download_accessions: Download indexes required for MetaScope ID and MetaBlast...

In compbiomed/MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Download indexes required for MetaScope ID and MetaBlast modules

Description

This is a necessary step for all samples utilizing NCBI and SILVA databases in the MetaScope pipeline. As specified by the user, download_accessions will automatically download the NCBI accessions database, the SILVA taxonomy database, and or the NCBI Blast 16S database and prepare consolidated databases for downstream use with the MetaID and MetaBLAST modules. This package relies on the taxonomizr package.

Usage

download_accessions(
  ind_dir,
  tmp_dir = file.path(ind_dir, "tmp"),
  remove_tmp_dir = TRUE,
  NCBI_accessions_database = TRUE,
  NCBI_accessions_name = "accessionTaxa",
  silva_taxonomy_database = TRUE,
  silva_taxonomy_name = "all_silva_headers",
  blast_16S_database = TRUE,
  blast_16S_name = "16S_ribosomal_RNA"
)

Arguments

ind_dir	Character string. Directory filepath where indices should be saved. Required.
tmp_dir	Character path to directory for storing temp files. (Useful to avoid redownloading) Defaults to file.path(ind_dir, "tmp")
remove_tmp_dir	Delete tmp_dir after downloads are complete? Defaults to TRUE
NCBI_accessions_database	Logical. Download taxonomizr NCBI accessions database? Defaults to TRUE.
NCBI_accessions_name	Character string. Filename (with or without extension) to save taxonomizr NCBI accessions database. Defaults to "accessionTaxa.sql".
silva_taxonomy_database	Logical. Download SILVA taxonomy database? Defaults to TRUE.
silva_taxonomy_name	Character string. Filename (with or without extension) to save SILVA taxonomy database. Defaults to the file supplied with the package, "all_silva_headers.rds".
blast_16S_database	Download NCBI 16S Blast database? Defaults to TRUE.
blast_16S_name	Character string. Filename (without extension) to save SILVA taxonomy database. Defaults to "16S_ribosomal_RNA".

Value

Exports database(s) with names and to location specified by the user.

Examples

## Not run: 
  download_accessions(
    ind_dir = "C:/Users/JohnSmith/Research",
    tmp_dir = file.path(ind_dir, "tmp"),
    remove_tmp_dir = TRUE,
    NCBI_accessions_database = TRUE,
    NCBI_accessions_name = "accessionTaxa.sql",
    silva_taxonomy_database = TRUE,
    silva_taxonomy_name = "all_silva_headers.rds",
    blast_16S_database = TRUE,
    blast_16S_name = "16S_ribosomal_RNA")

## End(Not run)

compbiomed/MetaScope documentation built on Jan. 16, 2025, 10:23 p.m.