NewYear_bugfix

.github/workflows/r.yml

@@ -22,7 +22,7 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          #- {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
 
@@ -49,3 +49,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          error-on: '"error"'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: LDWeaver
 Type: Package
 Title:Genomewide Epistasis Analysis on Bacteria
-Version: 1.3.1
+Version: 1.3.2
 Authors@R: person("Sudaraka", "Mallawaarachchi", email = "[email protected]", role = c("aut", "cre"))
 Maintainer: Sudaraka Mallawaarachchi <[email protected]>
 Description:Perform genomewide epistasis analysis by evaluating the LD structure in bacteria.

R/BacGWES.R

@@ -30,6 +30,7 @@
 #' modelling since all links are used. However, setting a threshold > 2 will generally reduce the memory usage, plotting time (default = 3, i.e. corresponding to p = 0.001),
 #' and run time for ARACNE. If all links are required to be returned, set to 0 (i.e. corresponding to p = 1), range 0 - 5
 #' @param tanglegram_break_segments specify the number of genome segments to prepare - one tanglegram per segment (default = 5), range 1 - 10. Set NULL to skip tanglegram
+#' @param write_gwesExplorer specify whether output for GWESExplorer is required (default = T)
 #' @param multicore specify whether to use parallel processing (default = T)
 #' @param ncores specify the number of cores to use for parallel processing (default = NULL), will auto detect if NULL
 #' @param max_blk_sz specify maximum block size for MI computation (default = 10000), larger sizes require more RAM, range 1000 - 100000
@@ -48,7 +49,8 @@ LDWeaver = function(dset, aln_path, aln_has_all_bases = T, pos = NULL, gbk_path
                     gap_freq = 0.15, maf_freq = 0.01, hdw_threshold = 0.1, perform_SR_analysis_only = F,
                     SnpEff_Annotate = T, sr_dist = 20000, lr_retain_links = 1e6,
                     max_tophits = 250, num_clusts_CDS = 3, srp_cutoff = 3, tanglegram_break_segments = 5,
-                    multicore = T, max_blk_sz = 10000, ncores = NULL, save_additional_outputs = F){
+                    write_gwesExplorer = T, multicore = T, max_blk_sz = 10000, ncores = NULL,
+                    save_additional_outputs = F){
   # Build blocks
   # BLK1: Extract SNPs and create sparse Mx from MSA (fasta)
   # BLK2: Parse GBK or GFF+REF
@@ -65,6 +67,8 @@ LDWeaver = function(dset, aln_path, aln_has_all_bases = T, pos = NULL, gbk_path
   #TODO: Provide the option to skip SNP extraction and use the whole provided alignment (redundant if pre-filtered)
   #TODO: Add the option to provide genbank file without reference sequence
   #TODO: Count through blocks and automate the displayed BLOCK NUMBER
+  #TODO: genbankr is being droped from the newest bioconductor, add alternative (https://github.com/gmbecker/genbankr)
+  #TODO: Add Hamming Distance plot, can we have a SNP Tree + Hamming Distance weights to show population structure control?
 
   #NOTE: SnpEff does not parse the GBK and GFF3 file from the same refseq reference genome the same way. There might be differences between annotations/tophits/etc.
   # # Welcome message # #
@@ -164,6 +168,12 @@ LDWeaver = function(dset, aln_path, aln_has_all_bases = T, pos = NULL, gbk_path
 
   # setup paths
   if(!file.exists(dset)) dir.create(dset) # save everything in here
+
+  # Save console output as a text file
+  info_file = file.path(dset, paste("LDW_run_",format(Sys.time(), "%Y%m%d%H%M%S"), ".txt", sep = ""))
+  suppressWarnings(sink(file= NULL))
+  sink(info_file, split = T)
+
   add_path = file.path(dset, "Additional_Outputs") # Additional Outputs
   if(save_additional_outputs) {
     if(!file.exists(add_path)) dir.create(file.path(dset, "Additional_Outputs"))
@@ -205,7 +215,8 @@ LDWeaver = function(dset, aln_path, aln_has_all_bases = T, pos = NULL, gbk_path
     cat(paste("All outputs will be saved to:", normalizePath(dset), "\n"))
     cat(paste("\n *** Input paths *** \n\n"))
     cat(paste("* Alignment:", aln_path, "\n"))
-    cat(paste("* GenBank Annotation:", gbk_path, "\n"))
+    if(!is.null(gbk_path)) cat(paste("* GenBank Annotation:", gbk_path, "\n"))
+    if(!is.null(gff3_path)) cat(paste("* GFF3 Annotation:", gff3_path, "\n"))
     if(!is.null(snpeff_jar_path)) cat(paste("* SnpEff Annotations will be performed on short-range links. SnpEff path:", snpeff_jar_path, "\n"))
 
     cat(paste("\n *** Parameters *** \n\n"))
@@ -358,6 +369,7 @@ LDWeaver = function(dset, aln_path, aln_has_all_bases = T, pos = NULL, gbk_path
 
 
   if(nrow(sr_links) == 0){
+    suppressWarnings(sink(file= NULL)) ### output info to text file
     stop("No potentially important sr_links were identified! Cannot continue analysis...")
   }
 
@@ -385,26 +397,30 @@ LDWeaver = function(dset, aln_path, aln_has_all_bases = T, pos = NULL, gbk_path
     tophits = LDWeaver::read_TopHits(top_hits_path = tophits_path)
   }
 
-  # Additional paths if annotations are requested
-  # tanglegram
-  tanglegram_path = file.path(dset, "SR_Tanglegram")
-  if(!file.exists(tanglegram_path)) dir.create(tanglegram_path)
-  # GWESExplorer
-  gwesexplorer_path = file.path(dset, "SR_GWESExplorer")
-  if(!file.exists(gwesexplorer_path)) dir.create(gwesexplorer_path)
-  # NetworkPlot
-  netplot_path = file.path(dset, "SR_network_plot.png")
 
   # BLK8
   if(!is.null(tanglegram_break_segments)){
+    # tanglegram
+    tanglegram_path = file.path(dset, "SR_Tanglegram")
+    if(!file.exists(tanglegram_path)) dir.create(tanglegram_path)
     cat("\n\n #################### BLOCK 9 #################### \n\n")
     LDWeaver::create_tanglegram(tophits = tophits, gbk = gbk, gff = gff, tanglegram_folder = tanglegram_path, break_segments = tanglegram_break_segments)
   }
   # BLK9
-  cat("\n\n #################### BLOCK 10 #################### \n\n")
-  LDWeaver::write_output_for_gwes_explorer(snp.dat = snp.dat, tophits = tophits, gwes_explorer_folder = gwesexplorer_path)
+  if(write_gwesExplorer){
+    # GWESExplorer
+    gwesexplorer_path = file.path(dset, "SR_GWESExplorer")
+    if(!file.exists(gwesexplorer_path)) dir.create(gwesexplorer_path)
+    cat("\n\n #################### BLOCK 10 #################### \n\n")
+    LDWeaver::write_output_for_gwes_explorer(snp.dat = snp.dat, tophits = tophits, gwes_explorer_folder = gwesexplorer_path)
+  }
+
 
   # BLK10
+  # Additional paths if annotations are requested
+  # NetworkPlot
+  netplot_path = file.path(dset, "SR_network_plot.png")
+
   cat("\n\n #################### BLOCK 11 #################### \n\n")
   LDWeaver::create_network(tophits = tophits, netplot_path = netplot_path, plot_title = paste("Networks in short-range tophits for", dset))
 

R/io_functions.R

@@ -250,7 +250,7 @@ cleanup = function(dset, delete_after_moving = F){
     mv_success = c(mv_success, idx)
   }
 
-  idx = c(grep("cds_var.rds", files), grep("hdw.rds", files), grep("parsed_gbk.rds", files), grep("snp_ACGTN.rds", files))
+  idx = c(grep("cds_var.rds", files), grep("hdw.rds", files), grep("parsed_gbk.rds", files), grep("parsed_gff3.rds", files), grep("snp_ACGTN.rds", files))
   if(length(idx) > 0){
     fldr = file.path(dset, "Additional_Outputs")
     cleanup_support(files = file.path(dset, files[idx]), fldr)
@@ -298,7 +298,7 @@ cleanup = function(dset, delete_after_moving = F){
   }
 
   #### Temp folder ####
-  idx = c(grep("snpEff", files), grep("*.vcf", files), grep("*annotations.tsv", files), grep("*_links.tsv", files))
+  idx = c(grep("snpEff", files), grep("*.vcf", files), grep("*annotations.tsv", files), grep("*_links.tsv", files), grep("LDW_run_*", files))
   if(length(idx) > 0){
     fldr = file.path(dset, "Temp")
     cleanup_support(files = file.path(dset, files[idx]), fldr)

R/lr_analyser.R

@@ -44,16 +44,14 @@ analyse_long_range_links = function(dset, lr_links_path, sr_links_path, are_lrli
   # NOTE: spydrpick does not add clusters, add them from paint (requires cds_var)
 
   if(SnpEff_Annotate == T) {
-    if( (is.null(gbk_path) & is.null(gff3_path)) | (!is.null(gbk_path) & !is.null(gff3_path)) ) stop("Either gbk_path or gff3_path must be provided.
-                                                                                                     To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F") # only one of gbk or gff can be NULL
-    if(!is.null(gff3_path) & is.null(ref_fasta_path)) stop("Reference fasta file must be provided for gff3 annoations.
-                                                           To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F") # only one of gbk or gff can be NULL
-    if(is.null(snpeff_jar_path)) stop("You must specify <snpeff_jar_path> for annotations. To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F")
-    if(!file.exists(snpeff_jar_path)) stop(paste("<SnpEff.jar> not found at:", snpeff_jar_path, "please check the path provided"))
-    if(is.null(snpeff_jar_path)) stop("You must specify <snpeff_jar_path> for annotations. To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F")
+    if( (is.null(gbk_path) & is.null(gff3_path)) | (!is.null(gbk_path) & !is.null(gff3_path)) ) stop("Either gbk_path or gff3_path must be provided. To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F") # only one of gbk or gff can be NULL
+    if(!is.null(gff3_path) & is.null(ref_fasta_path)) stop("Reference fasta file must be provided for gff3 annoations. To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F") # only one of gbk or gff can be NULL
+    # if(is.null(snpeff_jar_path)) stop("You must specify <snpeff_jar_path> for annotations. To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F")
+    # if(!file.exists(snpeff_jar_path)) stop(paste("<SnpEff.jar> not found at:", snpeff_jar_path, "please check the path provided"))
+    # if(is.null(snpeff_jar_path)) stop("You must specify <snpeff_jar_path> for annotations. To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F")
     # if(is.null(gbk_path)) stop("You must specify <gbk_path> for annotations. To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F")
-    if(is.null(snp.dat)) stop("You must specify <gbk_path> for annotations. To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F")
-    if(is.null(cds_var)) stop("You must specify <gbk_path> for annotations. To run without annotations, re-run analyse_long_range_links() with SnpEff_Annotate = F")
+    if(is.null(snp.dat)) stop("You must provide snp.dat to perform annotations.")
+    if(is.null(cds_var)) stop("You must specify cds_var to perform for annotations.")
   }
 
   # lr_links_path = "~/Desktop/LDWeaver_RUN/maela/lr_links.tsv"