/plugins/plugin_adapters_old.rb
 lib/seqtrimnext/plugins/plugin_amplicons.rb
 lib/seqtrimnext/plugins/plugin_contaminants.rb
+lib/seqtrimnext/plugins/plugin_classify.rb
 lib/seqtrimnext/plugins/plugin_extract_inserts.rb
 lib/seqtrimnext/plugins/plugin_find_poly_at.rb
 lib/seqtrimnext/plugins/plugin_ignore_repeated.rb

data/lib/seqtrimnext/actions/action_classify.rb

@@ -0,0 +1,23 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Almudena Bocinos Rioboo                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionClassify < SeqtrimAction
+      
+   def initialize(start_pos,end_pos)
+     super(start_pos,end_pos)    
+     @cut =false
+   end
+
+   def apply_decoration(char)
+     return char.yellow
+  
+   end       
+
+
+end

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

@@ -144,6 +144,7 @@ class SeqtrimWorker <  ScbiMapreduce::Worker
       # find mids
       mid = seq.get_actions(ActionMid).first
       
+      
       if (seq.seq_rejected)           # sequence rejected
       
       	#save to rejected sequences 

data/lib/seqtrimnext/classes/seqtrim.rb

@@ -203,6 +203,8 @@ class Seqtrim
         format = :sanger
       end
       
+      $LOG.info("Used FastQ format for input files: #{format}")
+      
       sequence_reader = FastqFile.new(seqs_path,'r',format, true)
       # cd_hit_input_file = 'cd-hit-input.fasta'
       cd_hit_input_file = seqs_path

data/lib/seqtrimnext/plugins/plugin.rb

@@ -79,7 +79,6 @@ class Plugin
       c=merged_hits.find{|c| overlapX?(hit.q_beg, hit.q_end,c.q_beg,c.q_end)}
       # puts " c #{c.inspect}"
 
-
       if (c.nil?)
         # add new contaminant
         #puts "NEW HIT #{hit.inspect}"

data/lib/seqtrimnext/plugins/plugin_classify.rb

@@ -0,0 +1,143 @@
+require "plugin"
+
+require "make_blast_db"
+########################################################
+# Author: Almudena Bocinos Rioboo
+#
+# Defines the main methods that are necessary to execute Pluginclassify
+# Inherit: Plugin
+########################################################
+
+class PluginClassify < Plugin
+
+
+  MAX_TARGETS_SEQS=4 #MAXIMUM NUMBER OF DIFFERENT ALIGNED SEQUENCES TO  KEEP FROM BLAST DATABASE
+
+
+  def near_to_extrem(c,seq,min_cont_size)
+    max_to_extreme=(min_cont_size/2).to_i
+    return ((c.q_beg-max_to_extreme<0) || (( c.q_end+max_to_extreme)>=seq.seq_fasta.size-1) ) #return if vector is very near to the extremes of insert)
+  end
+  
+  def sum_hits_by_id(hits)
+    res={}
+    
+    hits.each do |c|
+      hit_size=c.q_end - c.q_beg + 1
+      
+      res[c.definition] = (res[c.definition]||0)+hit_size
+      
+    end
+    
+    puts res.to_json
+    return res
+  end
+
+  #Begins the plugin1's execution to warn that there are classify in the sequence "seq"
+  def execute(seqs)
+    blasts= do_blasts(seqs)
+
+    seqs.each_with_index do |s,i|
+      exec_seq(s,blasts.querys[i])
+    end
+  end
+
+  def do_blasts(seqs)
+
+    # TODO - Culling limit = 2 porque el blast falla con este comando cuando se le pasa cl=1 y dust=no
+    # y una secuencia de baja complejidad como entrada
+
+    blast = BatchBlast.new("-db #{@params.get_param('classify_db')}",'blastn'," -task blastn -evalue #{@params.get_param('blast_evalue_classify')} -perc_identity #{@params.get_param('blast_percent_classify')} -culling_limit 1")  #get classify -max_target_seqs #{MAX_TARGETS_SEQS}
+
+    $LOG.debug('BLAST:'+blast.get_blast_cmd(:xml))
+
+    fastas=[]
+
+    seqs.each do |seq|
+      fastas.push ">"+seq.seq_name
+      fastas.push seq.seq_fasta
+    end
+
+
+    blast_table_results = blast.do_blast(fastas,:xml)
+
+    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
+
+    $LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: looking for classify into the sequence"
+
+    type = "ActionClassify"
+
+    classify={}
+
+    # classify_ids=[]
+
+    classify=sum_hits_by_id(blast_query.hits)
+
+    actions=[]
+    classify_size=0
+
+    min_cont_size=@params.get_param('min_classify_hit_size').to_i
+    
+    biggest_classify = classify.sort {|c1,c2| c1[1]<=>c2[1]}
+    
+    if !biggest_classify.empty?
+
+      definition,classify_size = biggest_classify.last
+      
+      
+      a = seq.new_action(-1,-1,type) # adds the correspondent action to the sequence
+
+      a.message = definition
+      
+      a.tag_id = definition.gsub(' ','_')
+
+      # a.found_definition = c.definition    # save the classify definitions, each separately
+      
+      #save to this file
+      seq.add_file_tag(1, a.tag_id, :file)
+      
+      
+      actions.push a
+
+      add_stats('classify_size',classify_size)
+      add_stats('classify_ids',definition)
+  
+      seq.add_actions(actions)
+    end
+
+  end
+
+  #Returns an array with the errors due to parameters are missing
+  def self.check_params(params)
+    errors=[]
+
+
+    comment='Blast E-value used as cut-off when searching for contaminations'
+    default_value = 1e-10
+    params.check_param(errors,'blast_evalue_classify','Float',default_value,comment)
+
+    comment='Minimum required identity (%) for a reliable classify'
+    default_value = 85
+    params.check_param(errors,'blast_percent_classify','Integer',default_value,comment)
+
+    comment='Minimum hit size (nt) for considering to classify'
+    default_value = 30 # era 40
+    params.check_param(errors,'min_classify_hit_size','Integer',default_value,comment)
+
+    comment='Path for classify database'
+    default_value = File.join($FORMATTED_DB_PATH,'classify.fasta')
+    params.check_param(errors,'classify_db','DB',default_value,comment)
+
+
+    return errors
+  end
+
+
+end

data/lib/seqtrimnext.rb

@@ -30,7 +30,7 @@ module Seqtrimnext
   # SEQTRIM_VERSION_STAGE = 'b'
   # SEQTRIM_VERSION = "2.0.0#{SEQTRIM_VERSION_STAGE}#{SEQTRIM_VERSION_REVISION}"
   
-   VERSION = '2.0.49'
+   VERSION = '2.0.50'
   
   SEQTRIM_VERSION = VERSION
   

metadata

@@ -2,7 +2,7 @@
 name: seqtrimnext
 version: !ruby/object:Gem::Version 
   prerelease: 
-  version: 2.0.49
+  version: 2.0.50
 platform: ruby
 authors: 
 - Dario Guerrero & Almudena Bocinos
@@ -10,7 +10,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-05-24 00:00:00 Z
+date: 2012-06-13 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: narray
@@ -201,6 +201,7 @@ files:
 - lib/seqtrimnext/actions/action_ab_adapter.rb
 - lib/seqtrimnext/actions/action_ab_far_adapter.rb
 - lib/seqtrimnext/actions/action_ab_left_adapter.rb
+- lib/seqtrimnext/actions/action_classify.rb
 - lib/seqtrimnext/actions/action_empty_insert.rb
 - lib/seqtrimnext/actions/action_ignore_repeated.rb
 - lib/seqtrimnext/actions/action_indetermination.rb
@@ -254,6 +255,7 @@ files:
 - lib/seqtrimnext/plugins/plugin_adapters_old.rb
 - lib/seqtrimnext/plugins/plugin_amplicons.rb
 - lib/seqtrimnext/plugins/plugin_contaminants.rb
+- lib/seqtrimnext/plugins/plugin_classify.rb
 - lib/seqtrimnext/plugins/plugin_extract_inserts.rb
 - lib/seqtrimnext/plugins/plugin_find_poly_at.rb
 - lib/seqtrimnext/plugins/plugin_ignore_repeated.rb
@@ -319,7 +321,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: seqtrimnext
-rubygems_version: 1.7.2
+rubygems_version: 1.8.24
 signing_key: 
 specification_version: 3
 summary: SeqtrimNEXT is a customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data