From 555b0edc37902f67efb6a49c1fb46e13d952f2cc Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 7 Dec 2023 10:30:18 +0100
Subject: [PATCH] kmerclust_load.R: fix columns names
---
src/bin/kmerclust_load.R | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/src/bin/kmerclust_load.R b/src/bin/kmerclust_load.R
index d8afb0b..3185e83 100644
--- a/src/bin/kmerclust_load.R
+++ b/src/bin/kmerclust_load.R
@@ -2,9 +2,15 @@ library(kmerclust)
library(vroom)
args <- commandArgs(trailingOnly = TRUE)
-data <- vroom::vroom(args[2], show_col_types = FALSE)
-format(object.size(data), units = "Mb")
-annotation <- parse_annotation(args[1])
-count <- annotate_counts(annotation, data, args[3]) %>% dplyr::ungroup() %>% dplyr::select(-c("files"))
+count <- vroom::vroom(
+ args[2],
+ show_col_types = FALSE,
+ col_names = c("kmer", "count_m", "count_f"),
+ skip = 1) %>%
+ mutate(
+ count_m = as.integer(count_m),
+ count_f = as.integer(count_f),
+ specie = as.factor(args[3])
+ )
format(object.size(count), units = "Mb")
save(count, file = paste0(args[3], ".Rdata"))
--
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