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--helpflag.
gget blat 🎯
Find the genomic location of a nucleotide or amino acid sequence using BLAT.
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
-st --seqtype
'DNA', 'protein', 'translated%20RNA', or 'translated%20DNA'.
Default: 'DNA' for nucleotide sequences; 'protein' for amino acid sequences.
-a --assembly
'human' (hg38) (default), 'mouse' (mm39), 'zebrafinch' (taeGut2),
or any of the species assemblies available here (use short assembly name).
-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
-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
gget blat -a taeGut2 MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR
# Python
gget.blat("MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRIQLPSEKAIFLFVDKTVPQSR", assembly="taeGut2")
→ Returns BLAT results for assembly taeGut2 (zebra finch). In the above example, gget blat automatically detects this sequence as an amino acid sequence and therefore sets the BLAT seqtype to protein.
| genome | query_size | aligned_start | aligned_end | matches | mismatches | %_aligned | ... |
|---|---|---|---|---|---|---|---|
| taeGut2 | 88 | 12 | 88 | 77 | 0 | 87.5 | ... |
More examples
References
If you use gget blat 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
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Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. doi: 10.1101/gr.229202. PMID: 11932250; PMCID: PMC187518.