stepB: Step B: Search and Download Sequences
In heibl/megaptera: MEGAPhylogeny Techniques in R

Description Usage Arguments Details Value References See Also

For any given project (see megapteraProj), this step searches the Nucleotide database on GenBank, downloads all sequences and stores them in a postgreSQL database table.

1	stepB(x, update.seqs = "no")

x

An object of class megapteraProj.

update.seqs

A character string determining the behaviour of stepB when it is run repeatedly on the same locus/taxon combination: "no" means that only sequences that have been made available on GenBank since the last execution stepB will be downloaded; "all" means the database table with all sequences will be removed and all sequences will be downloaded de novo. Naturely, this option has no effect if stepB is called for the first time.

All accessions are stored under their species name as appearing in the organism field at GenBank, but information about infrageneric ranks is stripped off the taxon names before they are stored in the database.

None. stepB is called for its side effects: (1) strings of DNA sequences with attribute data are stored in a pgSQL database; (2) a log file is written to the current working directory.

http://www.ncbi.nlm.nih.gov/books/NBK25501/

megapteraProj; stepA for the preceeding and stepC for the subsequent step; stepBX for the addition of external sequences to the database.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.