From 61f2438d16f4606ae4811b78e1597493139d4d25 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Mon, 8 Oct 2018 12:17:41 +0200
Subject: [PATCH] intersect_SNP.R: small script to return SNP in arg2 not found
in arg1
---
src/intersect_SNP.R | 19 +++++++++++++++++++
1 file changed, 19 insertions(+)
create mode 100755 src/intersect_SNP.R
diff --git a/src/intersect_SNP.R b/src/intersect_SNP.R
new file mode 100755
index 00000000..6d2649fe
--- /dev/null
+++ b/src/intersect_SNP.R
@@ -0,0 +1,19 @@
+#!/usr/bin/Rscript
+library("tidyverse")
+
+args <- commandArgs(trailingOnly = TRUE)
+snp_a <- read_delim(args[1], delim = "\t") %>%
+ mutate(cords = paste0(CHROM, POS))
+snp_b <- read_delim(args[2], delim = "\t") %>%
+ mutate(cords = paste0(CHROM, POS))
+
+
+only_b <- snp_b %>%
+ select(cords) %>%
+ setdiff(snp_a %>% select(cords)) %>%
+ pull(cords)
+
+snp_b %>%
+ filter(cords %in% only_b) %>%
+ write_csv(paste0("only_", args[2]))
+
--
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