fai_query4: Extract a part of a FASTA sequence.
In WhopGenome: High-Speed Processing of VCF, FASTA and Alignment Data

Description Usage Arguments Details Value Author(s) See Also Examples

Return a part of the a FASTA sequence.

1 2	fai_query4( faifh, sequencename, beginpos, endpos ) fai_query5( faifh, sequencename, beginpos, endpos, resultstring )

`faifh`	FAIhandle as returned by fai_open
`sequencename`	Identifier of a sequence in the fasta file
`beginpos`	Start position of the subsequence to extract
`endpos`	End position of the subsequence to extract
`resultstring`	Variable to store the results into

Note: the fai_query3 and fai_query5 methods are DEPRECATED : to be as fast as possible, they modified a given variable's contents (resultstring) which will cause issues in R's internals! Use .Call("FAI_query4", faifh, sequencename, beginpos, endpos ) to eliminate the overhead of using the R wrapper function. Use this function in combination with a while( ( seq = fai_query4(F,region) ) != FALSE ) if you need to loop. (This exploits the fact that only the string "FALSE" has a boolean value of FALSE, all others have a boolean value of TRUE.)

A string containing the (sub-)sequence, FALSE if it fails.

Ulrich Wittelsbuerger

fai_open

##
##	Example :
##
faifile  <- system.file("extdata", "ex.fasta", package = "WhopGenome")
faifh <- fai_open( faifile )
stopifnot( !is.null(faifh) )
result = fai_query4( faifh , "1", 9 , 20 )
if( result != FALSE )
{
	print( result )
}
fai_close( faifh )