---
name: "positionDB"
section: "1"
platform: "linux"
package: "meryl"
version: "0~20150903+r2013-9+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/positionDB"
---

# positionDB(1)

management of posDB files

## 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.

## SEE ALSO

[**existDB**(1)](/existDB/1.md), [**meryl**(1)](/meryl/1.md)