snp-search 0.6.0 → 0.7.0

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Files changed (4) hide show
  1. data/README.rdoc +24 -24
  2. data/VERSION +1 -1
  3. data/snp-search.gemspec +1 -1
  4. metadata +16 -16
data/README.rdoc CHANGED
@@ -10,41 +10,41 @@ To install snp-search, do
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  == Requirements
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- * Nothing! You just need to run this in unix and it will install all the necessary gems for you.
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+ Nothing! You just need to run this in unix and it will install all the necessary gems for you.
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  == Running snp-search
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- * To run snp-search, you need to have 3 files:
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+ To run snp-search, you need to have 3 files:
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  1- Variant Call Format (.vcf) file (which contains the SNP information)
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  2- Your reference genome that you used to generate your .vcf file (in genbank or embl format, the script will automatically detect the format).
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  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.
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- '''
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- strain1
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- strain2
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- strain3
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- strain4
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- etc..
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- '''
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-
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- * Once you have these files ready, you may run snp-search with the following options:
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-
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- '''
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- -V Enable verbose mode
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- -n Name of your database Optional, default = snp_db.sqlite3
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- -v .vcf file Required
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- -r Reference genome file (The same file that was used in generating the .vcf file). This should be in genbank or embl format. Required
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- -s Text file that contains a list of the strain/sample names (The same strains/samples used in generating the .vcf file) Required
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- -c SNP quality cuttoff. A phred-scaled quality score. High quality scores indicate high confidence calls. Optional, default = 90
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- -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
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- -h help message
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- '''
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-
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- * Usage:
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+ strain1
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+ strain2
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+ strain3
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+ strain4
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+ etc..
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+
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+ Once you have these files ready, you may run snp-search with the following options:
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+
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+
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+ -V Enable verbose mode
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+ -n Name of your database Optional, default = snp_db.sqlite3
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+ -v .vcf file Required
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+ -r Reference genome file (The same file that was used in generating the .vcf file). This should be in genbank or embl format. Required
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+ -s Text file that contains a list of the strain/sample names (The same strains/samples used in generating the .vcf file) Required
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+ -c SNP quality cuttoff. A phred-scaled quality score. High quality scores indicate high confidence calls. Optional, default = 90
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+ -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
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+ -h help message
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+
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+
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+ Usage:
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  snp-search -n my_snp_db.sqlite3 -r my_ref.gbk -v my_vcf_file.vcf -s my_list_of_strains.txt
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+ Have fun snp-searching!
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+
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  == Copyright
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  Copyright (c) 2011 Ali Al-Shahib. See LICENSE.txt for
data/VERSION CHANGED
@@ -1 +1 @@
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- 0.6.0
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+ 0.7.0
data/snp-search.gemspec CHANGED
@@ -5,7 +5,7 @@
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  Gem::Specification.new do |s|
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  s.name = "snp-search"
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- s.version = "0.6.0"
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+ s.version = "0.7.0"
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  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
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  s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
metadata CHANGED
@@ -1,7 +1,7 @@
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  --- !ruby/object:Gem::Specification
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  name: snp-search
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  version: !ruby/object:Gem::Version
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- version: 0.6.0
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+ version: 0.7.0
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  prerelease:
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  platform: ruby
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  authors:
@@ -14,7 +14,7 @@ date: 2011-12-01 00:00:00.000000000Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: activerecord
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- requirement: &2154921840 !ruby/object:Gem::Requirement
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+ requirement: &2158814220 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
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  version: '0'
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154921840
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+ version_requirements: *2158814220
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  - !ruby/object:Gem::Dependency
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  name: bio
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- requirement: &2154921260 !ruby/object:Gem::Requirement
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+ requirement: &2158813620 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
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  version: '0'
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154921260
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+ version_requirements: *2158813620
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  - !ruby/object:Gem::Dependency
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  name: slop
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- requirement: &2154920680 !ruby/object:Gem::Requirement
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+ requirement: &2158813020 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
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  version: '0'
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  type: :runtime
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  prerelease: false
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- version_requirements: *2154920680
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+ version_requirements: *2158813020
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  - !ruby/object:Gem::Dependency
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  name: rspec
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- requirement: &2154920080 !ruby/object:Gem::Requirement
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+ requirement: &2158812420 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -55,10 +55,10 @@ dependencies:
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  version: 2.3.0
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  type: :development
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  prerelease: false
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- version_requirements: *2154920080
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+ version_requirements: *2158812420
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  - !ruby/object:Gem::Dependency
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  name: bundler
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- requirement: &2154919480 !ruby/object:Gem::Requirement
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+ requirement: &2158752840 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -66,10 +66,10 @@ dependencies:
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  version: 1.0.0
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  type: :development
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  prerelease: false
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- version_requirements: *2154919480
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+ version_requirements: *2158752840
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  - !ruby/object:Gem::Dependency
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  name: jeweler
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- requirement: &2154918880 !ruby/object:Gem::Requirement
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+ requirement: &2158752260 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ~>
@@ -77,10 +77,10 @@ dependencies:
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  version: 1.6.4
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  type: :development
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  prerelease: false
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- version_requirements: *2154918880
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+ version_requirements: *2158752260
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  - !ruby/object:Gem::Dependency
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  name: rcov
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- requirement: &2154918300 !ruby/object:Gem::Requirement
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+ requirement: &2158751780 !ruby/object:Gem::Requirement
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  none: false
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  requirements:
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  - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
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  version: '0'
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  type: :development
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  prerelease: false
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- version_requirements: *2154918300
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+ version_requirements: *2158751780
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  description: Use the snp-search toolset to query the SNP database
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  email: ali.al-shahib@hpa.org.uk
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  executables:
@@ -130,7 +130,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
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  version: '0'
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  segments:
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  - 0
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- hash: 2383223488984407940
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+ hash: -491927113428014191
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  required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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  requirements: