feat: Add the "--PERCENT,P" option

lgmgeo · Jul 23, 2024 · 1734618 · 1734618
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Showing 9 changed files with 49 additions and 15 deletions.
diff --git a/README.md b/README.md
@@ -36,9 +36,12 @@
 --OUTPUTFILE,-O <File>        The liftover SV VCF output file
                               Required
 
+--PERCENT,-P <float>          Variation in length authorized for a lifted SV (e.g. difference max between SVLEN < 5%)
+                              Default value: 0.05
+
 --REFFASTASEQ,-R <File>       The reference sequence (fasta) for the TARGET genome build (i.e., the new one after the liftover)
 ```
-## liftoverSV: version 1.0.0_beta
+## liftoverSV: version 0.1.1_beta
 
 * Lift over #CHROM and POS
 

diff --git a/bin/liftoverSV b/bin/liftoverSV
@@ -1,7 +1,7 @@
 #!/usr/bin/env tclsh
 
 ############################################################################################################
-# liftoverSV 1.0.0_beta                                                                                    #
+# liftoverSV 0.1.1_beta                                                                                    #
 #                                                                                                          #
 # Copyright (C) 2024-current Veronique Geoffroy ([email protected])                             #
 #                                                                                                          #

diff --git a/changeLog.txt b/changeLog.txt
@@ -1,15 +1,33 @@
 ############################################################################################################
-# liftoverSV 1.0.0_beta                                                                                    #
+# liftoverSV 0.1.1_beta                                                                                    #
 #                                                                                                          #
 # Copyright (C) 2024-current Veronique Geoffroy ([email protected])                             #
 #                                                                                                          #
+# This program is free software; you can redistribute it and/or                                            #
+# modify it under the terms of the GNU General Public License                                              #
+# as published by the Free Software Foundation; either version 3                                           #
+# of the License, or (at your option) any later version.                                                   #
+#                                                                                                          #
+# This program is distributed in the hope that it will be useful,                                          #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of                                           #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the                                             #
+# GNU General Public License for more details.                                                             #
+#                                                                                                          #
+# You should have received a copy of the GNU General Public License                                        #
+# along with this program; If not, see <http://www.gnu.org/licenses/>.                                     #
 ############################################################################################################
 
 
 For more details, please see the README file.
 
 
-July, 12, 2024, liftoverSV version 1.0.0_beta
+
+July, 23, 2024, liftoverSV version 0.1.1_beta
+
+	- Add the --PERCENT,P option
+
+
+July, 12, 2024, liftoverSV version 0.1.0_beta
 
 	liftoverSV: Lifts over a Structural Variation VCF file from one reference build to another.
 
@@ -24,6 +42,6 @@ July, 12, 2024, liftoverSV version 1.0.0_beta
 	Case4: the distance between the two lifted positions changes significantly (difference between both SVLENs > 5%)
 
 	- Lift over INFO/SVLEN, INFO/SVSIZE
- 
+
 
 
diff --git a/share/doc/liftoverSV/commandLineOptions.txt b/share/doc/liftoverSV/commandLineOptions.txt
@@ -15,8 +15,7 @@ OPTIONS
                               See http://hgdownload.soe.ucsc.edu/downloads.html#terms for where to download chain files.
                               Required
 
---help,-h <Boolean>           Display the help message  
-                              Default value: false. Possible values: {true, false}
+--help,-h                     Display the help message  
 
 --INPUTFILE,-I <File>         The SV VCF input file
                               Required
@@ -27,6 +26,9 @@ OPTIONS
 --OUTPUTFILE,-O <File>		  The liftover SV VCF output file
                               Required
 
+--PERCENT,-P <float>          Variation in length authorized for a lifted SV (e.g. difference max between SVLEN < 5%) 
+                              Default value: 0.05
+
 --REFFASTASEQ,-R <File>       The reference sequence (fasta) for the TARGET genome build (i.e., the new one after the liftover)
 
 

diff --git a/share/tcl/liftoverSV/liftoverSV-config.tcl b/share/tcl/liftoverSV/liftoverSV-config.tcl
@@ -1,5 +1,5 @@
 ############################################################################################################
-# liftoverSV 1.0.0_beta                                                                                    #
+# liftoverSV 0.1.1_beta                                                                                    #
 #                                                                                                          #
 # Copyright (C) 2024-current Veronique Geoffroy ([email protected])                             #
 #                                                                                                          #
@@ -29,12 +29,13 @@ proc configureLiftoverSV {argv} {
     #######################
     set g_liftoverSV(BEDTOOLS)      "bedtools"
 	set g_liftoverSV(LIFTOVER)      "liftOver"   
+    set g_liftoverSV(PERCENT)       "0.05"
 
 
     ##################################
     ## Load options given in arguments
     ##################################
-    set lOptionsOk "B BEDTOOLS C CHAIN h help I INPUTFILE L LIFTOVER O OUTPUTFILE R REFFASTASEQ"
+    set lOptionsOk "B BEDTOOLS C CHAIN h help I INPUTFILE L LIFTOVER O OUTPUTFILE P PERCENT R REFFASTASEQ"
 
     set i 0
     set j 1
@@ -54,6 +55,8 @@ proc configureLiftoverSV {argv} {
                 set optionName LIFTOVER
             } elseif {$optionName eq "O"} {
                 set optionName OUTPUTFILE
+            } elseif {$optionName eq "P"} {
+                set optionName PERCENT
             } elseif {$optionName eq "R"} {
                 set optionName REFFASTASEQ
             } elseif {$optionName eq "h" || $optionName eq "help"} {
@@ -163,4 +166,12 @@ proc configureLiftoverSV {argv} {
         } 
     }
 
+    ## PERCENT: should be defined between 0 and 1.
+    if {$g_liftoverSV(PERCENT) < 0 || $g_liftoverSV(PERCENT) > 1} {
+        puts "Bad option value: --PERCENT = $g_liftoverSV(PERCENT)"
+        puts "Should be in the \[0-1\] range values, default = 0.05"
+        exit 2
+    }
+
+
 }
diff --git a/share/tcl/liftoverSV/liftoverSV-extractDNAseq.tcl b/share/tcl/liftoverSV/liftoverSV-extractDNAseq.tcl
@@ -1,5 +1,5 @@
 ############################################################################################################
-# liftoverSV 1.0.0_beta                                                                                    #
+# liftoverSV 0.1.1_beta                                                                                    #
 #                                                                                                          #
 # Copyright (C) 2024-current Veronique Geoffroy ([email protected])                             #
 #                                                                                                          #

diff --git a/share/tcl/liftoverSV/liftoverSV-general.tcl b/share/tcl/liftoverSV/liftoverSV-general.tcl
@@ -1,5 +1,5 @@
 ############################################################################################################
-# LiftOver_SVs_from_VCF 1.0.0_beta                                                                         #
+# LiftOver_SVs_from_VCF 0.1.1_beta                                                                         #
 #                                                                                                          #
 # Copyright (C) 2024-current Veronique Geoffroy ([email protected])                             #
 #                                                                                                          #

diff --git a/share/tcl/liftoverSV/liftoverSV-help.tcl b/share/tcl/liftoverSV/liftoverSV-help.tcl
@@ -1,5 +1,5 @@
 ############################################################################################################
-# liftoverSV 1.0.0_beta                                                                                    #
+# liftoverSV 0.1.1_beta                                                                                    #
 #                                                                                                          #
 # Copyright (C) 2024-current Veronique Geoffroy ([email protected])                             #
 #                                                                                                          #

diff --git a/share/tcl/liftoverSV/liftoverSV-liftAndWrite.tcl b/share/tcl/liftoverSV/liftoverSV-liftAndWrite.tcl
@@ -1,5 +1,5 @@
 ############################################################################################################
-# liftoverSV 1.0.0_beta                                                                                    #
+# liftoverSV 0.1.1_beta                                                                                    #
 #                                                                                                          #
 # Copyright (C) 2024-current Veronique Geoffroy ([email protected])                             #
 #                                                                                                          #
@@ -210,7 +210,7 @@ proc writeTheLiftedVCF {} {
 				regsub "(^END|;END)=(\[^;\]+)(;|$)" $infos "\\1=$theNewEND\\3" infos
 				set svlen [expr {$end-$start}]
                 set svlenlifted [expr {$theNewEND-$theNewStart}]
-				if {$svlenlifted < [expr {$svlen*0.95}] || $svlenlifted > [expr {$svlen*1.05}]} {
+				if {$svlenlifted < [expr {$svlen*(1-$g_liftoverSV(PERCENT))}] || $svlenlifted > [expr {$svlen*(1+$g_liftoverSV(PERCENT))}]} {
 					# Case4
 					lappend L_unmappedToWrite "[join [lrange $Ls 0 7] "\t"]\tthe distance between the two lifted positions changes significantly (svlen diff > 5%)"
 					incr j
@@ -248,7 +248,7 @@ proc writeTheLiftedVCF {} {
 	            regsub "(^SVEND|;SVEND)=(\[^;\]+)(;|$)" $infos "\\1=$theNewSVEND\\3" infos
                 set svlen [expr {$svend-$start}]
 				set svlenlifted [expr {$theNewSVEND-$theNewStart}]
-                if {$svlenlifted < [expr {$svlen*0.95}] || $svlenlifted > [expr {$svlen*1.05}]} {
+                if {$svlenlifted < [expr {$svlen*(1-$g_liftoverSV(PERCENT))}] || $svlenlifted > [expr {$svlen*(1+$g_liftoverSV(PERCENT))}]} {
                     # Case4
                     lappend L_unmappedToWrite "[join [lrange $Ls 0 7] "\t"]\tthe distance between the two lifted positions changes significantly (svlen diff > 5%; $svlen # $svlenlifted)"
                     incr j