Initial implementation of ALStructure wrapper

Author: StuntsPT

structure_threader/wrappers/alstructure_wrapper.R

@@ -0,0 +1,57 @@
+#!/usr/bin/Rscript
+# Copyright 2019 Francisco Pina Martins <[email protected]>
+# This file is part of structure_threader.
+# structure_threader is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+
+# structure_threader is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with structure_threader. If not, see <http://www.gnu.org/licenses/>.
+
+ll = Sys.getenv()[ grep("R_LIBS_USER", names(Sys.getenv())) ]
+local_lib = gsub("^.*\t", "", ll)
+
+if(!require("alstructure")){
+  if(!require("devtools")){
+    install.packages("devtools", lib=.libPaths()[1])
+  }
+  library("devtools")
+  install_github("storeylab/alstructure", build_vignettes=FALSE, ref="e355411", lib=.libPaths()[1])
+  library(alstructure)
+}
+
+if(!require(lfa)){
+  if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager", lib=.libPaths()[1])
+  
+  BiocManager::install("lfa", lib=.libPaths()[1])
+  library(lfa)
+}
+
+alstructure_wrapper = function(input_prefix, K) {
+  #' ALStructure wrapper
+  #'
+  #' Small wrapper function that wraps ALStructure
+  #' Takes an input prefix (file minus the extension) and value of K
+  #' as arguments and returns a q-matrix
+
+  K = as.numeric(K)
+  input_data = lfa::read.bed(input_prefix)
+  fit <- alstructure(X = input_data, d_hat=K)
+  q_matrix = t(fit$Q_hat)
+
+  return(q_matrix)
+}
+
+args = commandArgs(trailingOnly=TRUE)
+
+if (sys.nframe() == 0){
+  Q_matrix = alstructure_wrapper(args[1], args[2])
+  write.csv(Q_matrix, args[3])
+}