---
title: "dada2 - taxonomy"
author: Chris
output:
   pdf_document: 
    toc: yes
    toc_depth: 2
    number_sections : yes
---

```{r knitr_init, echo=FALSE, warning=FALSE, cache=TRUE}
library(knitr)
#install.packages("rmdformats")
#library(rmdformats)
library("kableExtra")

## Global options
# The following line is necessary to make sure that 
# everything is not reevaluated each time the file is knit
# Note : in the case of this report it is necessary to leave cache= FALSE

options(max.print="75")
knitr::opts_chunk$set(fig.width=8, 
                      fig.height=6, 
                      eval=TRUE, 
                      cache=TRUE,
                      echo=TRUE,
                      prompt=FALSE,
                      tidy=TRUE,
                      comment=NA,
                      message=FALSE,
                      warning=FALSE)
opts_knit$set(width=85)
```

# load more packages
```{r libraries, message=FALSE}

library("dada2")
library("phyloseq")
library("ggplot2")      # graphics
library("readxl")       # necessary to import the data from Excel file
library("dplyr")        # filter and reformat data frames
library("tibble")       # Needed for converting column to row names

```

# load data
```{r}

getwd()
library(readr)

# asv from dada2 for otu creation
asv<- read_csv("/home/shared/8TB_HDD_02/cnmntgna/GitHub/YellowIsland2023/data/ASVtable.csv")

```

# read in reference files to create fasta format
```{r}

library(seqinr)

# Load your fasta sequences
fasta_seqs <- read.fasta("/home/shared/8TB_HDD_02/cnmntgna/GitHub/YellowIsland2023/data/18S_Euk.fa")

# Load the taxonomy table (assuming tab-delimited format)
taxonomy_table <- read.table("/home/shared/8TB_HDD_02/cnmntgna/GitHub/YellowIsland2023/data/18S_Euk.tax.tsv", sep = "\t", header = TRUE)

# Assuming that the fasta headers correspond to the first column in the taxonomy table
for (i in 1:length(fasta_seqs)) {
    seq_name <- attr(fasta_seqs[[i]], "name") # Get sequence name from fasta
    tax_info <- taxonomy_table[taxonomy_table$ID == seq_name, ] # Match with taxonomy table

    # Replace fasta header with taxonomy information (edit this part based on your table format)
    attr(fasta_seqs[[i]], "name") <- paste0(">", tax_info$taxonomy_path)
}

# Write the updated fasta file
write.fasta(fasta_seqs, names = names(fasta_seqs), file.out = "/home/shared/8TB_HDD_02/cnmntgna/GitHub/YellowIsland2023/data/18S_Euk.fasta")

```

# check the format
```{bash}


```


# taxonomy
```{r}

taxa <- assignTaxonomy(seqtab.nochim, "/home/shared/8TB_HDD_02/cnmntgna/GitHub/YellowIsland2023/data/18S_Euk.fasta", multithread=TRUE, taxLevels=c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus", "Species"))


```