seqtrimnext 2.0.61 → 2.0.62

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 0ccbee45f33fe72b0b26f542ec15a54e16e91090
-  data.tar.gz: d3637c75263534e59c4a4fc3f2175b15eb7745ac
+  metadata.gz: 1fb6845331e9b46e2a53f29312fce204869a91cf
+  data.tar.gz: 18d138fe1b899582daae2e4118cd6118853afc29
 SHA512:
-  metadata.gz: b76e76001e951d7e1d104e59dd20042cd50274ed313e8531620962a639c8f294cdd9eb7c558f4e79a336a9f58d1d87e5357c21c4ddb2129cdb4d5048ff7a97ce
-  data.tar.gz: e19042628ff07b65c4fd08c11b719175e1656a343d10e7811a434fbd8d6923f2a2b0060f8c74fec894e2a09e82d7a35fcad4b4aa074e63516d399c163554163c
+  metadata.gz: d22ad436ce0b15ff783d15b871491adaa5947f9c1da4a7247712f7d6e9e790978ad90ab22657dc7768b51a61d6122f874c7853e9d0279f0dd408702a681ca5f0
+  data.tar.gz: 67d4af5e0bb8dc2eba127b6fe1ff04684c7b96db3fbad9e94cb6a222d88d4da3b5b5fd204022f70c0e14d2511ae476a7814f3ec32d21900c73f2370462207faa

data/bin/resume_execution_times.rb

@@ -27,29 +27,40 @@ ARGV.each do |file_path|
 	stats=JSON::parse(File.read(file_path))
 
 	res={}
+	
+	total=0
+		
 
 	begin
 		stats.keys.each do |k|
 			if stats[k]['execution_time']
 				res[k]=stats[k]['execution_time']['total_seconds']
+				total+=res[k]
 			end
 		end
+
+		res["TOTAL_plugins"]=total
 		
 	rescue Excepcion => e
 
 	   puts "Error reading #{file_path}"
 	end
 
+	if stats['scbi_mapreduce']
+		res['TOTAL_workers']=stats['scbi_mapreduce']['connected_workers']
+		res['TOTAL_read']=stats['scbi_mapreduce']['total_read_time']
+		res['TOTAL_write']=stats['scbi_mapreduce']['total_write_time']
+		res['TOTAL_manager_idle']=stats['scbi_mapreduce']['total_manager_idle_time']
+		res['TOTAL_execution']=stats['scbi_mapreduce']['total_seconds']
+	end
+
 	if puts_json
 		puts JSON::pretty_generate(res)
 	else
-		total=0
 		res.keys.sort.each do |k|
 			puts "#{k}\t#{res[k]}"
-			total+=res[k]
 		end
-		puts "-"*20
-		puts "TOTAL (plugins):\t#{total}"
 	end
+
 end
 

data/bin/seqtrimnext

@@ -362,6 +362,7 @@ $LOG.datetime_format = "%Y-%m-%d %H:%M:%S"
 #DEBUG < INFO < WARN < ERROR < FATAL < UNKNOWN
 
 $LOG.info("SeqTrimNext version #{Seqtrimnext::SEQTRIM_VERSION}")
+$LOG.info("STN command: #{$0}")
 
 
 $LOG.info("Using BLASTDB: "+ $FORMATTED_DB_PATH)

data/lib/seqtrimnext/actions/action_trim.rb

@@ -0,0 +1,21 @@
+require "seqtrim_action"
+
+########################################################
+# Author: Dario Guerrero                      
+# 
+# Defines the main methods that are necessary to execute Plugin1                                                     
+# Inherit: Plugin
+########################################################
+
+class ActionTrim < SeqtrimAction
+  def initialize(start_pos,end_pos)
+    
+    super(start_pos,end_pos)
+    @cut =true 
+  end
+
+  def apply_decoration(char)
+  	return char.red.italic
+  end  
+
+end

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

@@ -87,13 +87,6 @@ class SeqtrimWorkManager < ScbiMapreduce::WorkManager
 
   def self.end_work_manager
 
-    puts "FULL STATS:\n" +JSON.pretty_generate(@@full_stats)
-
-    # create stats file
-    f = File.open(STATS_PATH,'w')
-    f.puts JSON.pretty_generate(@@full_stats)
-    f.close
-
     # if initial files doesn't exists, create it
     if !File.exists?(File.join(OUTPUT_PATH,'initial_stats.json'))
       File.open(File.join(OUTPUT_PATH,'initial_stats.json'),'w') do |f|
@@ -102,10 +95,10 @@ class SeqtrimWorkManager < ScbiMapreduce::WorkManager
     end
 
     # load stats
-    r=File.read(STATS_PATH)
-    stats=JSON::parse(r)
-
+    #r=File.read(STATS_PATH)
+    #stats=JSON::parse(r)
 
+    stats=@@full_stats
 
     # make graphs
     gs=GraphStats.new(stats)
@@ -120,11 +113,18 @@ class SeqtrimWorkManager < ScbiMapreduce::WorkManager
       file.close
     end
 
-    if File.exists?('scbi_drb_checkpoint')
-      File.delete('scbi_drb_checkpoint')
-    end
   end
 
+  def self.work_manager_finished
+    @@full_stats['scbi_mapreduce']=@@stats
+
+    puts "FULL STATS:\n" +JSON.pretty_generate(@@full_stats)
+
+    # create stats file
+    f = File.open(STATS_PATH,'w')
+    f.puts JSON.pretty_generate(@@full_stats)
+    f.close
+  end
 
   def error_received(worker_error, obj)
     @@errors_file.puts "Error while processing object #{obj.inspect}\n" + worker_error.original_exception.message + ":\n" +worker_error.original_exception.backtrace.join("\n")

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

@@ -82,6 +82,7 @@ class SeqtrimWorker <  ScbiMapreduce::Worker
 
     # $WORKER_LOG.level = Logger::ERROR
     $WORKER_LOG.level = Logger::WARN
+    #$WORKER_LOG.level = Logger::INFO
     $WORKER_LOG.info "Loading actions"
 
     @action_manager = ActionManager.new

data/lib/seqtrimnext/classes/seqtrim.rb

@@ -362,6 +362,7 @@ class Seqtrim
         server.retry_stuck_jobs=true
 				server.start_server
         
+        
         # close sequence reader
 				sequence_readers.each do |file|
 				  file.close

data/lib/seqtrimnext/plugins/plugin.rb

@@ -35,6 +35,9 @@ class Plugin
     return true
   end
 
+  def exec_seq(seq,blast_query)
+  end
+
   #Begins the plugin's execution whit the sequence "seq"
   def execute(seqs)
     blasts=do_blasts(seqs)

data/lib/seqtrimnext/plugins/plugin_size_trim.rb

@@ -0,0 +1,58 @@
+require "plugin"
+
+########################################################
+# Author: Dario Guerrero
+# 
+# Defines the main methods that are necessary to execute PluginSizeTrim
+# Inherit: Plugin
+# Trims the output sequences to a fixed size
+########################################################
+
+class PluginSizeTrim < Plugin 
+   
+  def exec_seq(seq,blast_query)
+    #$LOG.debug "[#{self.class.to_s}, seq: #{seq.seq_name}]: checking if insert of sequence has enought size" 
+    # puts "inserto #{seq.insert_start}, #{seq.insert_end} size #{seq.seq_fasta.size}" 
+    
+
+    tr_size = @params.get_param('trim_size_file_'+(seq.order_in_tuple+1).to_s)
+
+    trim_size=-1
+
+    if tr_size
+      trim_size=tr_size.to_i
+    end 
+
+   # $WORKER_LOG.info "TRIM_SIZE=#{trim_size}, #{seq.order_in_tuple+1}"
+
+    if trim_size>0
+
+      if (seq.seq_fasta.size > trim_size)
+      a_beg,a_end = trim_size, seq.seq_fasta.size  # position from an empty insert 
+    
+        actions=[]  
+    
+         type = "ActionTrim"
+         
+         a=seq.new_action(a_beg,a_end,type) 
+         actions.push a                     
+         add_stats('trim_sizes',a_end-a_beg+1)
+         
+        seq.add_actions(actions)  
+      end  
+    end
+          
+  end
+ 
+  #Returns an array with the errors due to parameters are missing 
+  def self.check_params(params)
+    errors=[]  
+    
+    self.check_param(errors,params,'trim_size_file_1','Integer',-1)
+    self.check_param(errors,params,'trim_size_file_2','Integer',-1)
+    
+    return errors
+  end
+  
+  
+end

data/lib/seqtrimnext/version.rb

@@ -1,4 +1,4 @@
 module Seqtrimnext
-  VERSION = "2.0.61"
+  VERSION = "2.0.62"
   SEQTRIM_VERSION = VERSION
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: seqtrimnext
 version: !ruby/object:Gem::Version
-  version: 2.0.61
+  version: 2.0.62
 platform: ruby
 authors:
 - Dario Guerrero
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-01-19 00:00:00.000000000 Z
+date: 2016-01-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -288,6 +288,7 @@ files:
 - lib/seqtrimnext/actions/action_sanger_left_adapter.rb
 - lib/seqtrimnext/actions/action_sanger_right_adapter.rb
 - lib/seqtrimnext/actions/action_short_insert.rb
+- lib/seqtrimnext/actions/action_trim.rb
 - lib/seqtrimnext/actions/action_unexpected_poly_t.rb
 - lib/seqtrimnext/actions/action_unexpected_vector.rb
 - lib/seqtrimnext/actions/action_user_contaminant.rb
@@ -331,6 +332,7 @@ files:
 - lib/seqtrimnext/plugins/plugin_mids.rb
 - lib/seqtrimnext/plugins/plugin_sanger_adapters.rb
 - lib/seqtrimnext/plugins/plugin_short_insert.rb
+- lib/seqtrimnext/plugins/plugin_size_trim.rb
 - lib/seqtrimnext/plugins/plugin_user_contaminants.rb
 - lib/seqtrimnext/plugins/plugin_vectors.rb
 - lib/seqtrimnext/plugins_old/.DS_Store