Add new file

Integron_Prediction/Integron.R

+#!/user/bin/env R
+
+library(tidyverse)
+
+attc <- read.delim(file = snakemake@input[["attc"]])
+attc$ID <- gsub(" ","",attc$ID)
+attc <- attc %>% filter(Vscore <=1)
+attc$attc_prediction <- "attc"
+
+intI <- read.table(file = snakemake@input[["intI"]], quote="\"") %>% select(3,13) %>% filter(V13 <= 1)
+colnames(intI) <- c("ID","E_value")
+intI$intI_prediction <- "intI"
+
+Integrons <- merge(attc, intI, by="ID", all=TRUE) %>% select(1,3,5)
+Integrons <- unique(Integrons)
+Integrons$attc_prediction <- fct_explicit_na(Integrons$attc_prediction, na_level = "-")
+Integrons$intI_prediction <- fct_explicit_na(Integrons$intI_prediction, na_level = "-")
+Integrons$Prediction <- ifelse(Integrons$attc_prediction == "attc" & Integrons$intI_prediction == "intI", "complete",
+                               ifelse(Integrons$attc_prediction == "attc" & Integrons$intI_prediction == "-", "intI_incomplete",
+                                      ifelse(Integrons$attc_prediction == "-" & Integrons$intI_prediction == "intI", "attc_incomplete", "incomplete")))
+
+write.table(Integrons, file = snakemake@output[["Integrons"]], sep="\t", row.names=FALSE, quote=FALSE)