snp-search 0.29.0 → 0.30.0

data/README.rdoc

@@ -1,9 +1,9 @@
 = 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 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.
+SNPsearch is a tool 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 environment.  It is made available as a gem. See the github site for more information (https://github.com/hpa-bioinformatics/snp-search).
+SNPsearch 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
@@ -12,7 +12,7 @@ To install snp-search, do
 
 Not much, you just need:
 
-* Unix. When installed it will install all the necessary gems for you from Rubygems (note that Rubygems requires admin privileges.  If you do not have admin privileges then we suggest you install RVM: (http://beginrescueend.com/rvm/install/) and then gem install snp-search).  
+* Unix. Once snp-search is installed, all the necessary gems to run snp-search will also be installed from Rubygems (note that Rubygems requires admin privileges.  If you do not have admin privileges then we suggest you install RVM: (http://beginrescueend.com/rvm/install/) and then gem install snp-search).  
 * ruby version 1.8.7 and above.
 
 Thats it!
@@ -42,7 +42,9 @@ Usage:
 The output is your database in sqlite3 format.  If you like to view your table(s) and perform queries you can type 
   sqlite3 snp_db.sqlite3
 
-Alternatively, you may download a SQL tool to view your database (e.g. SQLite sorcerer)
+Alternatively, you may download a SQL tool to view your database (e.g. SQLite sorcerer).
+
+Also, depending on the query, a concatenated SNP FASTA file may be outputed (see below).
 
 == Examples
 
@@ -54,12 +56,27 @@ Usage:
 
   ruby example1.rb -D your_db_name.sqlite3 -s list_of_your_species.txt -o output.fasta
 
+options:
+
+  -V,	Enable verbose mode
+  -D,	The name of the database you like to query, Required
+  -o,	output file, in fasta format
+  -s,	The strains/samples you like to query, Required
+  -a,	The gene you like to remove from analysis
+  -h,	Print this help message
+
 * Example2: This script queries the database and selects the number of unique SNPs within the list of the strains/samples provided.  The output is the number of unique SNPs.
 
 Usage:
 
   ruby example2.rb -D your_db_name.sqlite3 -s list_of_your_species.txt 
 
+options:
+
+  -V,	Enable verbose mode
+  -D,	The name of the database you like to query, Required
+  -s,	The strains/samples you like to query, Required
+  -h,	Print this help message
 
 == Contact
 

data/VERSION

@@ -1 +1 @@
-0.29.0
+0.30.0

data/bin/snp-search

@@ -11,7 +11,7 @@ opts = Slop.new :help do
 
   on :V, :verbose, 'Enable verbose mode'
   on :n, :name=, 'Name of database, Required', true 
-  on :r, :reference_file=, 'Reference genome file, in gbk or embl file format, Required', true
+  on :d, :database_reference_file=, 'Reference genome file, in gbk or embl file format, Required', true
   on :v, :vcf_file=, '.vcf file, Required', true
   on :c, :cuttoff_snp=, 'SNP quality cutoff, (default = 90)', :default => 90 
   on :t, :cuttoff_genotype=, 'Genotype quality cutoff (default = 30)', :default => 30
@@ -22,7 +22,7 @@ opts.parse
   error_msg = ""
 
   error_msg += "You must supply the -n option, it's a required field\n" unless opts[:name]
-  error_msg += "You must supply the -r option, it's a required field\n" unless opts[:reference_file]
+  error_msg += "You must supply the -d option, it's a required field\n" unless opts[:database_reference_file]
   error_msg += "You must supply the -v option, it's a required field" unless opts[:vcf_file]
   
   unless error_msg == "" 
@@ -31,7 +31,7 @@ opts.parse
     exit
   end
    
-  abort "#{opts[:reference_file]} file does not exist!" unless File.exist?(opts[:reference_file])
+  abort "#{opts[:database_reference_file]} file does not exist!" unless File.exist?(opts[:database_reference_file])
   
   abort "#{opts[:vcf_file]} file does not exist!" unless File.exist?(opts[:vcf_file])
 
@@ -42,15 +42,15 @@ establish_connection(opts[:name])
 # Schema will run here
 db_schema
 
-ref = opts[:reference_file]
+ref = opts[:database_reference_file]
 
 sequence_format = guess_sequence_format(ref)
 
       case sequence_format
       when :genbank
-        sequence_flatfile = Bio::FlatFile.open(Bio::GenBank,opts[:reference_file]).next_entry
+        sequence_flatfile = Bio::FlatFile.open(Bio::GenBank,opts[:database_reference_file]).next_entry
       when :embl
-        sequence_flatfile = Bio::FlatFile.open(Bio::EMBL,opts[:reference_file]).next_entry
+        sequence_flatfile = Bio::FlatFile.open(Bio::EMBL,opts[:database_reference_file]).next_entry
       else
         puts "All sequence files should be of genbank or embl format"
         exit
@@ -61,7 +61,7 @@ sequence_format = guess_sequence_format(ref)
 vcf_mpileup_file = opts[:vcf_file]
 
 # The populate_features_and_annotations method populates the features and annotations.  It uses the embl/gbk file.
-# populate_features_and_annotations(sequence_flatfile)
+populate_features_and_annotations(sequence_flatfile)
 
 #The populate_snps_alleles_genotypes method populates the snps, alleles and genotypes.  It uses the vcf file, and if specified, the SNP quality cutoff and genotype quality cutoff
 populate_snps_alleles_genotypes(vcf_mpileup_file, opts[:cuttoff_snp].to_i, opts[:cuttoff_genotype].to_i)

data/examples/example1.rb

@@ -10,7 +10,7 @@ opts = Slop.new :help do
   banner "ruby query.rb [OPTIONS]"
 
   on :V, :verbose, 'Enable verbose mode'
-  on :d, :database=, 'The name of the database you like to query', true
+  on :D, :database=, 'The name of the database you like to query', true
   on :o, :outfile=, 'output file, in fasta format', true  
   on :s, :strain=, 'The strains/samples you like to query', true
   on :a, :annotation=, 'The gene you like to remove from analysis', true
@@ -22,7 +22,7 @@ end
 opts.parse
 
   puts "You must supply the -s option, it's a required field" and exit unless opts[:strain] 
-  puts "You must supply the -d option, it's a required field" and exit unless opts[:database] 
+  puts "You must supply the -D option, it's a required field" and exit unless opts[:database] 
 
 begin 
 	puts "#{opts[:database]} file does not exist!" and exit unless File.exist?(opts[:database])

data/snp-search.gemspec

@@ -5,7 +5,7 @@
 
 Gem::Specification.new do |s|
   s.name = "snp-search"
-  s.version = "0.29.0"
+  s.version = "0.30.0"
 
   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: 0.29.0
+  version: 0.30.0
   prerelease: 
 platform: ruby
 authors:
@@ -14,7 +14,7 @@ date: 2012-01-05 00:00:00.000000000Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: activerecord
-  requirement: &2173599960 !ruby/object:Gem::Requirement
+  requirement: &2158653900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -22,10 +22,10 @@ dependencies:
         version: 3.1.3
   type: :runtime
   prerelease: false
-  version_requirements: *2173599960
+  version_requirements: *2158653900
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &2173599480 !ruby/object:Gem::Requirement
+  requirement: &2158653400 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -33,10 +33,10 @@ dependencies:
         version: 1.4.2
   type: :runtime
   prerelease: false
-  version_requirements: *2173599480
+  version_requirements: *2158653400
 - !ruby/object:Gem::Dependency
   name: slop
-  requirement: &2173599000 !ruby/object:Gem::Requirement
+  requirement: &2158652900 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -44,10 +44,10 @@ dependencies:
         version: 2.4.0
   type: :runtime
   prerelease: false
-  version_requirements: *2173599000
+  version_requirements: *2158652900
 - !ruby/object:Gem::Dependency
   name: sqlite3
-  requirement: &2173598520 !ruby/object:Gem::Requirement
+  requirement: &2158652340 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -55,10 +55,10 @@ dependencies:
         version: 1.3.4
   type: :runtime
   prerelease: false
-  version_requirements: *2173598520
+  version_requirements: *2158652340
 - !ruby/object:Gem::Dependency
   name: activerecord-import
-  requirement: &2173598040 !ruby/object:Gem::Requirement
+  requirement: &2158651840 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -66,10 +66,10 @@ dependencies:
         version: 0.2.8
   type: :runtime
   prerelease: false
-  version_requirements: *2173598040
+  version_requirements: *2158651840
 - !ruby/object:Gem::Dependency
   name: rspec
-  requirement: &2173597560 !ruby/object:Gem::Requirement
+  requirement: &2158651360 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -77,10 +77,10 @@ dependencies:
         version: 2.3.0
   type: :development
   prerelease: false
-  version_requirements: *2173597560
+  version_requirements: *2158651360
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &2173597080 !ruby/object:Gem::Requirement
+  requirement: &2158650880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -88,10 +88,10 @@ dependencies:
         version: 1.0.0
   type: :development
   prerelease: false
-  version_requirements: *2173597080
+  version_requirements: *2158650880
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &2173596600 !ruby/object:Gem::Requirement
+  requirement: &2158650380 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ~>
@@ -99,10 +99,10 @@ dependencies:
         version: 1.6.4
   type: :development
   prerelease: false
-  version_requirements: *2173596600
+  version_requirements: *2158650380
 - !ruby/object:Gem::Dependency
   name: rcov
-  requirement: &2173596100 !ruby/object:Gem::Requirement
+  requirement: &2158649880 !ruby/object:Gem::Requirement
     none: false
     requirements:
     - - ! '>='
@@ -110,7 +110,7 @@ dependencies:
         version: '0'
   type: :development
   prerelease: false
-  version_requirements: *2173596100
+  version_requirements: *2158649880
 description: Use the snp-search toolset to query the SNP database
 email: ali.al-shahib@hpa.org.uk
 executables:
@@ -155,7 +155,7 @@ required_ruby_version: !ruby/object:Gem::Requirement
       version: '0'
       segments:
       - 0
-      hash: 3565475857465083305
+      hash: -2678213948828856035
 required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
   requirements: