positionDB1
Management of posdb files
Usage
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.
-test2db.fasta sequence.fasta-
Builds a
positionDBfrom 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.
Releases
Unchanged in 5 releases since Debian 9 (Stretch).