bb_run_blast - ampinzonv/BB3 GitHub Wiki

Function: `bb_run_blast`

Run a BLAST search using a query file and an existing database. Supports automatic detection of query type and validation of compatible BLAST types.

🧬 Description

This function runs a BLAST search (e.g., blastn, blastp) using a provided query FASTA file and a BLAST-formatted database. It validates compatibility between the query type and the database type, supports multi-threading, and provides useful feedback and error handling.

🧾 Usage

bb_run_blast --input FILE --db PREFIX --blast_type TYPE [--outfile FILE|DIR] [--processors N] [--strict] [--quiet] [--force]

🧵 Options

Option	Description
`--input FILE`	Query FASTA file (required)
`--db PREFIX`	Prefix of the BLAST database (required)
`--blast_type`	One of `blastn`, `blastp`, `blastx`, `tblastn`, `tblastx` (required)
`--outfile`	Output file or directory (default: `<query>.blastout`)
`--processors`	Number of CPU threads (default: 1)
`--strict`	Return an error if no hits are found
`--quiet`	Suppress informational messages
`--force`	Overwrite output file if it exists

💡 Notes

The input and database types are auto-detected using bb_guess_sequence_type and bb_guess_db_type.
Output format is fixed as BLAST tabular (outfmt 6) with 14 columns.

🧪 Example

bb_run_blast --input query.fasta --db mydb --blast_type blastn --outfile results/blast.out --processors 4