snp-search 0.7.0 → 0.8.0

data/README.rdoc

@@ -3,18 +3,19 @@
 snp-search is a set of tools that manages SNP data and allows for data importing, manipulating, editing and complex querying of SNP data.  It can be used to evaluate the utility of SNPs for the assessment of genetic diversity between haploid strains and the management of genotype and phenotype data.  Once a query is performed, SNPsearch can be used to convert the selected SNP data into FASTA sequences.  SNPsearch is particularly useful in the analysis of phylogenetic trees that are based on SNP differences across whole core genomes.  Queries can be made to answer critical genomic questions such as the association of SNPs with particular phenotypes.
 
 == Obtaining and installing the code
-snp-search is written in Ruby and operates in a Unix enviroment.  It is made available as a gem. See the github site for more information (https://github.com/hpa-bioinformatics/snp-search).
+snp-search is written in Ruby and operates in a Unix environment.  It is made available as a gem. See the github site for more information (https://github.com/hpa-bioinformatics/snp-search).
 
 To install snp-search, do
   gem install snp-search
 
 == Requirements
 
-Nothing! You just need to run this in unix and it will install all the necessary gems for you.
+Nothing! You just need to run this in Unix and it will install all the necessary gems for you.
 
 == Running snp-search   
 
 To run snp-search, you need to have 3 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).
@@ -35,13 +36,13 @@ Once you have these files ready, you may run snp-search with the following optio
   -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 cuttoff.  A phred-scaled quality score. High quality scores indicate high confidence calls. Optional, default = 90
-  -t	Genotype Quality cuttoff. This is the probability that the genotype call is wrong under the condition that the site is being variant.	Optional, default = 30
+  -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 -s my_list_of_strains.txt
 
 Have fun snp-searching!
 

data/VERSION

@@ -1 +1 @@
-0.7.0
+0.8.0

data/bin/snp-search

@@ -14,8 +14,8 @@ opts = Slop.new :help do
   on :r, :reference_file=, 'Reference genome file, in gbk or embl file format', true
   on :v, :vcf_file=, '.vcf file', true
   on :s, :strain=, 'text file with a list of strains/samples', true
-  on :c, :cuttoff_snp=, 'SNP quality cuttoff', :default => 90 
-  on :t, :cuttoff_genotype=, 'Genotype quality cuttoff', :default => 30
+  on :c, :cuttoff_snp=, 'SNP quality cutoff', :default => 90 
+  on :t, :cuttoff_genotype=, 'Genotype quality cutoff', :default => 30
    
   on_empty do
     puts help

data/snp-search.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.7.0"
+  s.version = "0.8.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ali Al-Shahib", "Anthony Underwood"]

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: snp-search
 version: !ruby/object:Gem::Version
-  version: 0.7.0
+  version: 0.8.0
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2011-12-01 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2158814220 !ruby/object:Gem::Requirement
+  requirement: &2154643260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2158814220
+  version_requirements: *2154643260
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2158813620 !ruby/object:Gem::Requirement
+  requirement: &2154642660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2158813620
+  version_requirements: *2154642660
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2158813020 !ruby/object:Gem::Requirement
+  requirement: &2154642060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2158813020
+  version_requirements: *2154642060
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2158812420 !ruby/object:Gem::Requirement
+  requirement: &2154641460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2158812420
+  version_requirements: *2154641460
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2158752840 !ruby/object:Gem::Requirement
+  requirement: &2154640860 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2158752840
+  version_requirements: *2154640860
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2158752260 !ruby/object:Gem::Requirement
+  requirement: &2154640260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2158752260
+  version_requirements: *2154640260
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2158751780 !ruby/object:Gem::Requirement
+  requirement: &2154639660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2158751780
+  version_requirements: *2154639660
 description: Use the snp-search toolset to query the SNP database
 email: ali.al-shahib@hpa.org.uk
 executables:
@@ -130,7 +130,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: -491927113428014191
+      hash: 977817954600315423
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: