Seqs2DB: Add Sequences from Text File to Database

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

Description

Adds sequences to a database.

Usage

Seqs2DB(seqs,
        type,
        dbFile,
        identifier,
        tblName = "Seqs",
        chunkSize = 1e7,
        replaceTbl = FALSE,
        fields = c(accession = "ACCESSION", rank = "ORGANISM"),
        processors = 1,
        verbose = TRUE,
        ...)

Arguments

seqs	A connection object or a character string specifying the file path to the file containing the sequences, an XStringSet object if type is XStringSet, or a QualityScaledXStringSet object if type is QualityScaledXStringSet. Files compressed with gzip, bzip2, xz, or lzma compression are automatically detected and decompressed during import. Full URL paths (e.g., "http://" or "ftp://") to uncompressed text files or gzip compressed text files can also be used.
type	The type of the sequences (seqs) being imported. This should be (an unambiguous abbreviation of) one of "FASTA", "FASTQ", "GenBank", "XStringSet", or "QualityScaledXStringSet".
dbFile	A SQLite connection object or a character string specifying the path to the database file. If the dbFile does not exist then a new database is created at this location.
identifier	Character string specifying the "id" to give the imported sequences in the database.
tblName	Character string specifying the table in which to add the sequences.
chunkSize	Number of characters to read at a time.
replaceTbl	Logical indicating whether to overwrite the entire table in the database. If FALSE (the default) then the sequences are appended to any already existing in the tblName. If TRUE the entire table is dropped, removing any existing sequences before adding any new sequences.
fields	Named character vector providing the fields to import from a "GenBank" formatted file as text columns in the database (not applicable for other "type"s). The default is to import the "ACCESSION" field as a column named "accession" and the "ORGANISM" field as a column named "rank". Other uppercase fields, such as "LOCUS" or "VERSION", can be specified in similar manner. Note that the "DEFINITION" field is automatically imported as a column named "description" in the database.
processors	The number of processors to use, or NULL to automatically detect and use all available processors.
verbose	Logical indicating whether to display each query as it is sent to the database.
...	Further arguments to be passed directly to Codec for compressing sequence information.

Details

Sequences are imported into the database in chunks of lines specified by chunkSize. The sequences can then be identified by searching the database for the identifier provided. Sequences are added to the database verbatim, so that no sequence information is lost when the sequences are exported from the database. The sequence (record) names are recorded into a column named “description” in the database.

Value

The total number of sequences in the database table is returned after import.

Warning

If replaceTbl is TRUE then any sequences already in the table are overwritten, which is equivalent to dropping the entire table.

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

BrowseDB, SearchDB, DB2Seqs

Examples

gen <- system.file("extdata", "Bacteria_175seqs.gen", package="DECIPHER")
dbConn <- dbConnect(SQLite(), ":memory:")
Seqs2DB(gen, "GenBank", dbConn, "Bacteria")
BrowseDB(dbConn)
dna <- SearchDB(dbConn, nameBy="description")
dbDisconnect(dbConn)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: RSQLite

Reading GenBank file chunk 1

175 total sequences in table Seqs.
Time difference of 0.26 secs

Search Expression:
select description, _Seqs.sequence from Seqs join _Seqs on Seqs.row_names =
_Seqs.row_names where _Seqs.row_names in (select row_names from Seqs)

DNAStringSet of length: 175
Time difference of 0.02 secs

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