TabixFile {Rsamtools} | R Documentation

## Manipulate tabix indexed tab-delimited files.

### Description

Use `TabixFile()` to create a reference to a Tabix file (and its index). Once opened, the reference remains open across calls to methods, avoiding costly index re-loading.

`TabixFileList()` provides a convenient way of managing a list of `TabixFile` instances.

### Usage

    ## Constructors

    TabixFile(file, index = paste(file, "tbi", sep="."), ...,
        yieldSize=NA_integer_)
    TabixFileList(...)

    ## Opening / closing

    ## S3 method for class 'TabixFile'
    open(con, ...)
    ## S3 method for class 'TabixFile'
    close(con, ...)

    ## accessors; also path(), index(), yieldSize()

    ## S4 method for signature 'TabixFile'
    isOpen(con, rw="")

    ## actions

    ## S4 method for signature 'TabixFile'
    seqnamesTabix(file, ...)
    ## S4 method for signature 'TabixFile'
    headerTabix(file, ...)
    ## S4 method for signature 'TabixFile,GRanges'
    scanTabix(file, ..., param)
    ## S4 method for signature 'TabixFile,IntegerRangesList'
    scanTabix(file, ..., param)
    ## S4 method for signature 'TabixFile,missing'
    scanTabix(file, ..., param)
    ## S4 method for signature 'character,ANY'
    scanTabix(file, ..., param)
    ## S4 method for signature 'character,missing'
    scanTabix(file, ..., param)

    countTabix(file, ...)

### Arguments

`con` | An instance of `TabixFile`.
`file` | For TabixFile(), A character(1) vector to the tabix file path; can be remote (http://, ftp://). For `countTabix`, a character(1) or `TabixFile` instance. For others, a `TabixFile` instance.
`index` | A character(1) vector of the tabix file index.
`yieldSize` | Number of records to yield each time the file is read from using `scanTabix`. Only valid when `param` is unspecified. `yieldSize` does not alter existing yield sizes, include `NA`, when creating a `TabixFileList` from `TabixFile` instances.
`param` | An instance of GRanges or IntegerRangesList, used to select which records to scan.
`...` | Additional arguments. For `TabixFileList`, this can include `file`, `index`, and `yieldSize` arguments. The `file` can be a single character vector of paths to tabix files (and optionally a similarly lengthed vector of `index`), or several instances of `TabixFile` objects. The arguments can also include `yieldSize`, applied to all elements of the list.
`rw` | character() indicating mode of file; not used for `TabixFile`.

### Objects from the Class

Objects are created by calls of the form `TabixFile()`.

### Fields

The `TabixFile` class inherits fields from the `RsamtoolsFile` class.

### Functions and methods

`TabixFileList` inherits methods from `RsamtoolsFileList` and `SimpleList`.

Opening / closing:

open.TabixFile

  Opens the (local or remote) `path` and `index`. Returns a `TabixFile` instance. `yieldSize` determines the number of records parsed during each call to `scanTabix`; `NA` indicates that all records are to be parsed.

close.TabixFile

  Closes the `TabixFile` `con`; returning (invisibly) the updated `TabixFile`. The instance may be re-opened with `open.TabixFile`.

Accessors:

path

  Returns a character(1) vector of the tabix path name.

index

  Returns a character(1) vector of tabix index name.

yieldSize, yieldSize<-

  Return or set an integer(1) vector indicating yield size.

Methods:

seqnamesTabix

  Visit the path in `path(file)`, returning the sequence names present in the file.

headerTabix

  Visit the path in `path(file)`, returning the sequence names, column indicies used to sort the file, the number of lines skipped while indexing, the comment character used while indexing, and the header (preceeded by comment character, at start of file) lines.

countTabix

  Return the number of records in each range of `param`, or the count of all records in the file (when `param` is missing).

scanTabix

  For `signature(file="TabixFile")`, Visit the path in `path(file)`, returning the result of `scanTabix` applied to the specified path. For `signature(file="character")`, call the corresponding method after coercing `file` to `TabixFile`.

indexTabix

  This method operates on file paths, rather than `TabixFile` objects, to index tab-separated files. See `indexTabix`.

show

  Compactly display the object.

### Author(s)

Martin Morgan

### Examples

    fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools",
                      mustWork=TRUE)
    tbx <- TabixFile(fl)

    param <- GRanges(c("chr1", "chr2"), IRanges(c(1, 1), width=100000))
    countTabix(tbx)
    countTabix(tbx, param=param)
    res <- scanTabix(tbx, param=param)
    sapply(res, length)
    res[["chr1:1-100000"]][1:2]

    ## parse to list of data.frame's
    dff <- Map(function(elt) {
        read.csv(textConnection(elt), sep="\t", header=FALSE)
    }, res)
    dff[["chr1:1-100000"]][1:5,1:8]

    ## parse 100 records at a time
    length(scanTabix(tbx)[[1]]) # total number of records
    tbx <- open(TabixFile(fl, yieldSize=100))
    while(length(res <- scanTabix(tbx)[[1]]))
       cat("records read:", length(res), "\n")
    close(tbx)

[Package Rsamtools version 2.2.3 Index]