bio-gemma-wrapper 0.98 → 0.98.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d8f36b92e82dda9e1e592724204521f9f4f1a950
-  data.tar.gz: 077abf1c1a704ab93a27627d511aeba0dbf6b4c5
+  metadata.gz: b7a8bfe787236f397dba6e05aef202486ba53389
+  data.tar.gz: 9fe2398ed3fcd053e8258f73a64b1610bfddf9e2
 SHA512:
-  metadata.gz: b49bb2c9362eb7babd2cf20f640fc7806719a8c82e31f93a97b4517d5c2777bd4ae55b9e5a1fd37df5f22e63e2673fa01ca4afbc4e07de6955391d77bd7f90fb
-  data.tar.gz: 863ef847e4ddff6b544a733e001bcd2291c73ab394573a299d54a8f2581066fb423b40be052ce6a440c1daffbd6ddb7500c5f01b7ce2de0e38e4277c8ae9e53e
+  metadata.gz: 0a691906f13da3469597517d160874315f5962822b0273757d33c37283c2a9a98da9a41d08c51e4ed7854b3d3593f9d96ac81d59212690edd628a2677499d501
+  data.tar.gz: 5d4b898ff3566f52652cbb7db6597dc245e9a5da6b0d9da107de81deec0d51c02c822762e0ab921a2309c1dbc3455b55c1adc5fe94c891e31a9c32cb6d343f2e

data/README.md

@@ -1,4 +1,4 @@
-[![Gem Version](https://badge.fury.io/rb/bio-gemma-wrapper.svg)](https://badge.fury.io/rb/bio-gemma-wrapper)
+[![gemma-wrapper 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
 
@@ -128,6 +128,23 @@ default. If you want something else provide a --cache-dir, e.g.
 
 will store K in ~/.gemma-cache.
 
+### GWA
+
+Run the LMM using the K's captured in K.json using the --input
+switch
+
+    gemma-wrapper --json --loco --input K.json -- \
+        -g test/data/input/BXD_geno.txt.gz \
+        -p test/data/input/BXD_pheno.txt \
+        -c test/data/input/BXD_covariates2.txt \
+        -a test/data/input/BXD_snps.txt \
+        -lmm 2 -maf 0.1 \
+        -debug > GWA.json
+
+Running it twice should show that GWA is not recomputed.
+
+    /tmp/9e411810ad341de6456ce0c6efd4f973356d0bad.log.txt CACHE HIT!
+
 ### LOCO
 
 Recent versions of GEMMA have LOCO support for a single chromosome
@@ -163,6 +180,33 @@ GWA.json contains the file names of every chromosome
 The -k switch is injected automatically. Again output switches are not
 allowed (-o, -outdir)
 
+### Permutations
+
+Permutations can be run with and without LOCO. First create K
+
+    gemma-wrapper --json -- \
+        -g test/data/input/BXD_geno.txt.gz \
+        -p test/data/input/BXD_pheno.txt \
+        -gk \
+        -debug > K.json
+
+Next, using K.json, permute the phenotypes with something like
+
+    gemma-wrapper --json --loco --input K.json \
+        --permutate 100 --permute-phenotype test/data/input/BXD_pheno.txt -- \
+        -g test/data/input/BXD_geno.txt.gz \
+        -p test/data/input/BXD_pheno.txt \
+        -c test/data/input/BXD_covariates2.txt \
+        -a test/data/input/BXD_snps.txt \
+        -lmm 2 -maf 0.1 \
+        -debug > GWA.json
+
+This should get the 95% significant and 67% suggestive thresholds:
+
+    ["95 percentile (significant) ", 2.015475e-05, 4.7]
+    ["67 percentile (suggestive)  ", 2.015475e-05, 4.7]
+
+
 ## Copyright
 
-Copyright (c) 2017 Pjotr Prins. See [LICENSE.txt](LICENSE.txt) for further details.
+Copyright (c) 2017,2018 Pjotr Prins. See [LICENSE.txt](LICENSE.txt) for further details.

data/VERSION

@@ -1 +1 @@
-0.98
+0.98.1

data/bin/gemma-wrapper

@@ -40,7 +40,7 @@ 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
+# These are used for testing compatibility with the gemma tool
 GEMMA_V_MAJOR = 98
 GEMMA_V_MINOR = 0
 
@@ -213,15 +213,15 @@ 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]]
+    # Remove the phenotype file from the hash
     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]
+if DO_COMPUTE_GWA and options[:permute_phenotypes]
+  raise "Did not expect GEMMA -p phenotype whith permutations (only use --permutate-phenotypes)" if pheno_idx
+  hashme += ['-p', options[:permute_phenotypes]]
 end
 
 require 'digest/sha1'
@@ -254,7 +254,7 @@ invoke_gemma = lambda do |extra_args, cache_hit = false|
   cmd="#{GEMMA_COMMAND} #{GEMMA_ARGS.join(' ')} #{extra_args.join(' ')}"
   record[:gemma_command] = cmd
   return if cache_hit
-  # debug.call cmd
+  debug.call cmd
   errno =
     if options[:json]
       # capture output
@@ -350,7 +350,7 @@ else
   json_in = JSON.parse(File.read(options[:input]))
   raise "JSON problem, file #{options[:input]} is not -gk derived" if json_in["type"] != "K"
 
-  pfn = options[:phenotypes] # can be nil
+  pfn = options[:permute_phenotypes] # can be nil
   k_files = json_in["files"].map { |rec| [rec[0],rec[2]] }
   k_files.each do | chr, kfn | # call a GWA for each chromosome
     gwas.call(chr,kfn,pfn)
@@ -358,7 +358,7 @@ else
   # Permute
   if options[:permutate]
     ps = []
-    raise "You should supply --phenotype with gemma-wrapper --permutate" if not pfn
+    raise "You should supply --permute-phenotypes with gemma-wrapper --permutate" if not pfn
     File.foreach(pfn).with_index do |line, line_num|
       ps << line
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-gemma-wrapper
 version: !ruby/object:Gem::Version
-  version: '0.98'
+  version: 0.98.1
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-11-19 00:00:00.000000000 Z
+date: 2018-11-20 00:00:00.000000000 Z
 dependencies: []
 description: GEMMA wrapper adds LOCO and permutation support. Also caches K between
   runs with LOCO support