Last data update: 2014.03.03
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R: Read and Write DNA Sequences from/to PgSQL Database
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 .
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tab.name |
a character string giving the name of the database table (gene).
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taxon |
a character string giving the name of the taxon.
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regex |
logical: if TRUE , the string given via taxon will be interpreted as a regular expression (see regex ).
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seqs |
an object of class DNAbin to write to the database.
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enforce.binomial |
Logical.
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max.bp |
an integer, only sequences shorter equal or shorter than max.bp will be returned.
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max.dist |
an integer, only sequences equally or less distant to the benchmark than max.dist will be returned.
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status |
a character string to be written to the status field of the PgSQG table.
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ignore.excluded |
logical: if TRUE , dbReadDNA will return also sequences that are marked in the status field as 'excluded', 'too long', or 'too distant'.
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Author(s)
Christoph Heibl
Results
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