#!/usr/bin/env Rscript

rm(list = ls())

## ------------------------------------------------------------------------

require("optparse")

## ------------------------------------------------------------------------
suppressPackageStartupMessages(library("optparse"))


## ------------------------------------------------------------------------

prepare_faa_fna_PathoFact_orf <- function(aa_file_path = NULL, # aa_file_path = "~/Desktop/03.chicken.faa" 
                                          fasta_file_path = NULL, # fasta_file_path = "~/Desktop/01.chicken.fasta"
                                          output_dir = "~/Desktop/",
                                          length_fil = 1000,
                                          pat = "[[:space:]].*",
                                          sample_name = "Sample"){
  
  #######-------------------------- Loading required Packges
  require(Biostrings)
  require(tidyverse)
  require(Biostrings)
  
  #######-------------------------- Read faa
  
  aa_file_path %>% 
    Biostrings::readAAStringSet() -> sequences #https://support.bioconductor.org/p/87210/
  
  #######-------------------------- Simplify headers
  
  names(sequences) <- sub(pattern = pat, "", names(sequences))  # https://stackoverflow.com/questions/9319242/remove-everything-after-space-in-string
  
  #######-------------------------- get number of sequences
  
  names(sequences) %>% length() -> num_faa_seq
  
  #######--------------------------
  
  # sequences[width(sequences) >= length_fil,] -> sequences
  
  #######-------------------------- Read contigs fna
  
  fasta_file_path %>% 
    Biostrings::readDNAStringSet() -> fna_contigs
  
  names(fna_contigs) %>% length() -> num_fna_contigs
  
  #######-------------------------- Filter contigs fna
  
  fna_contigs[width(fna_contigs) >= length_fil,] -> fna_contigs
  
  names(fna_contigs) %>% length() -> num_fna_contigs_filt
  
  #######-------------------------- Get contigs header
  
  data.frame(names(fna_contigs)) -> df_fasta 
  rownames(df_fasta) <- NULL
  
  #######-------------------------- Get faa header
  
  data.frame(names(sequences)) -> df 
  rownames(df) <- NULL
  
  #######-------------------------- Simplify header faa and filter names based on contig kept after length filtering

  df %>% 
    mutate(CONTIG = sub("(.*?_.*?)_.*", "\\1", names.sequences.)) %>% 
    dplyr::rename("ORF" = "names.sequences.") %>% 
    rownames_to_column("id") %>% 
    select(CONTIG, ORF) %>% 
    filter(CONTIG %in% df_fasta$names.fna_contigs.) -> df
  
  #######--------------------------
  # fna_contigs[df$CONTIG]  %>% 
  fna_contigs %>% 
    Biostrings::writeXStringSet(paste0(output_dir,"/", sample_name, ".fna"), append=FALSE,
                                compress=FALSE, compression_level=NA, format="fasta")

  
  sequences[df$ORF]  %>% 
    Biostrings::writeXStringSet(paste0(output_dir,"/", sample_name, ".faa"), append=FALSE,
                                compress=FALSE, compression_level=NA, format="fasta")
  
  df %>% 
    add_count(CONTIG) %>% 
    distinct(CONTIG, .keep_all = TRUE) %>% 
    arrange(-n) %>% 
    write_tsv(paste0(output_dir,"/", sample_name, "_report.tsv"))
  
  colnames(df) <- NULL
  
  write_tsv(x = df , 
            col_names = FALSE,
            file = paste0(output_dir,"/", sample_name, ".contig"))
  
  #######--------------------------
  
  # system2("gsed ",
  #         args = c("-i ",paste(c(  's/\*//g' ))),
  #         args = c(" ",paste0(output_dir,"/orf.faa")),
  #         
  #         )
  
  system2("gsed",
          args = c("-i 's/*//g' ", paste0(output_dir,"/", sample_name, ".faa"))
  )
  
}



# prepare_faa_PathoFact_orf(aa_file_path = "~/Desktop/03.SqueezeHuman.faa",
# fasta_file_path = "~/Desktop/01.SqueezeHuman.fasta",
#                           length_fil = 10000)


## ------------------------------------------------------------------------

option_list = list(
  make_option(c("-f", "--aa_file_path"), type="character", default = NULL, 
              help="Path of the input aminoacid fasta of the orfs", metavar="character"),
  
  make_option(c("-g", "--contig_fasta_file_path"), type="character", default = NULL, 
              help="Path of the input contig fasta file", metavar="character"),
  
  make_option(c("-o","--output_dir"), type="character", default = "~/Desktop/", 
              help="Name of the output directory -  created before running the analysis", metavar="character"),
  
  make_option(c("-s","--sample_name"), type="character", default = "Sample", 
              help="sample_name for the output files", metavar="character"),
  
  make_option(c("-l","--length_fil"), type="numeric", default= 2000, 
              help="Length filtering of contig fasta file", metavar="character"),
  
  make_option(c("--pat"), type="character", default= "[[:space:]].*", 
              help="Default regex pattern for faa header cleangin", metavar="character")
)

opt_parser = OptionParser(option_list = option_list);
opt = parse_args(opt_parser)

## ------------------------------------------------------------------------
# parse_args(opt_parser, args = c("--help"))

## ------------------------------------------------------------------------
# 
# prepare_faa_fna_PathoFact_orf(aa_file_path = "~/Desktop/03.chicken.faa",
#                               fasta_file_path = "~/Desktop/01.chicken.fasta",
#                               sample_name = "chicken1_l1000")

prepare_faa_fna_PathoFact_orf(aa_file_path = opt$aa_file_path,
                              fasta_file_path = opt$contig_fasta_file_path,
                              output_dir = opt$output_dir,
                              length_fil = opt$length_fil,
                              pat = opt$pat,
                              sample_name = opt$sample_name)

## ------------------------------------------------------------------------


print(sessionInfo())

## ------------------------------------------------------------------------

print(Sys.time())

## ------------------------------------------------------------------------