readFasta-methods: reader for databases in Fasta file format.

In wolski/pairseqsim: pairwise sequence alignment similarity simple.

Description

Reads file in FASTA format. An sequence entry in the fasta dabase consists of a header line starting with the \">\" sign which contains the id of the sequence. It is followed by several lines of the protein sequence. Because the header line may vary the user can specify a function which will extract (grep) the id. infogrep <- function(x) { return(sub("^>([a-zA-Z0-9]+) .+","\1",x,perl=TRUE)) }

Arguments

object	either AASequence or AASequenceList
file	Path to the file
grepinfo	Function which extracts the id from the fasta description line.
grepseq	Function to pre-process the sequence.

Value

Returns an object of class AASequenceList.

Methods

object = "AASequenceList"

Read sequence database in FASTA format.

Author(s)

Witold E. Wolski [e-mail]

References

http://r4proteomics.sourceforge.net

See Also

AASequenceList-class

Examples

mySequlist <- new("AASequenceList",info="my sequence list")
#mySequlist<-readFasta(mySequlist,"ex.fasta",grepinfo=infogrep,grepseq=seqgrep)

wolski/pairseqsim documentation built on May 4, 2019, 9:47 a.m.