dbDNA: Read and Write DNA Sequences
In heibl/megaptera: MEGAPhylogeny Techniques in R

Read and write DNA Sequences from/to PostgreSQL Database.

dbReadDNA(
  x,
  tab.name,
  taxon,
  regex = TRUE,
  max.bp,
  max.evalue,
  min.identity,
  min.coverage,
  ignore.excluded = TRUE,
  subtree = FALSE,
  blocks = "ignore",
  reliability = 0
)

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

`x`	An object of class `megapteraProj`.
`tab.name`	A vector of mode `"character"` giving the name of the database table. For `dbReadDNA` and when the locus is defined (see `setLocus`) this can be omitted and the data will be read from the species-level (or genus-level) database table.
`taxon`	A vector of mode `"character"` used to choose a subset of available taxa. This can be either one or more taxon names or a regular expression.
`regex`	Logical: if `TRUE`, the string given via `taxon` will be interpreted as a regular expression (see `regex`).
`max.bp`	An integer, only sequences equal or shorter than `max.bp` will be returned.
`max.evalue`	A positive real number giving the highest accepted Expectation value (E-value).
`min.identity`	A real number between 0 and 1, only sequences with a fraction of at least `min.identity` nucleotides that are identical with the reference sequence will be returned.
`min.coverage`	A real number between 0 and 1, only sequences with a fraction of at least `min.coverage` base pairs (compared to the reference sequence) will be returned.
`ignore.excluded`	Logical: if `FALSE`, `dbReadDNA` will also return sequences that are marked in the status field as 'excluded', 'too long', or 'too distant'.
`subtree`	Logical.
`blocks`	A vector of mode `"character"` indicating how to handle alignment blocks: `"split"` causes blocks to be returned as elements of a list. `"concatenate"` means, blocks will be concatendated and returned as a single alignment. In order to get a (potentially unaligned) list of sequences, choose `"ignore"`.
`reliability`	A vector of mode `"numeric"` between 0 and 1 giving the minimum reliability score for each alignment column.
`conn`	A connection object as produced by `dbConnect`.
`dna`	An object of class `DNAbin` to write to the database.
`enforce.binomial`	Logical
`status`	A vector of mode `"character"` to be written to the status field of the PostgreSQL table.