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Merge pull request #123 from torres-alexis/DEV_GeneLab_Reference_Anno…
…tations_vGL-DPPD-7110-A [GL_RefAnnotTable] Add Docker/Singularity
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -136,9 +136,9 @@ The default columns in the annotation table are: | |
| | Program | Version | Relevant Links | | ||
| |:----------------|:-------:|:---------------| | ||
| | R | 4.4.0 | [https://www.r-project.org/](https://www.r-project.org/) | | ||
| | Bioconductor | 3.19.1 | [https://bioconductor.org](https://bioconductor.org) | | ||
| | Bioconductor | 3.19 | [https://bioconductor.org](https://bioconductor.org) | | ||
| | tidyverse | 2.0.0 | [https://www.tidyverse.org](https://www.tidyverse.org) | | ||
| | STRINGdb | 2.16.0 | [https://www.bioconductor.org/packages/release/bioc/html/STRINGdb.html](https://www.bioconductor.org/packages/release/bioc/html/STRINGdb.html) | | ||
| | STRINGdb | 2.16.4 | [https://www.bioconductor.org/packages/release/bioc/html/STRINGdb.html](https://www.bioconductor.org/packages/release/bioc/html/STRINGdb.html) | | ||
| | PANTHER.db | 1.0.12 | [https://bioconductor.org/packages/release/data/annotation/html/PANTHER.db.html](https://www.bioconductor.org/packages/release/data/annotation/html/PANTHER.db.html) | | ||
| | rtracklayer | 1.64.0 | [https://bioconductor.org/packages/release/bioc/html/rtracklayer.html](https://www.bioconductor.org/packages/release/bioc/html/rtracklayer.html) | | ||
| | org.At.tair.db | 3.19.1 | [https://bioconductor.org/packages/release/data/annotation/html/org.At.tair.db.html](https://www.bioconductor.org/packages/release/data/annotation/html/org.At.tair.db.html) | | ||
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@@ -182,6 +182,10 @@ Current GeneLab annotation tables are available on [figshare](https://figshare.c | |
| ## 0. Set Up Environment | ||
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| ```R | ||
| # Set R library path to current working directory | ||
| lib_path <- file.path(getwd()) | ||
| .libPaths(lib_path) | ||
|
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| # Define variables associated with current pipeline and annotation table versions | ||
| GL_DPPD_ID <- "GL-DPPD-7110-A" | ||
| ref_tab_path <- "https://raw.githubusercontent.com/nasa/GeneLab_Data_Processing/master/GeneLab_Reference_Annotations/Pipeline_GL-DPPD-7110_Versions/GL-DPPD-7110-A/GL-DPPD-7110-A_annotations.csv" | ||
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@@ -253,7 +257,7 @@ base_output_name <- str_replace(base_gtf_filename, ".gtf.gz", "") | |
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| # Add the species name to base_output_name if the reference source is not ENSEMBL | ||
| if (!(ref_source %in% c("ensembl_plants", "ensembl_bacteria", "ensembl"))) { | ||
| base_output_name <- paste(str_replace(target_species_designation, " ", "_"), base_output_name, sep = "_") | ||
| base_output_name <- paste(str_replace(target_organism, " ", "_"), base_output_name, sep = "_") | ||
| } | ||
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| out_table_filename <- paste0(base_output_name, "-GL-annotations.tsv") | ||
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@@ -294,42 +298,52 @@ if ( file.exists(out_table_filename) ) { | |
| # Use AnnotationForge's makeOrgPackageFromNCBI function with default settings to create the organism-specific org.db R package from available NCBI annotations | ||
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| # Try to download the org.db from Bioconductor, build it locally if installation fails | ||
| BiocManager::install(target_org_db, ask = FALSE) | ||
| if (!requireNamespace(target_org_db, quietly = TRUE)) { | ||
| BiocManager::install(target_org_db, ask = FALSE) | ||
| if (!requireNamespace(target_org_db, quietly = TRUE)) { | ||
| tryCatch({ | ||
| # Parse organism's name in the reference table to create the org.db name (target_org_db) | ||
| genus_species <- strsplit(target_organism, " ")[[1]] | ||
| if (length(genus_species) < 1) { | ||
| stop("Species designation is not correctly formatted: ", target_organism) | ||
| stop("Species designation is not correctly formatted: ", target_organism) | ||
| } | ||
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| genus <- genus_species[1] | ||
| species <- ifelse(length(genus_species) > 1, genus_species[2], "") | ||
| strain <- ref_table %>% | ||
| filter(species == target_organism) %>% | ||
| pull(strain) %>% | ||
| gsub("[^A-Za-z0-9]", "", .) | ||
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| if (!is.na(strain) && strain != "") { | ||
| species <- paste0(species, strain) | ||
| species <- paste0(species, strain) | ||
| } | ||
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| # Get package name or build it if not provided | ||
| target_org_db <- ref_table %>% | ||
| filter(species == target_organism) %>% | ||
| pull(annotations) | ||
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| if (is.na(target_org_db) || target_org_db == "") { | ||
| cat("\nNo annotation database specified. Constructing package name...\n") | ||
| target_org_db <- paste0("org.", substr(genus, 1, 1), species, ".eg.db") | ||
| } | ||
| target_org_db <- paste0("org.", substr(genus, 1, 1), species, ".eg.db") | ||
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| BiocManager::install(c("AnnotationForge", "biomaRt", "GO.db"), ask = FALSE) | ||
| BiocManager::install(c("AnnotationForge", "biomaRt", "GO.db"), ask = FALSE) | ||
| library(AnnotationForge) | ||
| makeOrgPackageFromNCBI( | ||
| version = "0.1", | ||
| author = "Your Name <[email protected]>", | ||
| maintainer = "Your Name <[email protected]>", | ||
| outputDir = "./", | ||
| tax_id = target_taxid, | ||
| genus = genus, | ||
| species = species | ||
| makeOrgPackageFromNCBI( | ||
| version = "0.1", | ||
| author = "Your Name <[email protected]>", | ||
| maintainer = "Your Name <[email protected]>", | ||
| outputDir = "./", | ||
| tax_id = target_taxid, | ||
| genus = genus, | ||
| species = species | ||
| ) | ||
| install.packages(file.path("./", target_org_db), repos = NULL, type = "source", quiet = TRUE) | ||
| cat(paste0("'", target_org_db, "' has been successfully built and installed.\n")) | ||
| }, error = function(e) { | ||
| stop("Failed to build and load the package: ", target_org_db, "\nError: ", e$message) | ||
| stop("Failed to build and load the package: ", target_org_db, "\nError: ", e$message) | ||
| }) | ||
| target_org_db <- install_annotations(target_organism, ref_tab_path) | ||
| } | ||
| ``` | ||
|
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||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -13,35 +13,36 @@ install_annotations <- function(target_organism, refTablePath) { | |
| filter(species == target_organism) %>% | ||
| pull(taxon) | ||
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| # Parse organism's name in the reference table to create the org.db name (target_org_db) | ||
| target_species_designation <- ref_table %>% | ||
| filter(species == target_organism) %>% | ||
| pull(species) %>% | ||
| gsub("\\s+", " ", .) %>% | ||
| gsub("[^A-Za-z0-9 ]", "", .) | ||
|
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| genus_species <- strsplit(target_species_designation, " ")[[1]] | ||
| if (length(genus_species) < 1) { | ||
| stop("Species designation is not correctly formatted: ", target_species_designation) | ||
| } | ||
|
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| genus <- genus_species[1] | ||
| species <- ifelse(length(genus_species) > 1, genus_species[2], "") | ||
| strain <- ref_table %>% | ||
| filter(species == target_organism) %>% | ||
| pull(strain) %>% | ||
| gsub("[^A-Za-z0-9]", "", .) | ||
|
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| if (!is.na(strain) && strain != "") { | ||
| species <- paste0(species, strain) | ||
| } | ||
|
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| # Get package name or build it if not provided | ||
| target_org_db <- ref_table %>% | ||
| filter(species == target_organism) %>% | ||
| pull(annotations) | ||
|
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| if (is.na(target_org_db) || target_org_db == "") { | ||
| cat("\nNo annotation database specified. Constructing package name...\n") | ||
| target_species_designation <- ref_table %>% | ||
| filter(species == target_organism) %>% | ||
| pull(species) %>% | ||
| gsub("\\s+", " ", .) %>% | ||
| gsub("[^A-Za-z0-9 ]", "", .) | ||
|
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| genus_species <- strsplit(target_species_designation, " ")[[1]] | ||
| if (length(genus_species) < 1) { | ||
| stop("Species designation is not correctly formatted: ", target_species_designation) | ||
| } | ||
|
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| genus <- genus_species[1] | ||
| species <- ifelse(length(genus_species) > 1, genus_species[2], "") | ||
| strain <- ref_table %>% | ||
| filter(species == target_organism) %>% | ||
| pull(strain) %>% | ||
| gsub("[^A-Za-z0-9]", "", .) | ||
|
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||
| if (!is.na(strain) && strain != "") { | ||
| species <- paste0(species, strain) | ||
| } | ||
|
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| target_org_db <- paste0("org.", substr(genus, 1, 1), species, ".eg.db") | ||
| } | ||
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@@ -56,25 +57,25 @@ install_annotations <- function(target_organism, refTablePath) { | |
| } else { | ||
| cat(paste0("\nInstallation from Bioconductor failed, attempting to build '", target_org_db, "'...\n")) | ||
| if (!dir.exists(target_org_db)) { | ||
| tryCatch({ | ||
| BiocManager::install(c("AnnotationForge", "biomaRt", "GO.db"), ask = FALSE) | ||
| library(AnnotationForge) | ||
| makeOrgPackageFromNCBI( | ||
| version = "0.1", | ||
| author = "Your Name <[email protected]>", | ||
| maintainer = "Your Name <[email protected]>", | ||
| outputDir = "./", | ||
| tax_id = target_taxid, | ||
| genus = genus, | ||
| species = species | ||
| ) | ||
| install.packages(file.path("./", target_org_db), repos = NULL, type = "source", quiet = TRUE) | ||
| cat(paste0("'", target_org_db, "' has been successfully built and installed.\n")) | ||
| }, error = function(e) { | ||
| stop("Failed to build and load the package: ", target_org_db, "\nError: ", e$message) | ||
| }) | ||
| tryCatch({ | ||
| BiocManager::install(c("AnnotationForge", "biomaRt", "GO.db"), ask = FALSE) | ||
| library(AnnotationForge) | ||
| makeOrgPackageFromNCBI( | ||
| version = "0.1", | ||
| author = "Your Name <[email protected]>", | ||
| maintainer = "Your Name <[email protected]>", | ||
| outputDir = "./", | ||
| tax_id = target_taxid, | ||
| genus = genus, | ||
| species = species | ||
| ) | ||
| install.packages(file.path("./", target_org_db), repos = NULL, type = "source", quiet = TRUE) | ||
| cat(paste0("'", target_org_db, "' has been successfully built and installed.\n")) | ||
| }, error = function(e) { | ||
| stop("Failed to build and load the package: ", target_org_db, "\nError: ", e$message) | ||
| }) | ||
| } else { | ||
| cat(paste0("Local annotation package ", target_org_db, " already exists. This local package will be installed.")) | ||
| cat(paste0("Local annotation package ", target_org_db, " already exists. This local package will be installed.\n")) | ||
| install.packages(file.path("./", target_org_db), repos = NULL, type = "source", quiet = TRUE) | ||
| } | ||
| } | ||
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@@ -83,4 +84,4 @@ install_annotations <- function(target_organism, refTablePath) { | |
| library(target_org_db, character.only = TRUE) | ||
| cat(paste0("Using Annotation Database '", target_org_db, "'.\n")) | ||
| return(target_org_db) | ||
| } | ||
| } | ||