save SNP pos/chr/id/ref/alt in output file and also remove tmp file d…

…uring init
OpenMendel · Feb 17, 2022 · 372c797 · 372c797 · biona001 · Feb 17, 2022
1 parent b93b778
commit 372c797
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Showing 2 changed files with 8 additions and 7 deletions.
diff --git a/src/MendelIHT.jl b/src/MendelIHT.jl
@@ -54,8 +54,9 @@ module MendelIHT
     # force Julia to precompile some common functions (only Gaussian case are handled here)
     function __init__()
         dir = normpath(MendelIHT.datadir())
-        cross_validate(joinpath(dir, "normal"), Normal, verbose=false)
-        cross_validate(joinpath(dir, "multivariate"), MvNormal, phenotypes=[6, 7], verbose=false)
+        cross_validate(joinpath(dir, "normal"), Normal, verbose=false, cv_summaryfile="_tmp_init_cv_file_.txt")
+        cross_validate(joinpath(dir, "multivariate"), MvNormal, phenotypes=[6, 7], verbose=false, cv_summaryfile="_tmp_init_cv_file_.txt")
+        rm("_tmp_init_cv_file_.txt", force=true)
     end
 
 end # end module
diff --git a/src/wrapper.jl b/src/wrapper.jl
@@ -85,21 +85,21 @@ function iht(
 
     show(io, result)
 
+    # save estimated beta to disk
     if is_multivariate(y)
         open(betafile, "w") do io
-            print(io, "SNPid")
+            print(io, "chr\tpos\tSNPid\tref\talt")
             for i in 1:size(y, 1)
                 print(io, '\t', "beta_$i")
             end
             print(io, '\n')
-            writedlm(io, [X_ids result.beta'])
+            writedlm(io, [X_chr X_pos X_ids X_ref X_alt result.beta'])
         end
-        # writedlm(betafile, DataFrame([X_ids result.beta'], ["SNPid", "Estimated_beta"]))
         writedlm(covariancefile, result.Σ)
     else
         open(betafile, "w") do io
-            println(io, "SNPid", '\t', "Estimated_beta")
-            writedlm(io, [X_ids result.beta])
+            println(io, "chr\tpos\tSNPid\tref\talt\tEstimated_beta")
+            writedlm(io, [X_chr X_pos X_ids X_ref X_alt result.beta])
         end
     end