positionDB - Online in the Cloud

PROGRAM:

NAME

positionDB - management of posDB files

SYNOPSIS

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

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.

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