From 476e9d7fd2bc6205d660774c117142247c2700f1 Mon Sep 17 00:00:00 2001
From: akrinos <akrinos@vt.edu>
Date: Mon, 24 Oct 2022 22:52:59 -0400
Subject: [PATCH 1/2] Adding simple script for data output processing

---
 scripts/process-output.R | 54 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 54 insertions(+)
 create mode 100644 scripts/process-output.R

diff --git a/scripts/process-output.R b/scripts/process-output.R
new file mode 100644
index 0000000..a1f11fb
--- /dev/null
+++ b/scripts/process-output.R
@@ -0,0 +1,54 @@
+pacman::p_load(ggplot2,dplyr,data.table)
+
+## FUNCTIONS ##
+
+process_sub_eukulele <- function(eukulele_dir, label_out, all_results, salmon_dir,
+                               salmon_format="num", is_protein=FALSE) {
+    curr_dir = file.path(eukulele_dir,"taxonomy_estimation")
+    for (curr_file in list.files(curr_dir)) {
+        eukulele_estimates = data.frame(fread(file.path(curr_dir, curr_file), sep = "\t")) %>%
+                dplyr::mutate(full_classification=case_when(!is.na(full_classification)~full_classification,
+                                                            TRUE~"Unclassified")) %>%
+                tidyr::separate(full_classification, sep = ";",
+                                                     into = c("Domain","Supergroup","Phylum","Class","Order",
+                                                              "Family","Genus","Species"))%>% 
+                dplyr::mutate(Domain = unlist(lapply(as.character(EUKulele_out$Domain),trimws)))%>% 
+                dplyr::mutate(Supergroup = unlist(lapply(as.character(EUKulele_out$Supergroup),trimws)))%>% 
+                dplyr::mutate(Phylum = unlist(lapply(as.character(EUKulele_out$Phylum),trimws)))%>% 
+                dplyr::mutate(Class = unlist(lapply(as.character(EUKulele_out$Class),trimws)))%>% 
+                dplyr::mutate(Order = unlist(lapply(as.character(EUKulele_out$Order),trimws)))%>% 
+                dplyr::mutate(Family = unlist(lapply(as.character(EUKulele_out$Family),trimws)))%>% 
+                dplyr::mutate(Genus = unlist(lapply(as.character(EUKulele_out$Genus),trimws)))%>% 
+                dplyr::mutate(Species = unlist(lapply(as.character(EUKulele_out$Species),trimws)))
+        
+        if (is_protein) {
+            eukulele_estimates = eukulele_estimates %>% tidyr::separate(transcript_name,sep="\\.p",
+                                                                        into=c("transcript_name",
+                                                                               "protein_id"))
+        }
+        number_file = unlist(strsplit(curr_file,"_"))[1]
+        salmon_file = read.csv(file.path(salmon_dir,paste0(salmon_format,as.character(number_file), "_quant"),
+                                 "quant.sf"), sep = "\t")
+        matched_file= salmon_file %>% dplyr::full_join(eukulele_estimates,by=c("Name"="transcript_name"))
+        matched_file["Sample"] = curr_file
+        matched_file["SplitSamp"] = number_file
+        matched_file["Type"] = label_out
+
+        matched_file =  matched_file %>%
+            tidyr::replace_na(list("Domain"="Uncertain",
+                                   "Supergroup"="Uncertain",
+                                   "Phylum"="Uncertain",
+                                   "Class"="Uncertain",
+                                   "Order"="Uncertain",
+                                   "Family"="Uncertain",
+                                   "Genus"="Uncertain",
+                                   "Species"="Uncertain"))
+        all_results = all_results %>% dplyr::bind_rows(matched_file)
+    }
+    return(all_results)
+}
+
+all_results=data.frame()
+all_results = process_sub_eukulele("CAG_eukulele_pleuro_metazoans", "Metazoan_DB", all_results, 
+                     "/vortexfs1/omics/alexander/akrinos/2021-remodeling-eukrhythmic/2021-09-ALOHA/intermediate-files/04-compare/09-CAG-mapping/salmon",
+                     salmon_format="num", is_protein=TRUE)

From 2a522873d56a221fe685c9e06c4c3518ca4de017 Mon Sep 17 00:00:00 2001
From: Harriet Alexander <harriet.xander@gmail.com>
Date: Mon, 5 Dec 2022 10:57:07 -0500
Subject: [PATCH 2/2] Update databaseandconfig.rst

---
 docs/source/databaseandconfig.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/source/databaseandconfig.rst b/docs/source/databaseandconfig.rst
index b654821..6bceaae 100644
--- a/docs/source/databaseandconfig.rst
+++ b/docs/source/databaseandconfig.rst
@@ -11,7 +11,7 @@ Four databases can be downloaded and formatted automatically when invoking ``EUK
 - `PhyloDB <https://drive.google.com/drive/u/0/folders/0B-BsLZUMHrDQfldGeDRIUHNZMEREY0g3ekpEZFhrTDlQSjQtbm5heC1QX2V6TUxBeFlOejQ>`_
 - `EukProt <https://figshare.com/articles/EukProt_a_database_of_genome-scale_predicted_proteins_across_the_diversity_of_eukaryotic_life/12417881/2>`_
 - `MMETSP <https://zenodo.org/record/1212585#.Xw3PoJNKhTZ>`_ 
-- `MMETSP <https://zenodo.org/record/1212585#.Xw3PoJNKhTZ>`_ and `MMETSP <https://mmp.sfb.uit.no/databases/marref/#/>`_ *Default*
+- `MMETSP <https://zenodo.org/record/1212585#.Xw3PoJNKhTZ>`_ and `MarRef <https://mmp.sfb.uit.no/databases/marref/#/>`_ *Default*
 - `EukZoo <https://github.com/zxl124/EukZoo-database>`_
 
 Note that the MMETSP database is generated using cleaned MMETSP assemblies originally derived from, but not identical to, the assemblies stored in full at the link above. In order to download the cleaned assemblies used to create the ``EUKulele`` MMETSP database, please follow the instructions recorded in `this Github repository <https://github.com/shu251/download-cleaned-mmetsp>`_.