DB2Seqs {DECIPHER} | R Documentation

## Export Database Sequences to a FASTA or FASTQ File

### Description

Exports a database containing sequences to a FASTA or FASTQ formatted file of sequence records.

### Usage

    DB2Seqs(file,
             dbFile,
             tblName = "Seqs",
             identifier = "",
             type = "BStringSet",
             limit = -1,
             replaceChar = NA,
             nameBy = "description",
             orderBy = "row_names",
             removeGaps = "none",
             append = FALSE,
             width = 80,
             compress = FALSE,
             chunkSize = 1e5,
             sep = "::",
             clause = "",
             verbose = TRUE)

### Arguments

`file` | Character string giving the location where the file should be written.
`dbFile` | A SQLite connection object or a character string specifying the path to the database file.
`tblName` | Character string specifying the table in which to extract the data.
`identifier` | Optional character string used to narrow the search results to those matching a specific identifier. If "" then all identifiers are selected.
`type` | The type of `XStringSet` (sequences) to export to a FASTA formatted file or `QualityScaledXStringSet` to export to a FASTQ formatted file. This should be (an unambiguous abbreviation of) one of `"DNAStringSet"`, `"RNAStringSet"`, `"AAStringSet"`, `"BStringSet"`, `"QualityScaledDNAStringSet"`, `"QualityScaledRNAStringSet"`, `"QualityScaledAAStringSet"`, or `"QualityScaledBStringSet"`. (See details section below.)
`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(s) for identifying each sequence record. If more than one column name is provided, the information in each column is concatenated, separated by `sep`, in the order specified.
`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.
`removeGaps` | Determines how gaps ("-" or "." characters) are removed in the sequences. This should be (an unambiguous abbreviation of) one of `"none"`, `"all"` or `"common"`.
`append` | Logical indicating whether to append the output to the existing `file`.
`width` | Integer specifying the maximum number of characters per line of sequence. Not applicable when exporting to a FASTQ formatted file.
`compress` | Logical specifying whether to compress the output file using gzip compression.
`chunkSize` | Number of sequences to write to the `file` at a time. Cannot be less than the total number of sequences if `removeGaps` is `"common"`.
`sep` | Character string providing the separator between fields in each sequence's name, by default pairs of colons (“::”).
`clause` | An optional character string to append to the query as part of a “where clause”.
`verbose` | Logical indicating whether to display status.

### Details

Sequences are exported into either a FASTA or FASTQ file as determined by the `type` of sequences. If `type` is an `XStringSet` then sequences are exported to FASTA format. Quality information for `QualityScaledXStringSet`s are interpreted as `PredQuality` scores before export to FASTQ format.

If `type` is `"BStringSet"` (the default) then sequences are exported to a FASTA file exactly the same as they were when imported. If `type` is `"DNAStringSet"` then all U's are converted to T's before export, 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.

### Value

Writes a FASTA or FASTQ formatted file containing the sequence records in the database.

Returns the number of sequence records written to the `file`.

### Author(s)

Erik Wright eswright@pitt.edu

### References

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

### Examples

    db <- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
    tf <- tempfile()
    DB2Seqs(tf, db, limit=10)
    file.show(tf) # press 'q' to exit
    unlink(tf)

[Package DECIPHER version 2.12.0 Index]