TabixFile-class: Manipulate tabix indexed tab-delimited files.

In Bioconductor/Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

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)

Bioconductor/Rsamtools documentation built on March 26, 2024, 7:21 a.m.