work_gff3_convert-strand-designations.Rmd

---
title: "work_gff3_convert-strand-designations.Rmd"
author: "KA"
email: "kalavatt@fredhutch.org"
output: html_notebook
---

## Get situated
### Set working directory
```{r, results='hide', message=FALSE}
p_local <- "/Users/kalavattam/Dropbox/FHCC"  # KrisMac
# p_local <- "/Users/kalavatt/projects-etc"  # WorkMac
p_wd <- "2022-2023_RRP6-NAB3/results/2023-0215"
setwd(paste(p_local, p_wd, sep = "/"))

rm(p_local, p_wd)
```
<br />

### Load necessary libraries
```{r, results='hide', message=FALSE}
library(rtracklayer)
library(tidyverse)
```
<br />
<br />

## Reverse strand + and - strand designations in "combined_SC_KL.gff3"
```{r}
#  "combined_SC_KL.gff3" was manually copied into the work directory from
#+ "${HOME}/genomes/combined_SC_KL_20S/gff3"
gff3_in <- rtracklayer::import.gff3("combined_SC_KL.gff3")
gff3_in@strand@values %>% head(n = 20)

#  Create an intermediate naming state to faciliate easy conversion of "+" to
#+ "-" and vice versa
intermediate <- ifelse(
    gff3_in@strand@values == "+",
    "change_to_minus",
    ifelse(
        gff3_in@strand@values == "-",
        "change_to_plus",
        "*"
    )
) %>%
    as.data.frame()
colnames(intermediate) <- "intermediate"

#  Create a factor vector of converted strand designations
final <- ifelse(
    intermediate$intermediate == "change_to_minus",
    "-",
    ifelse(
        intermediate$intermediate == "change_to_plus",
        "+",
        "*"
    )
) %>%
    as.factor()

#  Order the factor levels to match the order in the gff3 file
level_order <- c("+", "-", "*")
final <- ordered(final, levels = level_order)

#  Create a variable for the gff3 with converted strand designations to be
#+ written out
gff3_out <- gff3_in
gff3_out@strand@values <- final
gff3_out@strand@values %>% head(n = 20)

rm(intermediate, final, level_order)
```
<br />
<br />

## Write out gff3 with converted strand designations to work directory
```{r}
rtracklayer::export.gff3(gff3_out, "combined_SC_KL.antisense.gff3")
```
<br />