test final polyA

mspodda · May 27, 2024 · 6206232 · 6206232
1 parent 72cef92
commit 6206232
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/workflow/R/config_all.R b/workflow/R/config_all.R
@@ -40,10 +40,10 @@ group.colors_pie_chart <- c( "#708090", "#E6E6E6", "#D9D9D9", "#008bbf",
                                          "#cfcfc4")
 
 ## directories
-txt_samples <- "/home/runner/work/isoworm/isoworm/test_data"
-results_dir <- "/home/runner/work/isoworm/isoworm/results"
-polyA_bam_dir <- "/home/runner/work/isoworm/isoworm/results/polyA/bam"
-final_output <- "/home/runner/work/isoworm/isoworm/workflow/R"
+txt_samples   <- "/home/runner/work/isoworm/isoworm/test_data"
+results_dir   <- "/home/runner/work/isoworm/isoworm/results"
+polyA_bam_dir <- "/home/runner/work/isoworm/isoworm/results/polyA"
+final_output  <- "/home/runner/work/isoworm/isoworm/workflow/R"
 ## total salmon
 indexDir <- file.path("/home/runner/work/isoworm/isoworm/test_data/salmon_index_v43")
 fasta    <- file.path("/home/runner/work/isoworm/isoworm/test_data/chr7_transcripts.fa")

diff --git a/workflow/R/polyA.R b/workflow/R/polyA.R
@@ -4,10 +4,12 @@ source("config_all.R")
 lapply(my_packages, require, character.only = TRUE) 
 ##### open all the bed files ##################################################
 samples_dir <- list.dirs(polyA_bam_dir, recursive = FALSE)
+print(samples_dir)
 dataframes_peak <- list()
 for (i in samples_dir){
   setwd(i)
   in.list <- list.files(path= i, recursive = T, full.names = T)
+  print(in.list)
   j <- grep("_small_Aligned.sortedByCoord.out.bam$",in.list)
   name <- paste0("quant_",gsub(".*/(SRR[0-9]+).*", "\\1",in.list[j]))
   gal <- readGAlignments(in.list[j])