release v11.0.0

README.md

@@ -222,7 +222,7 @@ Gitlab developers
 
 ### v10.1.0
 
-1) D614G added as expected variants in B.1.1.7 and B.1.351 
+1) D614G added as expected variants in B.1.1.7 and B.1.351
 
 
 ### v10.0.0

dataset/20210326_voc.gmt → dataset/20210327_voc.gmt

-#name=20210322 VOC Variants
-B.1.1.7	B.1.1.7	MN908947_Ampliseq:3208-3218	MN908947_Ampliseq:5329-5339	MN908947_Ampliseq:6895-6905	MN908947_Ampliseq:11229-11247	MN908947_Ampliseq:21706-21721	MN908947_Ampliseq:21932-21944	MN908947_Ampliseq:23004-23014	MN908947_Ampliseq:23212-23222	MN908947_Ampliseq:23344-23354	MN908947_Ampliseq:23545-23555	MN908947_Ampliseq:23650-23660	MN908947_Ampliseq:24447-24457	MN908947_Ampliseq:24855-24865	MN908947_Ampliseq:27913-27923	MN908947_Ampliseq:27989-27999	MN908947_Ampliseq:28052-28062	MN908947_Ampliseq:28221-28233	MN908947_Ampliseq:28918-28928
+B.1.1.7	B.1.1.7	MN908947_Ampliseq:3208-3218	MN908947_Ampliseq:5329-5339	MN908947_Ampliseq:6895-6905	MN908947_Ampliseq:11228-11238	MN908947_Ampliseq:21705-21715	MN908947_Ampliseq:21931-21941	MN908947_Ampliseq:23004-23014	MN908947_Ampliseq:23212-23222	MN908947_Ampliseq:23344-23354	MN908947_Ampliseq:23545-23555	MN908947_Ampliseq:23650-23660	MN908947_Ampliseq:24447-24457	MN908947_Ampliseq:24855-24865	MN908947_Ampliseq:27913-27923	MN908947_Ampliseq:27989-27999	MN908947_Ampliseq:28052-28062	MN908947_Ampliseq:28221-28231	MN908947_Ampliseq:28222-28232	MN908947_Ampliseq:28223-28233	MN908947_Ampliseq:28918-28928
 B.1.351	B.1.351	MN908947_Ampliseq:1000-1010	MN908947_Ampliseq:5171-5181	MN908947_Ampliseq:10264-10274	MN908947_Ampliseq:11229-11239	MN908947_Ampliseq:21742-21752	MN908947_Ampliseq:22147-22157	MN908947_Ampliseq:22754-22764	MN908947_Ampliseq:22953-22963	MN908947_Ampliseq:23004-23014	MN908947_Ampliseq:23344-23354	MN908947_Ampliseq:23605-23615	MN908947_Ampliseq:25504-25514	MN908947_Ampliseq:25845-25855	MN908947_Ampliseq:26397-26407	MN908947_Ampliseq:28828-28838
-P1	P1	MN908947_Ampliseq:3769-3779	MN908947_Ampliseq:5589-5599	MN908947_Ampliseq:11229-11247	MN908947_Ampliseq:17200-17210	MN908947_Ampliseq:21555-21565	MN908947_Ampliseq:21562-21572	MN908947_Ampliseq:21579-21589	MN908947_Ampliseq:21915-21925	MN908947_Ampliseq:22073-22083	MN908947_Ampliseq:22753-22763	MN908947_Ampliseq:22953-22963	MN908947_Ampliseq:23004-23014	MN908947_Ampliseq:23466-23476	MN908947_Ampliseq:24583-24593	MN908947_Ampliseq:28108-28118	MN908947_Ampliseq:28210-28220	MN908947_Ampliseq:28453-28463
-B.1.1.7_Spike	B.1.1.7_Spike	MN908947_Ampliseq:21706-21721	MN908947_Ampliseq:21932-21944	MN908947_Ampliseq:23004-23014	MN908947_Ampliseq:23212-23222	MN908947_Ampliseq:23344-23354	MN908947_Ampliseq:23545-23555	MN908947_Ampliseq:23650-23660	MN908947_Ampliseq:24447-24457	MN908947_Ampliseq:24855-24865
-B.1.351_Spike	B.1.351_Spike	MN908947_Ampliseq:21742-21752	MN908947_Ampliseq:22147-22157	MN908947_Ampliseq:22754-22764	MN908947_Ampliseq:22953-22963	MN908947_Ampliseq:23004-23014	MN908947_Ampliseq:23344-23354	MN908947_Ampliseq:23605-23615
-P1_Spike	P1_Spike	MN908947_Ampliseq:21555-21565	MN908947_Ampliseq:21562-21572	MN908947_Ampliseq:21579-21589	MN908947_Ampliseq:21915-21925	MN908947_Ampliseq:22073-22083	MN908947_Ampliseq:22753-22763	MN908947_Ampliseq:22953-22963	MN908947_Ampliseq:23004-23014	MN908947_Ampliseq:23466-23476	MN908947_Ampliseq:24583-24593
-A.23.1	A.23.1	MN908947_Ampliseq:2943-2953	MN908947_Ampliseq:11171-11181	MN908947_Ampliseq:11207-11217	MN908947_Ampliseq:21808-21818	MN908947_Ampliseq:21974-21984	MN908947_Ampliseq:22602-22612	MN908947_Ampliseq:23342-23352	MN908947_Ampliseq:23545-23555	MN908947_Ampliseq:28085-28095	MN908947_Ampliseq:28108-28118	MN908947_Ampliseq:28819-28829	MN908947_Ampliseq:29468-29478
-A.23.1_Spike	A.23.1_Spike	MN908947_Ampliseq:21808-21818	MN908947_Ampliseq:21974-21984	MN908947_Ampliseq:22602-22612	MN908947_Ampliseq:23342-23352	MN908947_Ampliseq:23545-23555
-B.1.525	B.1.525	MN908947_Ampliseq:14348-14358	MN908947_Ampliseq:11229-11247	MN908947_Ampliseq:21706-21721	MN908947_Ampliseq:21658-21668	MN908947_Ampliseq:22953-22963	MN908947_Ampliseq:23534-23544	MN908947_Ampliseq:24165-24175	MN908947_Ampliseq:26246-26256	MN908947_Ampliseq:26708-26718	MN908947_Ampliseq:28219-28231
-B.1.525_Spike	B.1.525_Spike	MN908947_Ampliseq:21706-21721	MN908947_Ampliseq:21658-21668	MN908947_Ampliseq:22953-22963	MN908947_Ampliseq:23534-23544	MN908947_Ampliseq:24165-24175
+P.1	P.1	MN908947_Ampliseq:3769-3779	MN908947_Ampliseq:5589-5599	MN908947_Ampliseq:11228-11238	MN908947_Ampliseq:17200-17210	MN908947_Ampliseq:21555-21565	MN908947_Ampliseq:21562-21572	MN908947_Ampliseq:21579-21589	MN908947_Ampliseq:21915-21925	MN908947_Ampliseq:22073-22083	MN908947_Ampliseq:22753-22763	MN908947_Ampliseq:22953-22963	MN908947_Ampliseq:23004-23014	MN908947_Ampliseq:23344-23354	MN908947_Ampliseq:23466-23476	MN908947_Ampliseq:24583-24593	MN908947_Ampliseq:28108-28118	MN908947_Ampliseq:28210-28220	MN908947_Ampliseq:28453-28463
+A.23.1	A.23.1	MN908947_Ampliseq:11171-11181	MN908947_Ampliseq:11207-11217	MN908947_Ampliseq:21808-21818	MN908947_Ampliseq:21974-21984	MN908947_Ampliseq:22602-22612	MN908947_Ampliseq:23342-23352	MN908947_Ampliseq:23545-23555	MN908947_Ampliseq:28085-28095	MN908947_Ampliseq:28108-28118	MN908947_Ampliseq:28819-28829	MN908947_Ampliseq:29468-29478
+B.1.525	B.1.525	MN908947_Ampliseq:14348-14358	MN908947_Ampliseq:11228-11238	MN908947_Ampliseq:21705-21715	MN908947_Ampliseq:21658-21668	MN908947_Ampliseq:22953-22963	MN908947_Ampliseq:23344-23354	MN908947_Ampliseq:23534-23544	MN908947_Ampliseq:24165-24175	MN908947_Ampliseq:26246-26256	MN908947_Ampliseq:26708-26718	MN908947_Ampliseq:28218-28228
 B.1.427	B.1.427	MN908947_Ampliseq:1000-1010	MN908947_Ampliseq:9679-9689	MN908947_Ampliseq:14349-14359	MN908947_Ampliseq:16335-16345	MN908947_Ampliseq:16955-16965	MN908947_Ampliseq:21541-21551	MN908947_Ampliseq:21959-21969	MN908947_Ampliseq:22858-22868	MN908947_Ampliseq:23344-23354	MN908947_Ampliseq:25504-25514	MN908947_Ampliseq:28828-28838
-B.1.427_Spike	B.1.427_Spike	MN908947_Ampliseq:21541-21551	MN908947_Ampliseq:21959-21969	MN908947_Ampliseq:22858-22868	MN908947_Ampliseq:23344-23354
 B.1.429	B.1.429	MN908947_Ampliseq:1000-1010	MN908947_Ampliseq:12819-12829	MN908947_Ampliseq:14349-14359	MN908947_Ampliseq:16955-16965	MN908947_Ampliseq:21541-21551	MN908947_Ampliseq:21959-21969	MN908947_Ampliseq:22858-22868	MN908947_Ampliseq:23344-23354	MN908947_Ampliseq:25504-25514	MN908947_Ampliseq:28828-28838
-B.1.429_Spike	B.1.429_Spike	MN908947_Ampliseq:21959-21969	MN908947_Ampliseq:22858-22868	MN908947_Ampliseq:23344-23354

dev/convert.voc_gatk_2_gmt.R

+#########################################################################
+##                                                                     ##
+##     convert voc_gatk into gmt                                       ##
+##                                                                     ##
+##     Gael A. Millot                                                  ##
+##     Bioinformatics and Biostatistics Hub                            ##
+##     Computational Biology Department                                ##
+##     Institut Pasteur Paris                                          ##
+##                                                                     ##
+#########################################################################
+
+
+rm(list = ls())
+
+date <- "20210327"
+expanse <- 5
+file.in <- "_voc_gatk.txt"
+file.out <- "_voc.gmt"
+path <- "C:/Users/gael/Documents/Git_projects/cnr_curation/dataset/"
+
+in.path <- paste0(path, date, file.in)
+out.path <- paste0(path, date, file.out)
+txt <- read.table(in.path, header = TRUE, sep = "\t", stringsAsFactors = FALSE, comment.char = "#", fill = FALSE, check.names = FALSE, colClasses = "character")
+
+res <- data.frame()
+voc.names <- unique(txt$voc)
+for(i0 in 1:length(voc.names)){
+    tempo.txt <- txt[txt$voc == voc.names[i0], ]
+    pos <- as.integer(tempo.txt$gatk_pos)
+    pos <- paste0(unique(tempo.txt$gatk_chr), ":", pos - expanse, "-", pos + expanse)
+    final <- paste0(voc.names[i0], "\t", voc.names[i0], "\t", paste(pos, collapse = "\t"))
+    res <- rbind(res, final)
+}
+write.table(res, file = out.path, row.names = FALSE, col.names = FALSE, append = FALSE, quote = FALSE, sep = "\t")