Perform Sequence Alignment Using MUMmer

This function orchestrates the alignment of sequences in a specified directory using MUMmer, a tool for aligning large DNA or protein sequences. It can handle GenBank and FASTA file formats. and performs checks to ensure necessary files are present.

Usage

r

mummer_alignment(
  path,
  cluster = NULL,
  maptype = "many-to-many",
  seqtype = "protein",
  mummer_options = "",
  filter_options = "",
  remove_files = TRUE,
  output_dir = tempdir()
)

Arguments

Argument	Description
`path`	The directory containing the sequence files. Its path may contain spaces; the names of the files may not.
`cluster`	Optional vector of cluster names to consider for alignment. If NULL, clusters are inferred from file names. The order of names determines the alignment sequence.
`maptype`	The type of mapping to perform; "many-to-many" or "one-to-one". "many-to-many" allows for multiple matches between clusters, "one-to-one" restricts alignments to unique matches between a pair.
`seqtype`	The type of sequences, either "protein" or "nucleotide".
`mummer_options`	Additional command line options for MUMmer. To see all available options, you can run `nucmer --help` or `promer --help` in the terminal depending on whether you are aligning nucleotide or protein sequences.
`filter_options`	Additional options for filtering MUMmer results. To view all filtering options, run `delta-filter --help` in the terminal.
`remove_files`	Logical indicating whether to remove intermediate files generated during the process, defaults to TRUE.
`output_dir`	Parent directory for a unique working subdirectory, without spaces in its path (MUMmer cannot use it otherwise); defaults to `tempdir()`. With `remove_files = FALSE`, copied inputs and alignment files are retained in that subdirectory.

Value

A data frame combining all alignment results, or NULL if errors occur during processing.

References

Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004). Versatile and open software for comparing large genomes. Genome Biology, 5(R12).

Examples

r

## Not run:
# Requires the external MUMmer programs (nucmer or promer, delta-filter and
# show-coords) on the PATH.

# Basic alignment with default options
mummer_alignment(
  path = "/path/to/sequences",
  maptype = "many-to-many",
  seqtype = "protein"
)

# Alignment with specific MUMmer options
mummer_alignment(
  path = "/path/to/sequences",
  maptype = "one-to-one",
  seqtype = "protein",
  mummer_options = "--maxgap=500 --mincluster=100",
  filter_options = "-i 90"
)
## End(Not run)