Package 'ssw'

Title: Striped Smith-Waterman Algorithm for Sequence Alignment using SIMD
Description: Provides an R interface for 'SSW' (Striped Smith-Waterman) via its 'Python' binding 'ssw-py'. 'SSW' is a fast 'C' and 'C++' implementation of the Smith-Waterman algorithm for pairwise sequence alignment using Single-Instruction-Multiple-Data (SIMD) instructions. 'SSW' enhances the standard algorithm by efficiently returning alignment information and suboptimal alignment scores. The core 'SSW' library offers performance improvements for various bioinformatics tasks, including protein database searches, short-read alignments, primary and split-read mapping, structural variant detection, and read-overlap graph generation. These features make 'SSW' particularly useful for genomic applications. Zhao et al. (2013) <doi:10.1371/journal.pone.0082138> developed the original 'C' and 'C++' implementation.
Authors: Nan Xiao [aut, cre, cph]
Maintainer: Nan Xiao <[email protected]>
License: MIT + file LICENSE
Version: 0.2.1
Built: 2024-09-17 22:23:51 UTC
Source: https://github.com/nanxstats/ssw-r

Help Index

Perform Smith-Waterman alignment of a read against a reference sequence

Description

Perform Smith-Waterman alignment of a read against a reference sequence

Usage

align(
  read,
  reference,
  gap_open = 3L,
  gap_extension = 1L,
  start_idx = 0L,
  end_idx = 0L,
  match_score = 2L,
  mismatch_penalty = 2L
)

Arguments

read

A character string of the read.
reference

A character string of the reference.
gap_open

Penalty for opening a gap. Default is 3.
gap_extension

Penalty for extending a gap. Default is 1.
start_idx

Index to start the alignment search. Default is 0.
end_idx

Index to end the alignment search. The default value 0 means using the entire reference length.
match_score

An integer for scoring matches, ranging from 0 to 255. Default is 2.
mismatch_penalty

An integer for mismatch penalties, ranging from 0 to 255. Default is 2.

Value

A list of class ssw containing the ssw aligner object and the alignment results.

Examples

a <- align("ACGT", "TTTTACGTCCCCC")
a
a$alignment$optimal_score
a$alignment$sub_optimal_score

Perform forced alignment with increased gap open penalty

Description

Perform forced alignment with increased gap open penalty

Usage

force_align(
  read,
  reference,
  force_overhang = FALSE,
  match_score = 2L,
  mismatch_penalty = 2L
)

Arguments

read

A character string of the read.
reference

A character string of the reference.
force_overhang

Logical. If TRUE, ensures only one end of the alignment overhangs. Default is FALSE.
match_score

An integer for scoring matches, ranging from 0 to 255. Default is 2.
mismatch_penalty

An integer for mismatch penalties, ranging from 0 to 255. Default is 2.

Value

A list of class ssw containing the input sequences, the ssw aligner object, and the alignment results.

Examples

# Results are truncated
a <- force_align("ACTG", "TTTTCTGCCCCCACG")
a

# Format the results
b <- a |> formatter()
b

# Print the formatted results directly
a |> formatter(print = TRUE)

Format and pretty-print SSW forced alignment results without truncation

Description

Format and pretty-print SSW forced alignment results without truncation

Usage

formatter(x, print = FALSE)

Arguments

x

An object of class ssw containing the forced alignment results.
print

Pretty-print the results? Default is FALSE.

Value

The formatted forced alignment results.

Examples

a <- force_align("ACTG", "TTTTCTGCCCCCACG")
b <- a |> formatter()
b
a |> formatter(print = TRUE)

Install ssw-py and its dependencies

Description

Install ssw-py and its dependencies

Usage

install_ssw_py(
  ...,
  envname = "r-ssw-py",
  new_env = identical(envname, "r-ssw-py")
)

Arguments

...

Other arguments passed to reticulate::py_install().
envname

The name or full path of the environment in which ssw-py is installed. Default is r-ssw-py.
new_env

Logical. If TRUE, the specified Python environment will be deleted and recreated if it already exists. Defaults to TRUE only when using the default environment name.

Value

Invisibly returns NULL. Primarily used for its side effect of installing the Python package in the specified environment.

Examples

install_ssw_py()

Is ssw-py installed?

Description

Is ssw-py installed?

Usage

is_installed_ssw_py()

Value

TRUE if installed, FALSE if not.

Examples

is_installed_ssw_py()

Print SSW alignment results

Description

Print SSW alignment results

Usage

## S3 method for class 'ssw'
print(x, start_idx = 0L, ...)

Arguments

x

An object of class ssw.
start_idx

Index to start printing from.
...

Additional parameters for print() (not used).

Value

Invisibly returns the input object.

Examples

a <- align("ACGT", "TTTTACGTCCCCC")
a

Global reference to ssw-py

Description

Global reference to ssw-py which will be initialized in .onLoad.

Usage

ssw_py

Format

An object of class python.builtin.module (inherits from python.builtin.object) of length 0.

Value

ssw-py reference object