tempo

.gitignore

-docker
-docs
-other
-README.md
-.nextflow
-singularity
-work
\ No newline at end of file
+work/
+singularity/
+results/
+.nextflow/
+.nextflow*
\ No newline at end of file

bin/.Rhistory

-install.packages('dplyr')
-install.packages('ggplot2')
-install.packages('DESeq2')
-if (!requireNamespace("BiocManager", quietly = TRUE))
-install.packages("BiocManager")
-BiocManager::install("DESeq2")
-install.packages("tidyverse")
-if (!require("BiocManager", quietly = TRUE))
-install.packages("BiocManager")
-BiocManager::install(version = "3.14")
-install.packages('SARTools')
-install.packages('sartools')
-install.packages('sartool')
-library(ggplot2)
-ggplot2::guides(fill = FALSE, color = FALSE, alpha = FALSE)
-ggplot2::guides(fill = 'none', color = 'none', alpha = 'none')
-ggplot2::guides(fill = 'none', color = 'none', alpha = 'none')
-setwd("~/mia/gitlab/kocchi/bin")

bin/adj_mean.R

 #! /usr/bin/Rscript
 
-source(here::here("bin/intern_funct_check.R"))
 
-path_function1 =  "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/c1dd8832f14d76c1901a60ca2a7c87af01a82b61/cute_little_R_functions.R" 
-
-if(length(path.function1) != 1){
-    stop(paste0("\n\n============\n\nERROR IN SLITHERINE\npath.function1 PARAMETER MUST BE LENGTH 1: ", 
-                paste(path.function1, collapse = " "), "\n\n============\n\n"))
-}else if(grepl(x = path.function1, pattern = "^http")){
-    tempo.try <- try(suppressWarnings(source(path.function1, local = .GlobalEnv)), silent = TRUE)
-    if(any(grepl(x = tempo.try, pattern = "[Ee]rror"))){
-        stop(paste0("\n\n============\n\nERROR IN SLITHERINE\n
-  HTTP INDICATED IN THE path.function1 PARAMETER DOES NOT EXISTS: ", path.function1, "\n\n============\n\n"))
-    }else{
-        source(path.function1, local = .GlobalEnv) # source the fun_ functions used below
-    }
-}else if( ! grepl(x = path.function1, pattern = "^http")){
-    if( ! file.exists(path.function1)){
-        stop(paste0("\n\n============\n\nERROR IN SLITHERINE\n
-  FILE INDICATED IN THE path.function1 PARAMETER DOES NOT EXISTS: ", path.function1, "\n\n============\n\n"))
-    }else{
-        source(path.function1, local = .GlobalEnv) # source the fun_ functions used below
-    }
-}
 
 adj.mean.fun <- function(x_3fun, text_3fun){
     # AIM

bin/hiccompare_graph.R

@@ -2,7 +2,6 @@
 
 ## local function: graphs of HiC Compare
 
-source(here::here("bin/intern_funct_check.R"))
 
 hiccompare.graphs.fun <-
   function(hictable_5fun,

bin/intern_funct_check.R

-#! /usr/bin/Rscript
-
-path_function1 =  "https://gitlab.pasteur.fr/gmillot/cute_little_R_functions/-/raw/c1dd8832f14d76c1901a60ca2a7c87af01a82b61/cute_little_R_functions.R"
-
-if (length(path.function1) != 1) {
-  stop(
-    paste0(
-      "\n\n============\n\nERROR IN SLITHERINE\npath.function1 PARAMETER MUST BE LENGTH 1: ",
-      paste(path.function1, collapse = " "),
-      "\n\n============\n\n"
-    )
-  )
-} else if (grepl(x = path.function1, pattern = "^http")) {
-  tempo.try <-
-    try(suppressWarnings(source(path.function1, local = .GlobalEnv)), silent = TRUE)
-  if (any(grepl(x = tempo.try, pattern = "[Ee]rror"))) {
-    stop(
-      paste0(
-        "\n\n============\n\nERROR IN SLITHERINE\n
-  HTTP INDICATED IN THE path.function1 PARAMETER DOES NOT EXISTS: ",
-        path.function1,
-        "\n\n============\n\n"
-      )
-    )
-  } else{
-    source(path.function1, local = .GlobalEnv) # source the fun_ functions used below
-  }
-} else if (!grepl(x = path.function1, pattern = "^http")) {
-  if (!file.exists(path.function1)) {
-    stop(
-      paste0(
-        "\n\n============\n\nERROR IN SLITHERINE\n
-  FILE INDICATED IN THE path.function1 PARAMETER DOES NOT EXISTS: ",
-        path.function1,
-        "\n\n============\n\n"
-      )
-    )
-  } else{
-    source(path.function1, local = .GlobalEnv) # source the fun_ functions used below
-  }
-}
-
-internal.function.check.fun <-
-  function(expect.arg.values_fun,
-           req.functions_fun,
-           function.name_fun) {
-    # AIM
-    # check the arguments of the other local functions of this script
-    # WARNING
-    # use the object of the checked function
-    # ARGUMENTS
-    # expect.arg.values_fun: a list of character strings made of the authorized values of the arguments of the checked function
-    # req.functions_fun: a vector of character strings made of the names of the cute little toolbox required functions. Write NULL is no functions required
-    # function.name_fun: a character string of the name of the parental function
-    # REQUIRED PACKAGES
-    # none
-    # REQUIRED FUNCTIONS FROM CUTE_LITTLE_R_FUNCTION
-    # non
-    # RETURN
-    # error messages
-    # EXAMPLES
-    # internal.function.check.fun(expect.arg.values_fun = list("a"), req.functions_fun = "b")
-    # DEBUGGING
-    # expect.arg.values_fun = list("a") ; req.functions_fun = "b"
-    # function name
-    function.name_intern <-
-      paste0(as.list(match.call(expand.dots = FALSE))[[1]], "()")
-    function.name_intern <-
-      paste0(function.name_intern, " INTERNAL FUNCTION OF SLITHERINE")
-    # end function name
-    # argument checking
-    if (!all(class(expect.arg.values_fun) == "list")) {
-      tempo.cat <-
-        paste0(
-          "\n\n================\n\nERROR IN ",
-          function.name_intern,
-          ":\n
-  ARGUMENT expect.arg.values_fun MUST BE CLASS LIST AND NOT:\n",
-          paste(class(expect.arg.values_fun) , collapse = "\n"),
-          "\n\n================\n\n"
-        )
-      stop(tempo.cat)
-    } else{
-      for (i2 in 1:length(expect.arg.values_fun)) {
-        if (!all(class(expect.arg.values_fun[[i2]]) == "character")) {
-          tempo.cat <-
-            paste0(
-              "\n\n================\n\nERROR IN ",
-              function.name_intern,
-              ":\nCOMPARTMENT ",
-              i2,
-              " OF ARGUMENT expect.arg.values_fun MUST BE A VECTOR OF CLASS CHARACTER AND NOT:\n",
-              paste(class(expect.arg.values_fun[[i2]]) , collapse = "\n"),
-              "\n\n================\n\n"
-            )
-          stop(tempo.cat)
-        }
-      }
-    }
-    if (!is.null(req.functions_fun)) {
-      if (!all(class(req.functions_fun) == "character")) {
-        tempo.cat <-
-          paste0(
-            "\n\n================\n\nERROR IN ",
-            function.name_intern,
-            ":\nARGUMENT req.functions_fun MUST BE A VECTOR OF CLASS CHARACTER AND NOT:\n",
-            paste(class(req.functions_fun) , collapse = "\n"),
-            "\n\n================\n\n"
-          )
-        stop(tempo.cat)
-      }
-    }
-    if (!all(class(function.name_fun) == "character")) {
-      tempo.cat <-
-        paste0(
-          "\n\n================\n\nERROR IN ",
-          function.name_intern,
-          ":\nARGUMENT function.name_fun MUST BE A VECTOR OF CLASS CHARACTER AND NOT:\n",
-          paste(class(function.name_fun) , collapse = "\n"),
-          "\n\n================\n\n"
-        )
-      stop(tempo.cat)
-    }
-    # end argument checking
-    # main code using the object of the function evaluated
-    if (!is.null(req.functions_fun)) {
-      for (i2 in 1:length(req.functions_fun)) {
-        if (length(find(req.functions_fun[i2], mode = "function")) == 0) {
-          tempo.cat <-
-            paste0(
-              "\n\n================\n\nERROR IN ",
-              function.name,
-              ": REQUIRED ",
-              req.functions_fun[i2],
-              " FUNCTION IS MISSING IN THE R ENVIRONMENTS\n\n================\n\n"
-            )
-          stop(tempo.cat)
-        }
-      }
-    }
-    arg.list <-
-      {
-        # this call the arguments of the parental function. To have the arguments of the current function: arg.list <- as.list(match.call(definition = sys.function(sys.parent(n = 2))))[-1] # recover the argument names with attributed values. -1 to remove the function name compartment. sys.function(sys.parent(n = 2)) to recover the agument beyond sys.function(). See also debugging_tools_for_r_dev for other kind of calling
-        cl <- sys.call(-1)
-        
-        f <-
-          get(as.character(cl[[1]]), mode = "function", sys.frame(-2))
-        
-        cl <- match.call(definition = f, call = cl)
-        
-        as.list(cl)[-1]
-      }
-    arg.names <- names(arg.list)
-    arg.values <- unlist(as.character(arg.list))
-    default.arg.list <-
-      formals(fun = sys.function(sys.parent()), envir = parent.frame(n = 1)) # list of all the arguments of the parental function with their default values (not the values of the user !). Use formals(fun = sys.function(sys.parent(n = 2))) for arguments of the current function
-    arg.with.default.value <-
-      !sapply(default.arg.list, is.symbol) &
-      sapply(sapply(default.arg.list, as.character), identical, "") # logical indicating which of the default.arg.list have default values
-    if (any(arg.with.default.value) == TRUE) {
-      tempo.cat <-
-        paste0(
-          "\n\n================\n\nERROR IN ",
-          function.name_fun,
-          ":\nARGUMENTS WITH DEFAULT VALUE NOT ALLOWED IN INTERNAL FUNCTIONS (FOR CODE SAFETY):\n",
-          paste(names(default.arg.list)[arg.with.default.value] , collapse = "\n"),
-          "\n\n================\n\n"
-        )
-      stop(tempo.cat)
-    }
-    expect.arg.names <- names(default.arg.list)
-    tempo.test <-
-      expect.arg.names[expect.arg.names %in% unlist(mapply(FUN = ls, pos = 1:10))]
-    if (length(tempo.test) > 0) {
-      # check that argument name are not in the R evironment
-      tempo.cat <-
-        paste0(
-          "\n\n================\n\nERROR IN ",
-          function.name_fun,
-          ":\nARGUMENT NAME OF THIS INTERNAL FUNCTION ALSO PRESENT IN THE R ENVIRONMENT,
-                            WHICH IS NOT ALLOWED FOR CODE SAFETY:\n",
-          paste(tempo.test, collapse = "\n"),
-          "\n\n================\n\n"
-        )
-      stop(tempo.cat)
-    }
-    if (!(
-      all(arg.names %in% expect.arg.names) &
-      length(arg.names) == length(expect.arg.names)
-    )) {
-      tempo.cat <-
-        paste0(
-          "\n\n================\n\nERROR IN ",
-          function.name_fun,
-          ": ARGUMENTS OF THIS FUNCTION MUST BE LENGTH:\n",
-          length(expect.arg.names),
-          "\nAND MUST HAVE THESE NAMES:\n",
-          paste(expect.arg.names, collapse = "\n"),
-          "\n\nHERE, IT IS LENGTH:\n",
-          length(arg.names),
-          "\nWITH NAMES:\n",
-          paste(arg.names, collapse = "\n"),
-          "\n\n================\n\n"
-        )
-      stop(tempo.cat)
-    }
-    if (length(arg.values) != length(expect.arg.values_fun)) {
-      tempo.cat <-
-        paste0(
-          "\n\n================\n\nERROR IN ",
-          function.name_fun,
-          ": ARGUMENTS OF THIS FUNCTION MUST BE LENGTH:\n",
-          length(expect.arg.values_fun),
-          "\n\nBUT HERE, IT IS LENGTH:\n",
-          length(arg.values),
-          "\n\n================\n\n"
-        )
-      stop(tempo.cat)
-    }
-    for (i1 in 1:length(expect.arg.values_fun)) {
-      if (!all(arg.values[i1] %in% expect.arg.values_fun[[i1]])) {
-        tempo.cat <-
-          paste0(
-            "\n\n================\n\nERROR IN ",
-            function.name_fun,
-            ": VALUE OF ARGUMENT ",
-            arg.names[i1],
-            " MUST BE:\n",
-            paste(dQuote(expect.arg.values_fun[[i1]], q = FALSE), collapse = "\n"),
-            "\n\nBUT HERE, IT IS VALUE:\n",
-            paste(arg.values[i1], collapse = "\n"),
-            "\n\n================\n\n"
-          )
-        stop(tempo.cat)
-      }
-    }
-  }

bin/mask_plot.R

@@ -2,7 +2,6 @@
 
 ## local function: heatmap + mask plotting
 
-source(here::here("bin/intern_funct_check.R"))
 
 mask.plot.fun <-
   function(mask_4fun,

bin/slith_part2.R

@@ -34,8 +34,7 @@ warn.secu <- as.logical(args[28])
 serp.symmet.input <- as.logical(toupper(args[29]))
 adj_mean <- args[30]
 hiccompare_graph <- args[31]
-intern_funct_check <- args[32]
-mask_plot <- args[33]
+mask_plot <- args[32]
 
 warning.message <- NULL
 ini.date <- Sys.time()

bin/use_serp.py

@@ -22,11 +22,22 @@ matB_theo = np.loadtxt(sys.argv[4])
 if len(sys.argv) == 7:
     thr_tot = int(sys.argv[5])
     thr_min = int(sys.argv[6])
+    iter_nb = int(sys.argv[7])
 
 # binning des 2 matrices
-matA_b, matB_b, mat_ratio = sp.serpentin_binning(matA, matB, thr_tot, thr_min)
+matA_b, matB_b, mat_ratio = sp.serpentin_binning(
+    A = matA, 
+    B = matB, 
+    threshold = thr_tot, 
+    minthreshold = thr_min, 
+    iterations = iter_nb
+)
 matA_theo_b, matB_theo_b, mat_theo_ratio = sp.serpentin_binning(
-    matA_theo, matB_theo, thr_tot, thr_min
+    A = matA_theo, 
+    B = matB_theo, 
+    threshold = thr_tot, 
+    minthreshold = thr_min, 
+    iterations = iter_nb
 )
 
 # output