seqtrimnext_report 0.0.5 → 0.0.7

checksums.yaml

@@ -0,0 +1,7 @@
+--- 
+SHA1: 
+  metadata.gz: c42cf93e60bfc81a51b415541d88f9a4ffd13213
+  data.tar.gz: 8a0719b08465f02570155488f32d8c92f10b947e
+SHA512: 
+  metadata.gz: 969f6bdcde2eb8e932532e35193f84260567113aaad17ac5476a877437af66cfe5e4b98d58d99caa4e6e4a5bcddb41ba3a93b469b351ac9e562b4ad5cd7812b0
+  data.tar.gz: aaf73a28e860db09598eb353fbcdd513b1b88726ae2ade0fd7a6e9ba62a4196fa3ae59e35e9650877dd14174bbd5e1c24da1f73e6ee56e4a72a0cc88ee81ec1c

data/History.txt

@@ -1,3 +1,11 @@
+=== 0.0.7 2013-07-19
+
+Fix to work with incomplete initial stats
+
+=== 0.0.6 2012-12-05
+
+Fix not found Initial stats for illumina
+
 === 0.0.5 2012-03-01
 
 Fixed bug with report generation

data/bin/generate_report.rb

@@ -39,6 +39,23 @@ def get_json_data(file)
   return data
 end
 
+def fix_initial_stats(initial_stats)
+  
+    initial_stats['sequence_count']=0 if initial_stats['sequence_count'].nil?
+    initial_stats['smallest_sequence_size']=0 if initial_stats['smallest_sequence_size'].nil?
+    initial_stats['biggest_sequence_size']=0 if initial_stats['biggest_sequence_size'].nil?    
+    initial_stats['min_sequence_size_raw']=0 if initial_stats['min_sequence_size_raw'].nil?    
+    initial_stats['max_sequence_size_raw']=0 if initial_stats['max_sequence_size_raw'].nil?    
+    initial_stats['coefficient_of_variance']=0 if initial_stats['coefficient_of_variance'].nil?    
+    initial_stats['nucleotide_count']=0 if initial_stats['nucleotide_count'].nil?    
+    initial_stats['mode_of_sizes']=0 if initial_stats['mode_of_sizes'].nil?    
+    initial_stats['mean_of_sequence_sizes']=0 if initial_stats['mean_of_sequence_sizes'].nil?    
+    initial_stats['qv']=[] if initial_stats['qv'].nil?    
+    initial_stats['used_key']='XXXX' if initial_stats['used_key'].nil?
+    initial_stats['all_keys']={'XXXX'=>0} if initial_stats['all_keys'].nil?
+    
+end
+
 if ARGV.count!=1
   puts "Usage: #{File.basename($0)} output_files_folder"
   exit(-1)
@@ -52,12 +69,37 @@ if !Dir.exists?(output_files)
   exit(-1)
 end
 
+
+
 if !File.exist?(File.join(output_files,'used_params.txt'))
   puts "used_params.txt file not found.\n"
   exit(-1)
 elsif !File.exist?(File.join(output_files,'initial_stats.json'))
-  puts "initial_stats.json file not found.\n"
-  exit(-1)
+  puts "initial_stats.json file not found. Using an empty file\n"
+  
+  f=File.open(File.join(output_files,'initial_stats.json'),'w')
+  
+  s='{
+    "sequence_count": 0,
+    "smallest_sequence_size": 0,
+    "biggest_sequence_size": 0,
+    "min_sequence_size_raw": 0,
+    "max_sequence_size_raw": 0,
+    "coefficient_of_variance": 0,
+    "nucleotide_count": 0,
+    "mode_of_sizes": 0,
+    "mean_of_sequence_sizes": 0,
+    "qv": [],
+    "used_key": "XXXX",
+    "all_keys": {
+      "XXXX": 0
+    }
+  }'
+  
+  f.puts(s)
+  f.close
+  
+  # exit(-1)
 elsif !File.exist?(File.join(output_files,'stats.json'))
   puts "stats.json file not found.\n"
   exit(-1)
@@ -76,6 +118,8 @@ begin
   
   # load initial and final stats
   initial_stats = get_json_data(File.join(output_files,'initial_stats.json'))
+  fix_initial_stats(initial_stats)
+  
   stats = get_json_data(File.join(output_files,'stats.json'))
   
 	if (initial_stats.nil?)

data/lib/seqtrimnext_report.rb

@@ -8,5 +8,5 @@ ROOT_PATH=File.join(File.dirname(__FILE__),'seqtrimnext_report')
 $: << File.expand_path(File.join(ROOT_PATH, 'classes'))
 
 module SeqtrimnextReport
-   VERSION = '0.0.5'
+   VERSION = '0.0.7'
 end

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: seqtrimnext_report
 version: !ruby/object:Gem::Version 
-  prerelease: 
-  version: 0.0.5
+  version: 0.0.7
 platform: ruby
 authors: 
 - Noe Fernandez & Dario Guerrero
@@ -10,13 +9,12 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2012-03-01 00:00:00 Z
+date: 2013-07-19 00:00:00 Z
 dependencies: 
 - !ruby/object:Gem::Dependency 
   name: seqtrimnext
   prerelease: false
   requirement: &id001 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -27,7 +25,6 @@ dependencies:
   name: hoe
   prerelease: false
   requirement: &id002 !ruby/object:Gem::Requirement 
-    none: false
     requirements: 
     - - ">="
       - !ruby/object:Gem::Version 
@@ -73,6 +70,8 @@ files:
 homepage: http://www.scbi.uma.es/downloads
 licenses: []
 
+metadata: {}
+
 post_install_message: PostInstall.txt
 rdoc_options: 
 - --main
@@ -80,23 +79,20 @@ rdoc_options:
 require_paths: 
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
-  - - ">="
+  - &id003 
+    - ">="
     - !ruby/object:Gem::Version 
       version: "0"
 required_rubygems_version: !ruby/object:Gem::Requirement 
-  none: false
   requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      version: "0"
+  - *id003
 requirements: []
 
 rubyforge_project: seqtrimnext_report
-rubygems_version: 1.7.2
+rubygems_version: 2.0.3
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: A PDF report generator for SeqtrimNEXT preprocessing software from SCBI.
 test_files: 
 - test/test_helper.rb