Squashed commit of the following:

commit 631eef6e
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Wed Jul 29 14:41:00 2020 +0300

    Switch to stringi to improve performance.

commit 99a6589b
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Wed Jul 29 14:39:44 2020 +0300

    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).

commit a044ac9f
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Wed Jul 29 14:19:03 2020 +0300

    updated 20200714

commit cd79464c
Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
Date:   Wed Jul 29 13:12:47 2020 +0300

    Squashed commit of the following:

    commit 23f5db8f
    Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
    Date:   Wed Jul 29 13:12:26 2020 +0300

        Changed to Apache License 2.0

    commit 21ad1ee7
    Author: Deepankar Chakroborty <deepankar.chakroborty@utu.fi>
    Date:   Wed Jul 29 13:12:05 2020 +0300

        Update info section

MutSiteFind.R

+# #<---------------------------->
+# # 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) 
+
+MutSiteFind <- function(MutationColumn){
+  return(unlist(x = stringi::stri_extract_first_regex(str = MutationColumn,pattern = "[[:digit:]]+"), use.names = F))
+}
+
+

unparalogMutations.R

 # #<---------------------------->
-# # Please include this when distributing and/or using this code. 
-# # I hope you will read and respect the terms of the included LICENSE
+# # 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
@@ -29,12 +29,12 @@
 
 # <--------------->
 
-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)
 
+unparalog <- function(DATA, paralog_separator = ";", annotation_separator = ",", GeneColName , AnnotationColName ){
    # 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))