bb_blast_on_the_fly - ampinzonv/BB3 GitHub Wiki
Function: bb_blast_on_the_fly
Run BLAST directly from two FASTA files without creating a permanent database.
๐ Description
This function performs a BLAST search between two FASTA files without requiring the user to create a database manually. It creates a temporary BLAST database from the subject file, runs the search, and deletes the temporary files afterward.
๐ฅ Input
--query: FASTA file containing the query sequences.--subject: FASTA file containing the subject sequences to search against.
๐ค Output
- Tabular BLAST results (outfmt 6 with 14 columns) printed to STDOUT or saved to a file.
๐งช Examples
Basic usage:
bb_blast_on_the_fly --query query.fasta --subject subject.fasta
Save output:
bb_blast_on_the_fly --query query.fasta --subject subject.fasta --outfile results.tsv
Use 4 CPU threads:
bb_blast_on_the_fly --query query.fasta --subject subject.fasta --processors 4
โ๏ธ Usage
bb_blast_on_the_fly --query FILE --subject FILE [--outfile FILE] [--processors N] [--quiet] [--force]
๐งต Options
| Option | Description |
|---|---|
--query FILE |
Input FASTA file with query sequences (required) |
--subject FILE |
Input FASTA file with subject sequences (required) |
--outfile FILE |
Output file (default: STDOUT) |
--processors N |
Number of CPU threads to use (default: 1) |
--quiet |
Suppress informational messages |
--force |
Overwrite output file if it exists |
๐ Notes
- A temporary BLAST database is created and automatically deleted after the search.
- Requires
makeblastdband appropriate BLAST+ tools (e.g.,blastn,blastp) in$PATH.