From 54566bf05ffa9fad3418f35835d1801af0d8f239 Mon Sep 17 00:00:00 2001
From: Tim <tbarry2@andrew.cmu.edu>
Date: Mon, 30 Aug 2021 21:34:46 -0400
Subject: [PATCH] prepare large-scale computations

---
 .DS_Store                                     | Bin 10244 -> 10244 bytes
 sceptre_paper/.DS_Store                       | Bin 14340 -> 14340 bytes
 sceptre_paper/analysis_drivers/.DS_Store      | Bin 6148 -> 6148 bytes
 .../run_monocle_nb_at_scale.R                 |   6 ++++--
 .../sceptre_function_args.R                   |   4 ++--
 sceptre_paper/utilities/run_xie_analysis.bash |  12 ++++++------
 6 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index e34fb84a7a1ac9f7d65881aa604228116a88c68a..61aaf1755c3ca270c9f87024fe3ea142ba11cc6c 100644
GIT binary patch
delta 53
zcmZn(XbISGQ;6}*<T}9y9_i|8T_Y0{9R))}^T~<A@{DsPHv-AIn->Zv@@!^T_{FmM
Ij|ej}0PGkMm;e9(

delta 56
zcmV-80LTA?P=rvh*%ATAlYS9^2o`&LFf1TBGm{At9s!q=C=wq5n3J#)9<#&~Lky9C
O1+xbr`UJBE6$1ktA`zhg

diff --git a/sceptre_paper/.DS_Store b/sceptre_paper/.DS_Store
index fdaaac167d31504ff70ec31b1b0781d027de17af..3975cfa32f554b403e5147fc5a2168b38daac49b 100644
GIT binary patch
delta 62
zcmV-E0Kxx+aD;HMdmsVKlOPg+4I6uVEiyDTEFdv4H#3uw86E+gldu^d0iBa@AtbYB
UA)5}f2Qc;olYkQ^vmYhk0*Pr9iU0rr

delta 37
tcmZoEXeroGtuUEG>GWiN1;x!dinIA9Hn47HH~7XfdA_>iW@pu7OaK!f4gUZD

diff --git a/sceptre_paper/analysis_drivers/.DS_Store b/sceptre_paper/analysis_drivers/.DS_Store
index 90ead10a1a171b25af0510f663428a8f40d7a2d9..f54540582e3ef221bb769a7eb806f7f8a4b8fb88 100644
GIT binary patch
delta 52
zcmZoMXffE(&%$_S@&uL!9_i|8T_Y0{9R))}^U3Gg<QeBoeh(z)PVQsX+uX`p%e0xD
H<1aq|%S#b3

delta 34
qcmZoMXffE(&obGE?KGq4<cqAzlWSSnH+QktGEHn?-OSGMmmdJsE(^W@

diff --git a/sceptre_paper/analysis_drivers/analysis_drivers_xie/run_monocle_nb_at_scale.R b/sceptre_paper/analysis_drivers/analysis_drivers_xie/run_monocle_nb_at_scale.R
index 2e8bb08..5304f86 100644
--- a/sceptre_paper/analysis_drivers/analysis_drivers_xie/run_monocle_nb_at_scale.R
+++ b/sceptre_paper/analysis_drivers/analysis_drivers_xie/run_monocle_nb_at_scale.R
@@ -4,7 +4,9 @@ offsite_dir <- .get_config_path("LOCAL_SCEPTRE_DATA_DIR")
 library(monocle)
 source(paste0(code_dir, "/sceptre_paper/analysis_drivers/analysis_drivers_xie/paths_to_dirs.R"))
 source(paste0(code_dir, "/sceptre_paper/analysis_drivers/analysis_drivers_xie/gasp_custom_functs.R"))
-cds <- readRDS(paste0(processed_dir, "/monocole_obj.rds"))
+analysis_ready_dir <- paste0(offsite_dir, "data/xie/analysis_ready")
+
+cds <- readRDS(paste0(analysis_ready_dir, "/monocole_obj.rds"))
 pairs <- fst::read_fst(paste0(processed_dir, "/gRNA_gene_pairs.fst"))
 pairs <- pairs[1:100,]
 
@@ -32,4 +34,4 @@ res <- purrr::map_dfr(.x = seq(1, nrow(pairs)), .f = function(i) {
   return(out)
 })
 
-saveRDS(res, paste0(results_dir_negative_binomial, "/monocle_nb_results.rds"))
\ No newline at end of file
+saveRDS(res, paste0(results_dir_negative_binomial, "/monocle_nb_results.rds"))
diff --git a/sceptre_paper/analysis_drivers/analysis_drivers_xie/sceptre_function_args.R b/sceptre_paper/analysis_drivers/analysis_drivers_xie/sceptre_function_args.R
index be24898..a5ada71 100644
--- a/sceptre_paper/analysis_drivers/analysis_drivers_xie/sceptre_function_args.R
+++ b/sceptre_paper/analysis_drivers/analysis_drivers_xie/sceptre_function_args.R
@@ -1,11 +1,11 @@
 # offsite_dir <- .get_config_path("LOCAL_SCEPTRE_DATA_DIR")
-small_example <- FALSE
+small_example <- TRUE
 library(sceptre)
 
 processed_dir <- paste0(offsite_dir, "/data/xie/processed")
 analysis_ready_dir <- paste0(offsite_dir, "/data/xie/analysis_ready")
 results_dir_negbin <- paste0(offsite_dir, "/results/xie/negative_binomial")
-bulk_regions <- readRDS(paste0(processed_dir, "/bulk_region_names.rds"))
+bulk_regions <- readRDS(paste0(plrocessed_dir, "/bulk_region_names.rds"))
 gRNA_gene_pairs <- fst::read.fst(paste0(processed_dir, "/gRNA_gene_pairs.fst"))
 covariate_matrix <- fst::read.fst(paste0(analysis_ready_dir, "/covariate_model_matrix.fst"))
 cell_gene_expression_matrix_info <- readRDS(paste0(analysis_ready_dir, "/exp_mat_sub_metadata.rds")) 
diff --git a/sceptre_paper/utilities/run_xie_analysis.bash b/sceptre_paper/utilities/run_xie_analysis.bash
index 9743b3a..7a73192 100644
--- a/sceptre_paper/utilities/run_xie_analysis.bash
+++ b/sceptre_paper/utilities/run_xie_analysis.bash
@@ -7,6 +7,7 @@ source ~/.research_config
 # Set the number of processors.
 n_processors=50
 machine=$MACHINE_NAME
+precomputation_complete=FALSE
 
 echo Running on machine $machine with $n_processors processors.
 
@@ -22,23 +23,22 @@ bash build_and_install_package.bash sceptre $machine
 bash build_and_install_package.bash katsevich2020 $machine
 
 echo Initialize the offsite directory structure.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"check_directory_structure_1.R
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"check_directory_structure_1.R
 
 echo Download the data.
 # Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"download_data_2.R
 
 echo Pre-process the data.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"pre_process_data_3.R
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"pre_process_data_3.R
 
 echo Construct model covariate matrix and perform quality control.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"quality_control_4.R
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"quality_control_4.R
 
 echo Determine the gene-gRNA pairs to analyze.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"select_gRNA_gene_pair_5.R
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"select_gRNA_gene_pair_5.R
 
 echo Create monocole object for monocole NB analysis.
-Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"create_monocle_object_5.1.R
-
+# Rscript $code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"create_monocle_object_5.1.R
 
 # Locate the parameter file
 parameter_file=$code_dir"/sceptre_paper/analysis_drivers/analysis_drivers_xie/"sceptre_function_args.R