fai_query2: 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 a FASTA sequence.

1 2	fai_query2( faifh, regionstring ) fai_query3( faifh, regionstring , resultstring )

`faifh`	FAIhandle as returned by fai_open
`regionstring`	String of the form sequencename:beginpos-endpos e.g. "MTRR1mouse:20-40" specifying the sequence and region
`resultstring`	String variable to store 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_query2", faifh, regionstring ) to eliminate the overhead of using the R wrapper function. Use this function in combination with a while( ( seq = fai_query2(F,region) ) != FALSE ) if you need to loop. 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_query2( faifh , "1:100-200" )
if( result != FALSE )
{
	print( result )
}
fai_close( faifh )