fai_query2 {WhopGenome} | R Documentation |
Return a part of a FASTA sequence.
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 )