seqtrimnext 2.0.60 → 2.0.61

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: a3858c7d16c231f2bd9a8a20a79e71793fa4a26b
-  data.tar.gz: 8737fb4a873639ccf4784fa0b0f4add4778df20f
+  metadata.gz: 0ccbee45f33fe72b0b26f542ec15a54e16e91090
+  data.tar.gz: d3637c75263534e59c4a4fc3f2175b15eb7745ac
 SHA512:
-  metadata.gz: 8885fc85c63703652371ecc1a4bc67670de700b8151ba0cf3e3e706904b979a4eeb777b289c2553b229832a556887572c0c8760978f7f6306b099a085a850ab1
-  data.tar.gz: a9c3c18e94a240720afd44840ba297259ec888c28381ec4855eec68b38dba3387b76df33c5211b2a91f9fec5d23e03645b792ae4fa71e8c82ea36dfc965e2e1e
+  metadata.gz: b76e76001e951d7e1d104e59dd20042cd50274ed313e8531620962a639c8f294cdd9eb7c558f4e79a336a9f58d1d87e5357c21c4ddb2129cdb4d5048ff7a97ce
+  data.tar.gz: e19042628ff07b65c4fd08c11b719175e1656a343d10e7811a434fbd8d6923f2a2b0060f8c74fec894e2a09e82d7a35fcad4b4aa074e63516d399c163554163c

data/bin/resume_execution_times.rb

@@ -0,0 +1,55 @@
+#!/usr/bin/env ruby
+
+require 'json'
+
+if ARGV.count<1 
+  puts "Usage: #{$0} [-t] [-j] stats1.json"
+  exit -1
+end
+
+# print header  
+if ARGV[0]=='-t'
+	heads=['Plugin name','execution_time (s)']
+	puts heads.join("\t")   
+	ARGV.shift
+end
+
+puts_json=false
+if ARGV[0]=='-j'
+	puts_json=true
+	ARGV.shift
+end
+
+
+ARGV.each do |file_path|
+	sample_name = File.basename(File.expand_path(File.join(file_path,'..','..')))
+
+	stats=JSON::parse(File.read(file_path))
+
+	res={}
+
+	begin
+		stats.keys.each do |k|
+			if stats[k]['execution_time']
+				res[k]=stats[k]['execution_time']['total_seconds']
+			end
+		end
+		
+	rescue Excepcion => e
+
+	   puts "Error reading #{file_path}"
+	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/resume_stn_stats.rb

@@ -0,0 +1,40 @@
+#!/usr/bin/env ruby
+
+require 'json'
+
+if ARGV.count<1 
+  puts "Usage: #{$0} stats1.json [stats2.json stats3.json,...]"
+  exit -1
+end
+
+# print header  
+if ARGV[0]=='-t'
+	heads=['sample_name','input_count','sequence_count_paired','sequence_count_single','rejected','rejected_percent']
+	puts heads.join("\t")   
+	ARGV.shift
+end
+
+ARGV.each do |file_path|
+	sample_name = File.basename(File.expand_path(File.join(file_path,'..','..')))
+
+	stats=JSON::parse(File.read(file_path))
+
+	res=[]
+
+	begin
+		res << sample_name
+		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) 
+		
+	rescue Excepcion => e
+
+	   puts "Error reading #{file_path}"
+	end
+
+	puts res.join("\t")
+
+end
+

data/lib/seqtrimnext/plugins/plugin.rb

@@ -20,9 +20,15 @@ class Plugin
     @stats ={}
     
     if can_execute?
+      t1=Time.now
       execute(seq)
+      t2=Time.now
     end
     
+    
+    @stats['execution_time']={}
+
+    @stats['execution_time']['total_seconds']=t2-t1
   end
 
   def can_execute?

data/lib/seqtrimnext/plugins/plugin_indeterminations.rb

@@ -148,6 +148,23 @@ class PluginIndeterminations < Plugin
      
      actions=[]
      
+    # find simple indeterminations at the beginning of sequence
+      match=seq.seq_fasta.match(/^[nN]+/)
+     
+     if !match.nil?
+       found=match[0].length
+       
+       a = seq.new_action(0,found-1,'ActionIndetermination')
+       actions.push a       
+
+       #Add actions  
+       seq.add_actions(actions)
+       actions=[]
+       add_stats('indetermination_size',found)
+  
+     end
+     
+
      # find simple indeterminations at end of sequence
 			match=seq.seq_fasta.match(/[nN]+$/)
      

data/lib/seqtrimnext/version.rb

@@ -1,4 +1,4 @@
 module Seqtrimnext
-  VERSION = "2.0.60"
+  VERSION = "2.0.61"
   SEQTRIM_VERSION = VERSION
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: seqtrimnext
 version: !ruby/object:Gem::Version
-  version: 2.0.60
+  version: 2.0.61
 platform: ruby
 authors:
 - Dario Guerrero
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-23 00:00:00.000000000 Z
+date: 2016-01-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -217,7 +217,9 @@ executables:
 - parse_json_results.rb
 - parse_params.rb
 - resume_clusters.rb
+- resume_execution_times.rb
 - resume_rejected.rb
+- resume_stn_stats.rb
 - reverse_paired.rb
 - seqtrimnext
 - split_fasta.rb
@@ -248,7 +250,9 @@ files:
 - bin/parse_json_results.rb
 - bin/parse_params.rb
 - bin/resume_clusters.rb
+- bin/resume_execution_times.rb
 - bin/resume_rejected.rb
+- bin/resume_stn_stats.rb
 - bin/reverse_paired.rb
 - bin/seqtrimnext
 - bin/split_fasta.rb
@@ -374,7 +378,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.4.8
+rubygems_version: 2.4.4
 signing_key: 
 specification_version: 4
 summary: Sequences preprocessing and cleaning software