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Read Protein Sequences in FASTA Format

Source: R/misc-01-readFASTA.R
readFASTA.Rd

This function reads protein sequences in FASTA format.

Usage

readFASTA(
  file = system.file("protseq/P00750.fasta", package = "protr"),
  legacy.mode = TRUE,
  seqonly = FALSE
)

Arguments

file

Path to the file containing the protein sequences in FASTA format. If it does not contain an absolute or relative path, the file name is relative to the current working directory, getwd. The default here is to read the P00750.fasta file which is present in the protseq directory of the protr package.

legacy.mode

If set to TRUE, lines starting with a semicolon (;) are ignored. Default value is TRUE.

seqonly

If set to TRUE, only sequences as returned without attempt to modify them or to get their names and annotations (execution time is divided approximately by a factor 3). Default value is FALSE.

Value

Character vector of the protein sequences.

The three returned argument are just different forms of the same output. If one is interested in a Mahalanobis metric over the original data space, the first argument is all she/he needs. If a transformation into another space (where one can use the Euclidean metric) is preferred, the second returned argument is sufficient. Using A and B is equivalent in the following sense.

References

Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America, 85: 2444–2448.

See also

See getUniProt for retrieving protein sequences from uniprot.org.

Author

Nan Xiao <https://nanx.me>

Examples

P00750 <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))