readFASTA: Read Protein/DNA Sequences in FASTA Format

In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Read Protein/DNA Sequences in FASTA Format

Usage

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

Arguments

file	The name of the file which the sequences in fasta format are to be read from. 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 BioMedR 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.

Details

This function reads protein sequences in FASTA format.

Value

The result character vector

Note

Note that any different sets of instances (chunklets), e.g. 1, 3, 7 and 4, 6, might belong to the same class and might belong to different classes.

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

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 readPDB for reading protein sequences in PDB format.

Examples

P00750 = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))

wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.