Package 'Rbowtie2'

Make system call for binaries

Description

Function that makes a system call for the bowtie binaries. Note it is not intended to be used outside of the package.

Usage

.callbinary(
  bin1,
  args1,
  op = NULL,
  bin2 = NULL,
  args2 = NULL,
  path = NULL,
  lang = NULL
)

Arguments

bin1	Character. The binary used for the system call.
args1	Character. The arguments to pass to the binary.
op	Character. Optional: Generally used if needed to pipe to another binary.
bin2	Character. Optional: Another binary that can be used in the system call. Generally the output of the first binary is piped to the this binary.
args2	Character Optional: The arguments to pass to the second binary.
path	Character Optional: If passed to function, returns the path. Needed for Rsamtools to convert from sam to bam.
lang	Character. The interpreter used to execute the binary

Value

The output of the system call or the path provided.

Author(s)

Zheng Wei

---

Print available arguments for adapterremoval

Description

Print available arguments for adapterremoval. Note that some arguments to the adapterremoval are invalid if they are already handled as explicit function arguments.

Usage

adapterremoval_usage()

Value

AdapterRemoval available arguments and their usage.

Author(s)

Zheng Wei

References

Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88.

Examples

adapterremoval_usage()

---

Print version information of adapterremoval

Description

Print version information of adapterremoval

Usage

adapterremoval_version()

Value

An invisible Integer of call status. The value is 0 when there is not any mistakes

Author(s)

Zheng Wei

References

Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88.

Examples

adapterremoval_version()

---

Interface to bowtie2 of bowtie2-2.2.3

Description

This function can be use to call wrapped bowtie2 binary.

Usage

bowtie2(
  bt2Index,
  samOutput,
  seq1,
  ...,
  seq2 = NULL,
  interleaved = FALSE,
  overwrite = FALSE
)

Arguments

bt2Index	Character scalar. bowtie2 index files prefix: 'dir/basename' (minus trailing '.*.bt2' of 'dir/basename.*.bt2').
samOutput	Character scalar. A path to a SAM file used for the alignment output.
seq1	Character vector. For single-end sequencing, it contains sequence file paths. For paired-end sequencing, it can be file paths with #1 mates paired with file paths in seq2. And it can also be interleaved file paths when argument interleaved=TRUE
...	Additional arguments to be passed on to the binaries. See below for details.
seq2	Character vector. It contains file paths with #2 mates paired with file paths in seq1. For single-end sequencing files and interleaved paired-end sequencing files(argument interleaved=TRUE), it must be NULL.
interleaved	Logical. Set TRUE when files are interleaved paired-end sequencing data.
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. All of them should be Character or Numeric scalar. You can put all aditional arguments in one Character(e.g. "–threads 8 –no-mixed") with white space splited just like command line, or put them in different Character (e.g. "–threads","8","–no-mixed"). Note that some arguments("-x","–interleaved","-U","-1","-2","-S") to the bowtie2 are invalid if they are already handled as explicit function arguments. See the output of bowtie2_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)
bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
"--threads 4 --quiet",overwrite=TRUE)
## Alignments
reads_1 <- system.file(package="Rbowtie2", "extdata", "bt2", "reads",
"reads_1.fastq")
reads_2 <- system.file(package="Rbowtie2", "extdata", "bt2", "reads",
"reads_2.fastq")
if(file.exists(file.path(td, "lambda_virus.1.bt2"))){
    cmdout<-bowtie2(bt2Index = file.path(td, "lambda_virus"),
       samOutput = file.path(td, "result.sam"),
       seq1=reads_1,seq2=reads_2,overwrite=TRUE,"--threads 3");cmdout
    head(readLines(file.path(td, "result.sam")))
}

---

Print available arguments that can be passed to bowtie2_build()

Description

Calling bowtie2_build_usage() prints the available arguments that can be passed to the ... argument of the bowtie2_build() function of the package. Note that some arguments are invalid if they are already handled as explicit function arguments.

Usage

bowtie2_build_usage()

Value

Information about available arguments that can be passed to bowtie2_build()

Author(s)

Zheng Wei

References

Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012, 9:357-359.

Examples

bowtie2_build_usage()

---

Interface to bowtie2-2.4.4 align function

Description

This function can be use to call the bowtie2 wrapper which wraps the bowtie2-align-s and the bowtie2-align-l binaries.

Usage

bowtie2_samtools(
  bt2Index,
  output,
  outputType = "sam",
  seq1 = NULL,
  seq2 = NULL,
  bamFile = NULL,
  ...,
  interleaved = FALSE,
  overwrite = FALSE
)

Arguments

bt2Index	Character scalar. The path where the bowtie2 index files are located. Include the basename of the index files at the end of the path (i.e. path_to_index_dir/index_basename). Do not include the bowtie2 index file extension (.bt2 or .bt2l)
output	Character scalar. The path where the alignment output file should be created. Include the basename of the alignment file at the end of the path (i.e. path_to_output_dir/output_basename). Do not include the alignment file extension (.sam or .bam).
outputType	Character scalar. Specify the output alignment file type. Default is set to "sam" but can also be changed to "bam".
seq1	Character vector. For single-end sequencing, it contains sequence file paths. For paired-end sequencing, it can be file paths with #1 mates paired with file paths in seq2. And it can also be interleaved file paths when argument interleaved=TRUE.
seq2	Character vector. It contains file paths with #2 mates paired with file paths in seq1. For single-end sequencing files and interleaved paired-end sequencing files (argument interleaved=TRUE), it must be NULL.
bamFile	Character vector. A path to a bam file that contains unaligned reads. If a bam file is provided then seq1 and seq2 must be set to NULL
...	Additional arguments to be passed on to the bowtie2 wrapper. See below for details.
interleaved	Logical. Set TRUE when files are interleaved paired-end sequencing data.
overwrite	Logical. Force overwriting of existing files if setting TRUE.

Details

All additional arguments in ... are interpreted as additional parameters to be passed to bowtie2 wrapper. All of them should be Character or Numeric scalar. You can put all additional arguments in one Character (e.g. "–threads 8 –no-mixed") with white space separation, or put them in different Character (e.g. "–threads","8","–no-mixed"). Note that some arguments ("-x","–interleaved","-U","-1","-2","-b","-S") are invalid if they are already handled as explicit function arguments. See the output of bowtie2_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)
bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),"--threads 4 --quiet",overwrite=TRUE)

## Alignments
reads_1 <- system.file(package="Rbowtie2", "extdata", "bt2", "reads", "reads_1.fastq")
reads_2 <- system.file(package="Rbowtie2", "extdata", "bt2", "reads", "reads_2.fastq")

## Sam file created
bowtie2_samtools(bt2Index = file.path(td,"lambda_virus"), output = file.path(td,"example"), seq1 = reads_1,
seq2 = reads_2, overwrite = TRUE)

## Bam file created
bowtie2_samtools(bt2Index = file.path(td,"lambda_virus"), output = file.path(td,"example"), outputType = "bam", 
seq1 = reads_1, seq2 = reads_2, overwrite = TRUE)

---

Print available arguments that can be passed to bowtie2()

Description

Calling bowtie2_usage() prints the available arguments that can be passed to the ... argument of the bowtie2() function of the package. Note that some arguments are invalid if they are already handled as explicit function arguments.

Usage

bowtie2_usage()

Value

Information about available arguments that can be passed to bowtie2().

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

bowtie2_usage()

---

Print version information of bowtie2-2.4.4

Description

Calling bowtie2_version() prints the version information of the bowtie package used.

Usage

bowtie2_version()

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

bowtie2_version()

---

Interface to bowtie2-2.4.4 build function

Description

This function can be use to call the bowtie2-build wrapper which wraps the bowtie2-build-s and the bowtie2-build-l binaries.

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. The path where the bowtie2 index files should be created. Include the basename of the index file at the end of the path (i.e. path_to_index_dir/index_basename).
...	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 wrapper. All of them should be Character or Numeric scalar. You can put all additional arguments in one Character (e.g. "–threads 8 –quiet") with white space separation, 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)

bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
"--threads 4 --quiet",overwrite=TRUE)

## Use additional arguments in another way

bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
"--threads",4,"--quiet",overwrite=TRUE)

## The function will print the output during the process without "--quiet" argument.
bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"),
overwrite=TRUE)

---

Check if file is creatable

Description

This is an internal function that is not meant to be used outside of the package. It determines whether the file at the end of the path can be created.

Usage

checkFileCreatable(filePath, argname, overwrite)

Arguments

filePath	Character scalar. Path to file to be created.
argname	Character scalar. Name of the argument passed.
overwrite	Logical Will warn user of overwriting if set TRUE.

Value

Indicates whether the file can be created at the path given.

Author(s)

Zheng Wei

---

Check if file exists

Description

This is an internal function that is not meant to be used outside of the package. It determines whether a specific file exists at the end of the path given to the function.

Usage

checkFileExist(filePath, argname)

Arguments

filePath	Character scalar. Path to file of interest.
argname	Character scalar. Name of the argument passed.

Value

Stops the function if the file does not exist.

Author(s)

Zheng Wei

---

Determine bowtie2 index type

Description

This is an internal function that is not meant to be used outside of the package. It determines whether the given index library comprises of small indexes (.bt2) or large indexes (.bt2l).

Usage

checkIndexType(filePath)

Arguments

filePath

Character scalar. The path where bowtie2 index files are located. Include the basename of the index files at the end of the path (i.e. path_to_index_dir/index_basename). Do not include the bowtie2 index file extension (.bt2 or .bt2l).

Details

The function first tries to determine whether path_to_index_dir/index_basename.1.bt2 exists and if it doesn't exist then it tries to determine whether path_to_index_dir/index_basename.1.bt2l exists. If neither of those files exist then there is an issue with the index files that must be addressed.

Value

Character scalar. Returns either "SMALL" if the .bt2 file is found, "LARGE" if the .bt2l file is found, or "ERROR" if neither the .bt2 nor .bt2l file is found.

---

Check if path exists

Description

This is an internal function that is not meant to be used outside of the package. It determines whether the path passed to the function exists.

Usage

checkPathExist(filePath, argname)

Arguments

filePath	Character scalar. Path of interest.
argname	Character scalar. Name of the argument passed.

Value

Stops the function if the path does not exist.

Author(s)

Zheng Wei

---

Check if samtools exists on the system

Description

This is an internal function that is not meant to be used outside of the package. It checks whether samtools exists on the system.

Usage

checkSamtoolsExists()

Value

Returns TRUE if samtools exists on the system, else FALSE

---

identify adapters for paired-end reads

Description

This function can be use to call wrapped AdapterRemoval binary for adapters identifying.

Usage

identify_adapters(file1, file2, ..., basename = NULL, overwrite = FALSE)

Arguments

file1	Character vector. It can be file paths with #1 mates paired with file paths in file2 And it can also be interleaved file paths when argument interleaved=TRUE
file2	Character vector. It contains file paths with #2 mates paired with file paths in file1. For interleaved paired-end sequencing files(argument interleaved=TRUE),it must to be setted to NULL.
...	Additional arguments to be passed on to the binaries. See below for details.
basename	Character. The outputfile path prefix. Default: your_output
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 identify_adapters. All of them should be Character or Numeric scalar. You can put all aditional arguments in one Character(e.g. "–threads 8") with white space splited just like command line, or put them in different Character(e.g. "–threads","8"). Note that some arguments("–identify-adapters", "–file1","–file2","–basename") to the identify_adapters are invalid if they are already handled as explicit function arguments. See the output of adapterremoval_usage() for details about available parameters.

Value

An invisible Character vector of adapters for each mate.

Author(s)

Zheng Wei

References

Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88.

Examples

td <- tempdir()
reads_1 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_1.fq")
reads_2 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_2.fq")
adapters <- identify_adapters(file1=reads_1,file2=reads_2,
basename = file.path(td,"reads")
,"--threads 2",overwrite=TRUE)
adapters

---

Interface to bowtie2 of adapterremoval-2.2.1a

Description

This function can be use to call wrapped AdapterRemoval binary.

Usage

remove_adapters(
  file1,
  ...,
  adapter1 = NULL,
  output1 = NULL,
  file2 = NULL,
  adapter2 = NULL,
  output2 = NULL,
  basename = NULL,
  interleaved = FALSE,
  overwrite = FALSE
)

Arguments

file1	Character vector. For single-end sequencing, it contains sequence file paths. For paired-end sequencing, it can be file paths with #1 mates paired with file paths in file2 And it can also be interleaved file paths when argument interleaved=TRUE
...	Additional arguments to be passed on to the binaries. See below for details.
adapter1	Character. It is an adapter sequence for file1. Default: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG
output1	Character. The trimmed mate1 reads output file path for file1. Defualt: basename.pair1.truncated (paired-end), basename.truncated (single-end), or basename.paired.truncated (interleaved)
file2	Character vector. It contains file paths with #2 mates paired with file paths in file1. For single-end sequencing files and interleaved paired-end sequencing files(argument interleaved=TRUE), it must be NULL.
adapter2	Character. It is an adapter sequence for file2. Defualt: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
output2	Character. The trimmed mate2 reads output file path for file2. Default: BASENAME.pair2.truncated (only used in PE mode, but not if –interleaved-output is enabled)
basename	Character. The outputfile path prefix. Default: your_output
interleaved	Logical. Set TRUE when files are interleaved paired-end sequencing data.
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 remove_adapters. All of them should be Character or Numeric scalar. You can put all aditional arguments in one Character(e.g. "–threads 8") with white space splited just like command line, or put them in different Character(e.g. "–threads","8"). Note that some arguments( "–file1","–file2","–adapter1","–adapter2","–output1","–output2", "–basename","–interleaved") to the identify_adapters are invalid if they are already handled as explicit function arguments. See the output of adapterremoval_usage() for details about available parameters.

Value

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

Author(s)

Zheng Wei

References

Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88.

Examples

td <- tempdir()

# Identify adapters
reads_1 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_1.fq")
reads_2 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_2.fq")
adapters <- identify_adapters(file1=reads_1,file2=reads_2,
basename=file.path(td,"reads"), "--threads 3",overwrite=TRUE)

# Remove adapters
cmdout<-remove_adapters(file1=reads_1,file2=reads_2,adapter1 = adapters[1],
adapter2 = adapters[2],
output1=file.path(td,"reads_1.trimmed.fq"),
output2=file.path(td,"reads_2.trimmed.fq"),
basename=file.path(td,"reads.base"),overwrite=TRUE,"--threads 3");cmdout

---