bowtie2-build: Interface to bowtie2-build of bowtie2-2.2.3

In Rbowtie2: An R Wrapper for Bowtie2 and AdapterRemoval

Description

This function can be use to call wrapped bowtie2-build binary

Usage

bowtie2_build(references, bt2Index, ..., overwrite = FALSE)

Arguments

references	Character vector. The path to the files containing the references for which to build a bowtie index.
bt2Index	Character scalar. Write bowtie2 index data to files with this prefix: 'dir/basename'. If the files with path like 'dir/basename.*.bt2' already exists, the function function will cast an error, unless argument overwrite is TRUE.
...	Additional arguments to be passed on to the binaries. See below for details.
overwrite	Logical. Force overwriting of existing files if setting TRUE.

Details

All additional arguments in ... are interpreted as additional parameters to be passed on to bowtie2_build. All of them should be Character or Numeric scalar. You can put all aditional arguments in one Character(e.g. "–threads 8 –quiet") with white space splited just like command line, or put them in different Character(e.g. "–threads","8","–quiet"). See the output of bowtie2_build_usage() for details about available parameters.

Value

An invisible Integer of call status. The value is 0 when there is not any mistakes Otherwise the value is non-zero.

Author(s)

Zheng Wei

References

Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.

Examples

td <- tempdir()
## Building a bowtie2 index
refs <- dir(system.file(package="Rbowtie2", "extdata", "bt2","refs"),
full=TRUE)
cmdout<-bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
"--threads 4 --quiet",overwrite=TRUE);cmdout
## Use additional arguments in another way
cmdout<-bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
"--threads",4,"--quiet",overwrite=TRUE);cmdout
## The function will print the output
## during the process without "--quiet" argument.
cmdout<-bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
overwrite=TRUE);cmdout

Example output

arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only
sh: 1: /usr/lib/R/site-library/Rbowtie2/bowtie2-build-s: Permission denied
Warning message:
In system(call, intern = TRUE, show.output.on.console = TRUE) :
  running command ''/usr/lib/R/site-library/Rbowtie2/bowtie2-build-s' --threads 4 --quiet /usr/lib/R/site-library/Rbowtie2/extdata/bt2/refs/lambda_virus.fa /work/tmp/tmp/RtmpdUaAjX/lambda_virus' had status 126
character(0)
attr(,"status")
[1] 126
arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only
sh: 1: /usr/lib/R/site-library/Rbowtie2/bowtie2-build-s: Permission denied
Warning message:
In system(call, intern = TRUE, show.output.on.console = TRUE) :
  running command ''/usr/lib/R/site-library/Rbowtie2/bowtie2-build-s' --threads 4 --quiet /usr/lib/R/site-library/Rbowtie2/extdata/bt2/refs/lambda_virus.fa /work/tmp/tmp/RtmpdUaAjX/lambda_virus' had status 126
character(0)
attr(,"status")
[1] 126
arguments 'show.output.on.console', 'minimized' and 'invisible' are for Windows only
sh: 1: /usr/lib/R/site-library/Rbowtie2/bowtie2-build-s: Permission denied
Warning message:
In system(call, intern = TRUE, show.output.on.console = TRUE) :
  running command ''/usr/lib/R/site-library/Rbowtie2/bowtie2-build-s' /usr/lib/R/site-library/Rbowtie2/extdata/bt2/refs/lambda_virus.fa /work/tmp/tmp/RtmpdUaAjX/lambda_virus' had status 126
character(0)
attr(,"status")
[1] 126

Rbowtie2 documentation built on Nov. 8, 2020, 5:35 p.m.