seqtrimnext 2.0.60 → 2.0.61
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
checksums.yaml
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@@ -1,7 +1,7 @@
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 0ccbee45f33fe72b0b26f542ec15a54e16e91090
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data.tar.gz: d3637c75263534e59c4a4fc3f2175b15eb7745ac
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SHA512:
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metadata.gz:
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metadata.gz: b76e76001e951d7e1d104e59dd20042cd50274ed313e8531620962a639c8f294cdd9eb7c558f4e79a336a9f58d1d87e5357c21c4ddb2129cdb4d5048ff7a97ce
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data.tar.gz: e19042628ff07b65c4fd08c11b719175e1656a343d10e7811a434fbd8d6923f2a2b0060f8c74fec894e2a09e82d7a35fcad4b4aa074e63516d399c163554163c
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@@ -0,0 +1,55 @@
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#!/usr/bin/env ruby
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require 'json'
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if ARGV.count<1
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puts "Usage: #{$0} [-t] [-j] stats1.json"
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exit -1
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end
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# print header
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if ARGV[0]=='-t'
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heads=['Plugin name','execution_time (s)']
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puts heads.join("\t")
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ARGV.shift
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end
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puts_json=false
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if ARGV[0]=='-j'
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puts_json=true
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ARGV.shift
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end
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ARGV.each do |file_path|
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sample_name = File.basename(File.expand_path(File.join(file_path,'..','..')))
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stats=JSON::parse(File.read(file_path))
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res={}
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begin
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stats.keys.each do |k|
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if stats[k]['execution_time']
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res[k]=stats[k]['execution_time']['total_seconds']
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end
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end
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rescue Excepcion => e
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puts "Error reading #{file_path}"
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end
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if puts_json
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puts JSON::pretty_generate(res)
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else
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total=0
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res.keys.sort.each do |k|
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puts "#{k}\t#{res[k]}"
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total+=res[k]
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end
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puts "-"*20
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puts "TOTAL (plugins):\t#{total}"
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end
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end
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#!/usr/bin/env ruby
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require 'json'
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if ARGV.count<1
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puts "Usage: #{$0} stats1.json [stats2.json stats3.json,...]"
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exit -1
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end
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# print header
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if ARGV[0]=='-t'
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heads=['sample_name','input_count','sequence_count_paired','sequence_count_single','rejected','rejected_percent']
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puts heads.join("\t")
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ARGV.shift
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end
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ARGV.each do |file_path|
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sample_name = File.basename(File.expand_path(File.join(file_path,'..','..')))
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stats=JSON::parse(File.read(file_path))
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res=[]
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begin
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res << sample_name
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res << stats['sequences']['count']['input_count']
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res << stats['sequences']['count']['output_seqs_paired']
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res << stats['sequences']['count']['output_seqs']
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res << stats['sequences']['count']['rejected']
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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)
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rescue Excepcion => e
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puts "Error reading #{file_path}"
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end
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puts res.join("\t")
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end
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@@ -148,6 +148,23 @@ class PluginIndeterminations < Plugin
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actions=[]
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# find simple indeterminations at the beginning of sequence
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match=seq.seq_fasta.match(/^[nN]+/)
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if !match.nil?
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found=match[0].length
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a = seq.new_action(0,found-1,'ActionIndetermination')
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actions.push a
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#Add actions
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seq.add_actions(actions)
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actions=[]
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add_stats('indetermination_size',found)
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end
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# find simple indeterminations at end of sequence
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match=seq.seq_fasta.match(/[nN]+$/)
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data/lib/seqtrimnext/version.rb
CHANGED
metadata
CHANGED
@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: seqtrimnext
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version: !ruby/object:Gem::Version
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version: 2.0.
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version: 2.0.61
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platform: ruby
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authors:
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- Dario Guerrero
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autorequire:
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bindir: bin
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cert_chain: []
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date:
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date: 2016-01-19 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bundler
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@@ -217,7 +217,9 @@ executables:
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- parse_json_results.rb
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- parse_params.rb
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- resume_clusters.rb
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- resume_execution_times.rb
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- resume_rejected.rb
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- resume_stn_stats.rb
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- reverse_paired.rb
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- seqtrimnext
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- split_fasta.rb
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@@ -248,7 +250,9 @@ files:
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- bin/parse_json_results.rb
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- bin/parse_params.rb
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- bin/resume_clusters.rb
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- bin/resume_execution_times.rb
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- bin/resume_rejected.rb
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- bin/resume_stn_stats.rb
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- bin/reverse_paired.rb
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- bin/seqtrimnext
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- bin/split_fasta.rb
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@@ -374,7 +378,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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version: '0'
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requirements: []
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rubyforge_project:
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rubygems_version: 2.4.
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rubygems_version: 2.4.4
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signing_key:
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specification_version: 4
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summary: Sequences preprocessing and cleaning software
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