SYNOPSIS
positionDB [-mersize k] [-merskip k] [-use a-b,c] [-merbegin b] [-merend e] -sequence s.fasta -output p.posDBpositionDB -dump datafile
positionDB -test1 sequence.fasta
positionDB -test2 db.fasta sequence.fasta
OPTIONS
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.