snp-search 0.4.0 → 0.5.0

data/README.rdoc

@@ -1,6 +1,6 @@
 = snp-search
 
-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 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.
+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).
@@ -10,27 +10,34 @@ To install snp-search, do
 
 == Requirements
 
-* ActiveRecord: The snp-search API is based on ActiveRecord to get the data from the database.  ActiveRecord is available as a gem:
-  gem install activerecord
-
-* SQLite3: The SQL engine used is sqlite3.  Most Linux operating systems come with sqlite3.  However if you do not have sqlite then you may download it from http://www.sqlite.org/download.html.  The installation instructions are available in the download page.
-
-* bio gem.
+* Nothing! You just need to run this in unix and it will install all the necessary gems for you.
 
 == Running snp-search   
 
-Step 1: 
-
-== Contributing to snp-search
- 
-* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
-* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
-* Fork the project
-* Start a feature/bugfix branch
-* Commit and push until you are happy with your contribution
-* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
-* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
-* 
+* 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).
+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 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
+-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
 
 == Copyright
 

data/VERSION

@@ -1 +1 @@
-0.4.0
+0.5.0

data/bin/snp-search

@@ -10,23 +10,26 @@ opts = Slop.new :help do
   banner "ruby snp-search [OPTIONS]"
 
   on :V, :verbose, 'Enable verbose mode'
-  on :n, :name=, 'Name of database', true 
-  on :r, :reference_file=, 'Path for the reference database, in gbk or embl file format'
-  on :v, :vcf_file=, 'Path for the .vcf file', true
-  on :s, :strain, 'Path for the list of strains text file', true
-  on :c, :cuttoff_snp=, 'cuttoff for SNP quality' 
-  on :t, :cuttoff_genotype=, 'cuttoff for genotype quality'
+  on :n, :name=, 'Name of database', :default => 'snp_db.sqlite3' 
+  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_empty do
     puts help
   end
 end
-
 opts.parse
 
+
+begin
 strains = []
-File.read(opts[:strain]).each_line do |line|
-  strains << line.chop
-end
+  File.read(opts[:strain]).each_line do |line| 
+    strains << line.chop
+  end
+ 
 
 # Enter the name of your database 
 establish_connection(opts[:name])
@@ -61,3 +64,6 @@ populate_features_and_annotations(sequence_flatfile)
 
 #The populate_snps_alleles_genotypes method populates the snps, alleles and genotypes.  It uses the strain names (array) and vcf file.
 populate_snps_alleles_genotypes(strains, vcf_mpileup_file, opts[:cuttoff_snp].to_i, opts[:cuttoff_genotype].to_i)
+
+rescue
+end

data/lib/snp-search.rb

@@ -37,7 +37,7 @@ def populate_features_and_annotations(sequence_file)
 			db_feature.strand = feature.locations.first.strand
 			db_feature.name = feature.feature
 			db_feature.save
-			puts "populated #{db_feature.name}, start: #{db_feature.start}, end: #{db_feature.end}, strand: #{db_feature.strand} for feature: #{db_feature.id}"
+			puts "populating #{db_feature.name}, start: #{db_feature.start}, end: #{db_feature.end}, strand: #{db_feature.strand} for feature: #{db_feature.id}"
 			# Populate the Annotation table with qualifier information from the genbank file
 			feature.qualifiers.each do |qualifier|
 				a = Annotation.new
@@ -45,7 +45,7 @@ def populate_features_and_annotations(sequence_file)
 				a.value = qualifier.value
 				a.save
 				db_feature.annotations << a
-				puts "populated #{a.qualifier} for feature: #{db_feature.id}"
+				puts "populating #{a.qualifier} for feature: #{db_feature.id}"
 			end
 		end
 	end

data/snp-search.gemspec

@@ -5,11 +5,11 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.4.0"
+  s.version = "0.5.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Ali Al-Shahib", "Anthony Underwood"]
-  s.date = "2011-11-30"
+  s.date = "2011-12-01"
   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: 0.4.0
+  version: 0.5.0
   prerelease: 
 platform: ruby
 authors:
@@ -10,11 +10,11 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2011-11-30 00:00:00.000000000Z
+date: 2011-12-01 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2155288080 !ruby/object:Gem::Requirement
+  requirement: &2158814260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -22,10 +22,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2155288080
+  version_requirements: *2158814260
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2155287480 !ruby/object:Gem::Requirement
+  requirement: &2158813660 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -33,10 +33,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2155287480
+  version_requirements: *2158813660
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2155286880 !ruby/object:Gem::Requirement
+  requirement: &2158813060 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -44,10 +44,10 @@ dependencies:
         version: '0'
   type: :runtime
   prerelease: false
-  version_requirements: *2155286880
+  version_requirements: *2158813060
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2155286300 !ruby/object:Gem::Requirement
+  requirement: &2158812460 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2155286300
+  version_requirements: *2158812460
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2155285700 !ruby/object:Gem::Requirement
+  requirement: &2158752880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2155285700
+  version_requirements: *2158752880
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2155285120 !ruby/object:Gem::Requirement
+  requirement: &2158752260 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2155285120
+  version_requirements: *2158752260
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2155284520 !ruby/object:Gem::Requirement
+  requirement: &2158751780 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -88,7 +88,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2155284520
+  version_requirements: *2158751780
 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: 3021040479965194059
+      hash: 2192451038165693366
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: