It is not advisable to download the entire GenBank database to your machine. Equally, it is best to limit the size of a database. Databases that are too large will be slow to query and are more likely to cause memory issues. For example, you may actually make a query that demands more memory than is available on your machine. One solution to instead set multiple restez
paths on your machine.
You can either set up a path for different domains. Or you could download for a single set of domains and then create a database from the same downloaded files using the alt_restez_path
argument.
# a larger database from the same download files in rodents_path db_create(alt_restez_path = rodents_path, max_length = 2000)
Another way to create smaller (i.e., more efficient) databases is to use the accession filter. This is particularly useful if the organisms you are interested in are only a small subset of a much larger domain. For example, you might be only interested in ferns, but since ferns are part of the plant domain (and the smallest domain including ferns is plants), this means you need to download the entire plant domain (638 GB as of release 251!). While restez cannot download just ferns, it can build a database only including ferns, which should be much more efficient for querying than a database of all plants.
To do this, use ncbi_acc_get()
first to obtain a vector of accessions (GenBank IDs). Construct the query as you would when searching on GenBank.
# Specify vector of GenBank accessions: # all ferns in GenBank between with sequence length between 10 to 200000 bases fern_accs <- ncbi_acc_get("Polypodiopsida[ORGN] AND 10:200000[SLEN]")
Next, use the vector of accessions as the accession filter (acc_filter
) for db_create()
.
One more tip: use scan
to speed up the process of building the database. Particularly in cases where the target sequences (here, ferns) are only a small part of the GenBank domain (here, plants), there are many GenBank files that do not contain any target sequences at all. Setting scan
to TRUE
will first check if any of the target accessions are present in the file and if not, skip processing that file further. This can significantly save on time but is only available on machines with zgrep
installed (typically Mac or Unix, but not Windows).
db_create(acc_filter = fern_accs, scan = TRUE)
The db_download
function lists the various possible GenBank domains that can be downloaded. You can work out which GenBank domain a sequence belongs to by its three letter code towards the end of its locus. For example, the top of the record for this sequence indicates it is in the rodent domain.
LOCUS LT548182 456 bp DNA linear ROD 23-NOV-2016 DEFINITION TPA_inf: Cavia porcellus GLNH gene for globin H. ACCESSION LT548182 VERSION LT548182.1
The restez
package database is built with duckdb
.
If you encounter any errors that include the phrase "Server says", then an issue is
likely to have occurred within the database. Please raise such issues with
GitHub. But keep the following
factors in mind:
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