ATB_ESGEM_orgs.Rmd

---
title: "Extract AMRfinderplus results for all ESGEM-AMR organisms"
output: html_document
date: "2024-10-24"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(dev = 'png', echo = TRUE, message = FALSE, warning = FALSE,
                      cache = FALSE, fig.align = 'center')
knitr::opts_knit$set(root.dir = getwd())

# Data wrangling
library(tidyverse)
library(dplyr)
source("AllTheBacteria_functions.R")
```

# set path to file of AMRFinderPlus from AllTheBacteria, downlaoded from https://osf.io/zgexh (0.5GB)
``` {r}
ATB_amrfp <- "AMRFP_results.tsv.gz"

```


# extract AMRfp data for a given species
``` {r}
# for a given species:
# extract amrfp results
# report number of rows, number of samples
# write out file
getAMRfp <- function(species) {
  amrfp <- atb_amrfp_filter_by_taxa(user_taxa=species, atb_armfp_results_path=ATB_amrfp)
  write_tsv(amrfp, file=paste0("AllTheBacteria/ATB_",species,"_AFP.tsv.gz"))
  as.data.frame(paste(species, dim(amrfp)[1], length(unique(amrfp$Name)))) %>%
    write_tsv(file=paste0("AllTheBacteria/ATB_",species,"_AFP_info.tsv"), col_names = F)
}
```

``` {r}
getAMRfp("Enterococcus")
```

``` {r}
getAMRfp("Enterobacter")
```

``` {r}
getAMRfp("Staphylococcus")
```

``` {r}
getAMRfp("Acinetobacter baumannii")
```

``` {r}
getAMRfp("Serratia")
```

``` {r}
getAMRfp("Neisseria gonorrhoeae")
getAMRfp("Streptococcus")
```

``` {r}
getAMRfp("Campylobacter")
getAMRfp("Haemophilus influenzae")
```

``` {r}
getAMRfp("Achromobacter")
getAMRfp("Aeromonas")
getAMRfp("Bordetella")
getAMRfp("Brucella")
getAMRfp("Burkholderia cepacia")
getAMRfp("Burkholderia pseudomallei")
```

``` {r}
getAMRfp("Chryseobacterium")
getAMRfp("Corynebacterium diphtheriae")
getAMRfp("Chryseobacterium")
getAMRfp("Edwardsiella")
getAMRfp("Legionella")
getAMRfp("Listeria")
```

``` {r}
getAMRfp("Mycoplasma")
getAMRfp("Ureaplasma")
getAMRfp("Neisseria meningitidis")
```

``` {r}
getAMRfp("Pasteurella")
getAMRfp("Proteus mirabilis")
getAMRfp("Shewanella")
getAMRfp("Stenotrophomonas")
```

``` {r}
getAMRfp("Treponema")
getAMRfp("Vibrio")
```

``` {r}
getAMRfp("Yersinia")
```

``` {r}
getAMRfp("Burkholderia mallei") # GTDB has mallei rather than pseudomallei
```

``` {r}
getAMRfp("Clostridioides difficile")
```

``` {r}
getAMRfp("Mycobacterium tuberculosis")
```

``` {r}
getAMRfp("Pseudomonas aeruginosa")
getAMRfp("Klebsiella pneumoniae")
getAMRfp("Klebsiella quasipneumoniae")
getAMRfp("Klebsiella variicola")
```

``` {r}
getAMRfp("Escherichia coli")
```

``` {r}
getAMRfp("Salmonella")
```

``` {r}
read_tsv("AllTheBacteria/ATB_Salmonella_AFP.tsv.gz") %>% 
  filter(`Element type`=="AMR") %>%
  select(Name, `Gene symbol`, `Hierarchy node`, `Element type`, `Element subtype`, Class, Subclass, `% Coverage of reference sequence`, `% Identity to reference sequence`, `Accession of closest sequence`, Species) %>% 
  write_tsv("AllTheBacteria/ATB_Salmonella_AFP.tsv.gz")
```

``` {r}
read_tsv("AllTheBacteria/ATB_Escherichia coli_AFP.tsv.gz") %>% 
  filter(`Element type`=="AMR") %>%
  select(Name, `Gene symbol`, `Hierarchy node`, `Element type`, `Element subtype`, Class, Subclass, `% Coverage of reference sequence`, `% Identity to reference sequence`, `Accession of closest sequence`, Species) %>% 
  write_tsv("AllTheBacteria/ATB_Escherichia coli_AFP.tsv.gz")
```



# get sample info for existing files

``` {r}
# for a given species:
# read in amrfp results
# report number of rows, number of samples
# write out file
getAMRfpinfo <- function(filepath) {
  amrfp <- read_tsv(filepath)
  infofile <- gsub("AFP.tsv.gz", "AFP_info.tsv", filepath)
  species <- gsub("_AFP.tsv.gz", "", filepath)
  species <- gsub("AllTheBacteria/ATB_","",species)
  as.data.frame(paste(species, dim(amrfp)[1], length(unique(amrfp$Name)))) %>%
    write_tsv(file=infofile, col_names = F)
}
```