stepBX: Step BX: Add External Sequences

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

This step adds external sequences, i.e. sequences that were not retrieved from GenBank with stepB, to the postgreSQL database table "acc_*" (where * is the SQL-compatible name of the locus). Cannot be called before stepB.

Usage

stepBX(x, dna, tag = "user-supplied", overwrite = FALSE)

Arguments

x	an object of class megapteraProj.
dna	a list of class DNAbin.
tag	a character string to tag the sequences in the database table.
overwrite	logical, indicating if existing sequences in the database should be overwritten.

Details

It is important that the names of the sequences in DNA conform to the pattern "Genus_species_ID". The occurance of a underscore inside the strings "Genus", "species", and "ID" is illegal, but letters, numbers and hyphens are allowed.

Value

None. stepBX 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.

Note

The function is under development and the results should always be checked.

Author(s)

Christoph Heibl

See Also

megapteraProj; stepB for the preceeding and stepC for the subsequent step.

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