Python arguments are equivalent to long-option arguments (--arg), unless otherwise specified. Flags are True/False arguments in Python. The manual for any gget tool can be called from the command-line using the -h --help flag.

gget blast 💥

BLAST a nucleotide or amino acid sequence to any BLAST database.
Return format: JSON (command-line) or data frame/CSV (Python).

Positional argument
sequence
Nucleotide or amino acid sequence, or path to FASTA or .txt file.

Optional arguments
-p --program
'blastn', 'blastp', 'blastx', 'tblastn', or 'tblastx'.
Default: 'blastn' for nucleotide sequences; 'blastp' for amino acid sequences.

-db --database
'nt', 'nr', 'refseq_rna', 'refseq_protein', 'swissprot', 'pdbaa', or 'pdbnt'.
Default: 'nt' for nucleotide sequences; 'nr' for amino acid sequences.
More info on BLAST databases

-l --limit
Limits number of hits to return. Default: 50.

-e --expect
Defines the expect value cutoff. Default: 10.0.

-o --out
Path to the file the results will be saved in, e.g. path/to/directory/results.csv (or .json). Default: Standard out.
Python: save=True will save the output in the current working directory.

Flags
-lcf --low_comp_filt
Turns on low complexity filter.

-mbo --megablast_off
Turns off MegaBLAST algorithm. Default: MegaBLAST on (blastn only).

-csv --csv
Command-line only. Returns results in CSV format.
Python: Use json=True to return output in JSON format.

-q --quiet
Command-line only. Prevents progress information from being displayed.
Python: Use verbose=False to prevent progress information from being displayed.

wrap_text
Python only. wrap_text=True displays data frame with wrapped text for easy reading (default: False).

Example

gget blast MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR

# Python
gget.blast("MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR")

→ Returns the BLAST result of the sequence of interest. gget blast automatically detects this sequence as an amino acid sequence and therefore sets the BLAST program to blastp with database nr.

BLAST from .fa or .txt file:

gget blast fasta.fa

# Python
gget.blast("fasta.fa")

→ Returns the BLAST results of the first sequence contained in the fasta.fa file.

More examples

References

If you use gget blast in a publication, please cite the following articles:

• Luebbert, L., & Pachter, L. (2023). Efficient querying of genomic reference databases with gget. Bioinformatics. https://doi.org/10.1093/bioinformatics/btac836

• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10. doi: 10.1016/S0022-2836(05)80360-2. PMID: 2231712.