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megaptera (version 1.0-0)

io.dna.db: Read and Write DNA Sequences from/to PgSQL Database

Description

DNA sequence alignment can be read from and written to a (alreay existing) pgSQL database table.

Usage

dbReadDNA(conn, tab.name, taxon, regex = FALSE, max.bp, max.dist, enforce.binomial = FALSE, ignore.excluded = TRUE)


dbWriteDNA(conn, tab.name, seqs, enforce.binomial = TRUE, status)

Arguments

conn
a connection object as produced by dbConnect.
tab.name
a character string giving the name of the database table (gene).
taxon
a character string giving the name of the taxon.
regex
logical: if TRUE, the string given via taxon will be interpreted as a regular expression (see regex).
seqs
an object of class DNAbin to write to the database.
enforce.binomial
Logical.
max.bp
an integer, only sequences shorter equal or shorter than max.bp will be returned.
max.dist
an integer, only sequences equally or less distant to the benchmark than max.dist will be returned.
status
a character string to be written to the status field of the PgSQG table.
ignore.excluded
logical: if TRUE, dbReadDNA will return also sequences that are marked in the status field as 'excluded', 'too long', or 'too distant'.