positionDB(1) management of posDB files


positionDB [-mersize k] [-merskip k] [-use a-b,c] [-merbegin b] [-merend e] -sequence s.fasta -output p.posDB

positionDB -dump datafile

positionDB -test1 sequence.fasta

positionDB -test2 db.fasta sequence.fasta


Building an image

-mersize k
The size of the mers, default=20.
-merskip k
The skip between mers, default=0
-use a-b,c
Specify which sequences to use, default=all
-merbegin b
Build on a subset of the mers, starting at mer #b, default=all mers
-merend e
Build on a subset of the mers, ending at mer #e, default=all mers
-sequence s.fasta
Input sequences.
-output p.posDB
Output filename.

Dumping information about an image

-dump datafile.posDB

Running sanity tests

-test1 sequence.fasta
Tests if each and every mer is found in the positionDB. Reports if it doesn't find a mer at the correct position. Doesn't report if table has too much stuff.
-test2 db.fasta sequence.fasta
Builds a positionDB from db.fasta, then searches the table for each mer in sequence.fasta. Reports all mers it finds.
This is a silly test and you shouldn't do it.