Read and Write DNA Sequences from/to PgSQL Database

Share:

Description

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

Usage

1
2
3
4
5
6
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'.

Author(s)

Christoph Heibl