make_BLAST_DB {DBTC}

Make a BLAST Database

Description

This function takes a fasta file (in MACER format) and establishes a database upon which a BLAST search can be completed.

Usage

make_BLAST_DB(
  fileLoc = NULL,
  makeblastdbPath = "makeblastdb",
  taxaDBLoc = NULL,
  dbName = NULL,
  minLen = 100,
  verbose = TRUE
)

Arguments

fileLoc

The location of a file in a directory where all fasta files will be used to construct a BLASTable database (Default NULL).

makeblastdbPath

The local path for the blast+ makeblastdbPath program (Default 'makeblastdb').

taxaDBLoc

The location of the NCBI taxonomic data base (Default NULL; for accessionTaxa.sql see the main DBTC page for details).

dbName

A short 6-8 alpha character name used when building a database (Default NULL).

minLen

The minimum sequence length used to construct the BLAST database (Default 100).

verbose

If set to TRUE then there will be output to the R console, if FALSE then this reporting data is suppressed (Default TRUE).

Details

The user inputs the location of a file in a directory that contains a properly formatted fasta file which can be used to construct a BLASTable database. The NCBI blast+ program, makeblastdb and the NCBI taxonomic database (accessionTaxa.sql) are required to run this script (see readme instructions for details).

The examples are present to display the syntax for the function. These examples are not run because there are files required to run the functions, in some cases multiple files are necessary and some of these are quite large. To get specific examples please see https://github.com/rgyoung6/DBTCShinyTutorial/blob/main/README.md

Value

The output from this function includes a folder with the BLAST database named according to the submitted dbName

Note

WARNING - NO WHITESPACE!

When running DBTC functions the paths for the files selected cannot have white space! File folder locations should be as short as possible (close to the root as some functions do not process long naming conventions.

Also, special characters should be avoided (including question mark, number sign, exclamation mark). It is recommended that dashes be used for separations in naming conventions while retaining underscores for use as information delimiters (this is how DBTC functions use underscore).

There are several key character strings used in the DBTC pipeline, the presence of these strings in file or folder names will cause errors when running DBTC functions.

The following strings are those used in DBTC and should not be used in file or folder naming: - _BLAST - _combinedDada - _taxaAssign - _taxaAssignCombined - _taxaReduced - _CombineTaxaReduced

Author(s)

Robert G. Young

References

<https://github.com/rgyoung6/DBTC> Young, R. G., Hanner, R. H. (Submitted October 2023). Dada-BLAST-Taxon Assign-Condense Shiny Application (DBTCShiny). Biodiversity Data Journal.

See Also

dada_implement() combine_dada_output() seq_BLAST() taxon_assign() combine_assign_output() reduce_taxa() combine_reduced_output()

Examples

## Not run: 
make_BLAST_DB()
make_BLAST_DB(fileLoc = NULL, makeblastdbPath = "makeblastdb", taxaDBLoc = NULL,
inputFormat = NULL, dbName = NULL, minLen = 100)

## End(Not run)