bb_create_blast_db - ampinzonv/BB3 GitHub Wiki

Function: bb_create_blast_db

Create a BLAST database from a FASTA file using makeblastdb.

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🔍 Description

This function generates a BLAST database from a given FASTA file. It automatically detects whether the sequences are nucleotide or protein and uses that to configure makeblastdb.

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📥 Input

• A FASTA file with nucleotide or protein sequences.

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📤 Output

• A set of files forming a BLAST database (e.g., .nsq, .nin, .nhr or .psq, .pin, .phr).

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🧪 Examples

Create a nucleotide database:

bb_create_blast_db --input genome.fasta

Create a protein database in a custom directory:

bb_create_blast_db --input proteins.fasta --outdir blastdb/ --db_name mydb

Dry run (show command only):

bb_create_blast_db --input sequences.fasta --dry_run

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⚙️ Usage

bb_create_blast_db --input FILE [--outdir DIR] [--db_name NAME] [--title TITLE] [--dry_run] [--quiet] [--force]

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🧵 Options

Option	Description
--input FILE	Input FASTA file (required)
--outdir DIR	Output directory (default: current directory)
--db_name NAME	Name of the BLAST database (default: derived from input file name)
--title TITLE	Human-readable title (default: derived from input)
--dry_run	Print the command instead of executing it
--quiet	Suppress informational messages
--force	Overwrite existing database files

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📌 Notes

• The function uses bb_guess_sequence_type to auto-detect if the database is nucleotide or protein.
• Compatible with downstream functions like bb_run_blast.