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 diamond 💎

Align multiple protein or translated DNA sequences using DIAMOND (DIAMOND is similar to BLAST, but this is a local computation).
Return format: JSON (command-line) or data frame/CSV (Python).

Positional argument
query
Sequences (str or list) or path to FASTA file containing sequences to be aligned against the reference.

Required arguments
-ref --reference
Reference sequences (str or list) or path to FASTA file containing reference sequences.

Optional arguments
-db --diamond_db
Path to save DIAMOND database created from reference (str).
Default: None -> Temporary db file will be deleted after alignment or saved in out if out is provided.

-s --sensitivity
Sensitivity of alignment (str). Default: "very-sensitive".
One of the following: fast, mid-sensitive, sensitive, more-sensitive, very-sensitive, or ultra-sensitive.

-t --threads
Number of threads used (int). Default: 1.

-db --diamond_binary
Path to DIAMOND binary (str). Default: None -> Uses DIAMOND binary installed with gget.

-o --out
Path to the folder to save results in (str), e.g. "path/to/directory". Default: Standard out; temporary files are deleted.

Flags
-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.

Example

# !!! Make sure to list the positional argument first here so it is not added as a reference sequence
gget diamond GGETISAWESQME ELVISISALIVE LQVEFRANKLIN PACHTERLABRQCKS -ref GGETISAWESQMEELVISISALIVELQVEFRANKLIN PACHTERLABRQCKS

# Python
gget.diamond(["GGETISAWESQME", "ELVISISALIVE", "LQVEFRANKLIN", "PACHTERLABRQCKS"], reference=["GGETISAWESQMEELVISISALIVELQVEFRANKLIN", "PACHTERLABRQCKS"])

→ Returns results in JSON (command-line) or data frame/CSV (Python) format:

query_accession	subject_accession	identity_percentage	query_seq_length	subject_seq_length	length	query_start	query_end	subject_start	subject_end	e-value	bit_score
Seq0	Seq0	100	13	37	13	1	13	1	13	2.82e-09	30.8
Seq2	Seq0	100	12	37	12	1	12	26	37	4.35e-08	27.7
Seq3	Seq1	100	15	15	15	1	15	1	15	2.01e-11	36.2

More examples

References

If you use gget diamond 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
Buchfink, B., Xie, C. & Huson, D. Fast and sensitive protein alignment using DIAMOND. Nat Methods 12, 59–60 (2015). https://doi.org/10.1038/nmeth.3176