Include MutSiteFind.R and improved installing dependencies

unparalogMutations checks & installs dependencies only when it is sourced, and not everytime the function was called (as previously).

MutSiteFind.R

@@ -0,0 +1,31 @@
+# #<---------------------------->
+# # Please include this section when distributing and/or using this code. 
+# # Please read and abide by the terms of the included LICENSE
+# #
+# #  Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
+# #  Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
+# #  License: https://gitlab.utu.fi/deecha/shared_scripts/-/blob/master/LICENSE
+# #
+# #  PURPOSE:
+# #  For a given vector of amino acid changes like A123T, V256F, E746_A750del
+# #  this function returns c(123, 256, 746) as amino acid positions of
+# #  the mutated residue. 
+# #     In case of indels, it doesn't return the range!! (returns only the start position)
+# #
+# #<---------------------------->
+
+dependencies <- c("stringi")
+missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
+if(length(missing_packages)) install.packages(missing_packages) 
+
+## ----- Legacy version relying on r::base --------
+MutSiteFind.legacy=function(MutationColumn){
+  MutationSite=c()
+  for(i in seq(1:length(MutationColumn))){
+    Site=regmatches(MutationColumn[i], gregexpr("[[:digit:]]+",MutationColumn[i]))[[1]][1]
+    MutationSite=c(MutationSite,Site)
+  }
+  return(MutationSite)
+}
+
+

unparalogMutations.R

@@ -1,6 +1,6 @@
 # #<---------------------------->
-# # Please include this when distributing and/or using this code. 
+# # Please include this section when distributing and/or using this code. 
-# # I hope you will read and respect the terms of the included LICENSE
+# # Please read and abide by the terms of the included LICENSE
 # #
 # #  Author : Deepankar Chakroborty (https://gitlab.utu.fi/deecha)
 # #  Report issues: https://gitlab.utu.fi/deecha/shared_scripts/-/issues
@@ -29,12 +29,12 @@
 
 # <--------------->
 
+# Installing missing dependencies
+dependencies <- c("stringi", "progress")
+missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
+if(length(missing_packages)) install.packages(missing_packages)
+
 unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
-   # Installing missing dependencies
-   dependencies <- c("stringi", "progress")
-   missing_packages <- dependencies[!(dependencies %in% installed.packages()[, "Package"])]
-   if(length(missing_packages)) install.packages(missing_packages)      
-   
    # Sanity checks
    check_paralog_sep <- !any(stringi::stri_detect_fixed(str = DATA$Gene.refGene,pattern = paralog_separator))
    check_annotation_sep <- !any(stringi::stri_detect_fixed(str =  DATA$AAChange.refGene, pattern = annotation_separator))