SearchDB: Obtain Specific Sequences from a Database

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

Description

Returns the set of sequences meeting the search criteria.

Usage

SearchDB(dbFile,
         tblName = "Seqs",
         identifier = "",
         type = "XStringSet",
         limit = -1,
         replaceChar = NA,
         nameBy = "row_names",
         orderBy = "row_names",
         countOnly = FALSE,
         removeGaps = "none",
         quality = "Phred",
         clause = "",
         processors = 1,
         verbose = TRUE)

Arguments

dbFile	A SQLite connection object or a character string specifying the path to the database file.
tblName	Character string specifying the table where the sequences are located.
identifier	Optional character string used to narrow the search results to those matching a specific identifier. If "" (the default) then all identifiers are selected.
type	The type of XStringSet (sequences) to return. This should be (an unambiguous abbreviation of) one of "XStringSet", "DNAStringSet", "RNAStringSet", "AAStringSet", "BStringSet", "QualityScaledXStringSet", "QualityScaledDNAStringSet", "QualityScaledRNAStringSet", "QualityScaledAAStringSet", or "QualityScaledBStringSet". If type is "XStringSet" or "QualityScaledXStringSet" then an attempt is made to guess the type of sequences based on their composition.
limit	Number of results to display. The default (-1) does not limit the number of results.
replaceChar	Optional character used to replace any characters of the sequence that are not present in the XStringSet's alphabet. Not applicable if type=="BStringSet". The default (NA) results in an error if an incompatible character exist. (See details section below.)
nameBy	Character string giving the column name for naming the XStringSet.
orderBy	Character string giving the column name for sorting the results. Defaults to the order of entries in the database. Optionally can be followed by " ASC" or " DESC" to specify ascending (the default) or descending order.
countOnly	Logical specifying whether to return only the number of sequences.
removeGaps	Determines how gaps ("-" or "." characters) are removed in the sequences. This should be (an unambiguous abbreviation of) one of "none", "all" or "common".
clause	An optional character string to append to the query as part of a “where clause”.
quality	The type of quality object to return if type is a QualityScaledXStringSet. This should be (an unambiguous abbreviation of) one of "Phred", "Solexa", or "Illumina". Note that recent versions of Illumina software provide "Phred" formatted quality scores.
processors	The number of processors to use, or NULL to automatically detect and use all available processors.
verbose	Logical indicating whether to display queries as they are sent to the database.

Details

If type is "DNAStringSet" then all U's are converted to T's before creating the DNAStringSet, and vise-versa if type is "RNAStringSet". All remaining characters not in the XStringSet's alphabet are converted to replaceChar or removed if replaceChar is "". Note that if replaceChar is NA (the default), it will result in an error when an unexpected character is found. Quality information is interpreted as PredQuality scores.

Value

An XStringSet or QualityScaledXStringSet with the sequences that meet the specified criteria. The names of the object correspond to the value in the nameBy column of the database.

Author(s)

Erik Wright [e-mail]

References

ES Wright (2016) "Using DECIPHER v2.0 to Analyze Big Biological Sequence Data in R". The R Journal, 8(1), 352-359.

See Also

Seqs2DB, DB2Seqs

Examples

db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
# get all sequences in the default table:
dna <- SearchDB(db)
# select a random sequence:
dna <- SearchDB(db, orderBy="random()", limit=1)
# remove gaps from "Mycobacterium" sequences:
dna <- SearchDB(db, identifier="Mycobacterium", removeGaps="all")
# provide a more complex query:
dna <- SearchDB(db, nameBy="description", orderBy="bases", removeGaps="common",
                clause="nonbases is 0")

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.