snp-search 0.22.0 → 0.23.0

data/README.rdoc

@@ -19,34 +19,25 @@ Thats it!
 
 == Running snp-search   
 
-To run snp-search, you need to have 3 files:
+To run snp-search, you need to have 2 files:
 
 1- Variant Call Format (.vcf) file (which contains the SNP information)
 
 2- Your reference genome that you used to generate your .vcf file (in genbank or embl format, the script will automatically detect the format).
 
-3- A text file with a list of your strain/sample names.  These should be the same strains/samples used in generating the .vcf file. In the text file, every strain/sample name should have a new line, e.g.
-
-  strain1
-  strain2
-  strain3
-  strain4
-  etc..
-
 Once you have these files ready, you may run snp-search with the following options:
 
   -V	Enable verbose mode
   -n	Name of your database	Optional, default = snp_db.sqlite3
   -v	.vcf file	Required
   -r	Reference genome file (The same file that was used in generating the .vcf file).  This should be in genbank or embl format.	Required
-  -s	Text file that contains a list of the strain/sample names (The same strains/samples used in generating the .vcf file)	Required
   -c	SNP quality cutoff.  A phred-scaled quality score. High quality scores indicate high confidence calls. Optional, default = 90
   -t	Genotype Quality cutoff. This is the probability that the genotype call is wrong under the condition that the site is being variant.	Optional, default = 30
   -h	help message
 
 
 Usage:
-  snp-search -n my_snp_db.sqlite3 -r my_ref.gbk -v my_vcf_file.vcf -s my_list_of_strains.txt
+  snp-search -n my_snp_db.sqlite3 -r my_ref.gbk -v my_vcf_file.vcf 
 
 == Output
 The output is your database in sqlite3 format.  If you like to view your table(s) and perform queries you can type 

data/VERSION

@@ -1 +1 @@
-0.22.0
+0.23.0

data/lib/snp-search.rb

@@ -4,6 +4,8 @@ require 'bio'
 require  'snp_db_models'
 #establish_connection
 
+GC.disable
+
 def guess_sequence_format(reference_genome)
   file_extension = File.extname(reference_genome).downcase
   file_format = nil

data/snp-search.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.22.0"
+  s.version = "0.23.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
-  s.date = "2011-12-07"
+  s.date = "2011-12-08"
   s.description = "Use the snp-search toolset to query the SNP database"
   s.email = "ali.al-shahib@hpa.org.uk"
   s.executables = ["snp-search"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: snp-search
 version: !ruby/object:Gem::Version
-  version: 0.22.0
+  version: 0.23.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-12-07 00:00:00.000000000Z
+date: 2011-12-08 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2158657440 !ruby/object:Gem::Requirement
+  requirement: &2158724720 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 3.1.3
   type: :runtime
   prerelease: false
-  version_requirements: *2158657440
+  version_requirements: *2158724720
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2158656840 !ruby/object:Gem::Requirement
+  requirement: &2158724140 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -33,10 +33,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2158656840
+  version_requirements: *2158724140
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2158645460 !ruby/object:Gem::Requirement
+  requirement: &2158723560 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -44,10 +44,10 @@ dependencies:
         version: 2.4.0
   type: :runtime
   prerelease: false
-  version_requirements: *2158645460
+  version_requirements: *2158723560
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2158644880 !ruby/object:Gem::Requirement
+  requirement: &2158722980 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 1.3.4
   type: :runtime
   prerelease: false
-  version_requirements: *2158644880
+  version_requirements: *2158722980
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2158644320 !ruby/object:Gem::Requirement
+  requirement: &2158722400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2158644320
+  version_requirements: *2158722400
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2158643800 !ruby/object:Gem::Requirement
+  requirement: &2158693340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2158643800
+  version_requirements: *2158693340
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2158643320 !ruby/object:Gem::Requirement
+  requirement: &2158692760 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +88,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2158643320
+  version_requirements: *2158692760
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2158642840 !ruby/object:Gem::Requirement
+  requirement: &2158692180 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -99,7 +99,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2158642840
+  version_requirements: *2158692180
 description: Use the snp-search toolset to query the SNP database
 email: ali.al-shahib@hpa.org.uk
 executables:
@@ -146,7 +146,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 534829390528662828
+      hash: 802966617095520080
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: