bio-gemma-wrapper 0.97.1 → 0.98

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,3 +1,5 @@
+[![Gem Version](https://badge.fury.io/rb/bio-gemma-wrapper.svg)](https://badge.fury.io/rb/bio-gemma-wrapper)
+
 # GEMMA wrapper caches K between runs with LOCO support
 
 ![Genetic associations identified in CFW mice using GEMMA (Parker et al,
@@ -39,10 +41,12 @@ Invoke the tool with
 
     gemma-wrapper --help
 
-and it will render
+and it will render something like
 
 ```
 Usage: gemma-wrapper [options] -- [gemma-options]
+        --permutate n                Permutate # times by shuffling phenotypes
+        --permute-phenotypes filen   Phenotypes to be shuffled in permutations
         --loco [x,y,1,2,3...]        Run full LOCO
         --input filen                JSON input variables (used for LOCO)
         --cache-dir path             Use a cache directory
@@ -95,7 +99,8 @@ Run it twice to see
 
 gemma-wrapper computes the unique HASH value over the command
 line switches passed into GEMMA as well as the contents of the files
-passed in (here the genotype and phenotype files).
+passed in (here the genotype and phenotype files - actually it ignores the phenotype with K because
+GEMMA always computes the same K).
 
 You can also get JSON output on STDOUT by providing the --json switch
 

data/VERSION

@@ -1 +1 @@
-0.97.1
+0.98

data/bin/gemma-wrapper

@@ -35,9 +35,13 @@ GEMMA wrapper example:
         -lmm 2 -maf 0.1 \\
         -debug > GWA.json
 
+Gemma gets used from the path. You can override by setting
+
+      env GEMMA_COMMAND=path/bin/gemma gemma-wrapper ...
+
 "
 # These are used for testing compatibility
-GEMMA_V_MAJOR = 97
+GEMMA_V_MAJOR = 98
 GEMMA_V_MINOR = 0
 
 basepath = File.dirname(File.dirname(__FILE__))
@@ -61,6 +65,7 @@ if not gemma_command
   end
 end
 
+
 require 'fileutils'
 require 'optparse'
 require 'tmpdir'
@@ -76,13 +81,13 @@ options = { show_help: false, source: 'https://github.com/genetics-statistics/ge
 opts = OptionParser.new do |o|
   o.banner = "\nUsage: #{File.basename($0)} [options] -- [gemma-options]"
 
-  o.on('--permutate n', Integer, 'Permutate by shuffling phenotypes') do |lst|
+  o.on('--permutate n', Integer, 'Permutate # times by shuffling phenotypes') do |lst|
     options[:permutate] = lst
     options[:force] = true
   end
 
-  o.on('--phenotypes filen',String, 'Phenotypes to be shuffled in permutations') do |phenotypes|
-    options[:phenotypes] = phenotypes
+  o.on('--permute-phenotypes filen',String, 'Phenotypes to be shuffled in permutations') do |phenotypes|
+    options[:permute_phenotypes] = phenotypes
     raise "Phenotype input file #{phenotypes} does not exist" if !File.exist?(phenotypes)
   end
 
@@ -176,6 +181,7 @@ info.call GEMMA_K_BANNER
 
 # Check gemma version
 GEMMA_COMMAND=options[:gemma_command]
+
 gemma_version_header = `#{GEMMA_COMMAND}`.split("\n").grep(/GEMMA|Version/)[0].strip
 info.call "Using ",gemma_version_header,"\n"
 gemma_version = gemma_version_header.split(/[,\s]+/)[1]
@@ -197,12 +203,26 @@ if RUBY_VERSION =~ /^1/
   warning "runs on Ruby 2.x only\n"
 end
 
+DO_COMPUTE_KINSHIP = gemma_args.include?("-gk")
+DO_COMPUTE_GWA = !DO_COMPUTE_KINSHIP
+
 # ---- Compute HASH on inputs
 hashme = []
 geno_idx = gemma_args.index '-g'
-raise "Expected GEMMA -g switch" if geno_idx == nil
-hashme = gemma_args
-hashme += ['-p', options[:phenotypes]] if options[:phenotypes]
+raise "Expected GEMMA -g genotype file switch" if geno_idx == nil
+pheno_idx = gemma_args.index '-p'
+hashme =
+  if DO_COMPUTE_KINSHIP and pheno_idx != nil
+    p [pheno_idx,gemma_args[pheno_idx+2..-1]]
+    gemma_args[0..pheno_idx-1] + gemma_args[pheno_idx+2..-1]
+  else
+    gemma_args
+  end
+
+if DO_COMPUTE_GWA
+  raise "Did not expect GEMMA -p phenotype file switch" if pheno_idx
+  hashme += ['-p', options[:permute_phenotypes]] if options[:permute_phenotypes]
+end
 
 require 'digest/sha1'
 debug.call "Hashing on ",hashme,"\n"
@@ -302,7 +322,7 @@ end
 # ---- Run GWA
 gwas = lambda do | chr, kfn, pfn |
   record[:type] = "GWA"
-  error.call "Do not use the GEMMA -k switch with gemma-wrapper!" if GEMMA_ARGS.include? '-k' # K is automatic
+  error.call "Do not use the GEMMA -k switch with gemma-wrapper - it is automatic!" if GEMMA_ARGS.include? '-k' # K is automatic
   hashi, cache_hit = cache.call chr,".assoc.txt"
   if not cache_hit
     args = [ '-k', kfn, '-o', hashi ]
@@ -313,7 +333,8 @@ gwas = lambda do | chr, kfn, pfn |
 end
 
 LOCO = options[:loco]
-if GEMMA_ARGS.include? '-gk'
+# if GEMMA_ARGS.include? '-gk'
+if DO_COMPUTE_KINSHIP
   # compute K
   info.call LOCO
   if LOCO != nil
@@ -325,7 +346,7 @@ if GEMMA_ARGS.include? '-gk'
     kinship.call # no LOCO
   end
 else
-  # GWAS
+  # DO_COMPUTE_GWA
   json_in = JSON.parse(File.read(options[:input]))
   raise "JSON problem, file #{options[:input]} is not -gk derived" if json_in["type"] != "K"
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-gemma-wrapper
 version: !ruby/object:Gem::Version
-  version: 0.97.1
+  version: '0.98'
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-07-19 00:00:00.000000000 Z
+date: 2018-11-19 00:00:00.000000000 Z
 dependencies: []
 description: GEMMA wrapper adds LOCO and permutation support. Also caches K between
   runs with LOCO support