snp-search 0.5.0 → 0.6.0
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- data/README.rdoc +6 -0
- data/VERSION +1 -1
- data/snp-search.gemspec +1 -1
- metadata +16 -16
data/README.rdoc
CHANGED
@@ -16,17 +16,22 @@ To install snp-search, do
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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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+
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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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* Once you have these files ready, you may run snp-search with the following options:
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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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@@ -35,6 +40,7 @@ etc..
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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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* 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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data/VERSION
CHANGED
@@ -1 +1 @@
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1
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-
0.
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1
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+
0.6.0
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data/snp-search.gemspec
CHANGED
metadata
CHANGED
@@ -1,7 +1,7 @@
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1
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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.
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+
version: 0.6.0
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prerelease:
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platform: ruby
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authors:
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@@ -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: &
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+
requirement: &2154921840 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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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: *
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+
version_requirements: *2154921840
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: &
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requirement: &2154921260 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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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: *
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+
version_requirements: *2154921260
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- !ruby/object:Gem::Dependency
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name: slop
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requirement: &
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+
requirement: &2154920680 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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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: *
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version_requirements: *2154920680
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- !ruby/object:Gem::Dependency
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name: rspec
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requirement: &
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requirement: &2154920080 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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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: *
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version_requirements: *2154920080
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- !ruby/object:Gem::Dependency
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name: bundler
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-
requirement: &
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requirement: &2154919480 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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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: *
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version_requirements: *2154919480
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- !ruby/object:Gem::Dependency
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name: jeweler
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requirement: &
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requirement: &2154918880 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ~>
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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: *
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version_requirements: *2154918880
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- !ruby/object:Gem::Dependency
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name: rcov
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-
requirement: &
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+
requirement: &2154918300 !ruby/object:Gem::Requirement
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none: false
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requirements:
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- - ! '>='
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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: *
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+
version_requirements: *2154918300
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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:
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@@ -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:
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+
hash: 2383223488984407940
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required_rubygems_version: !ruby/object:Gem::Requirement
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none: false
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requirements:
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