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Converting Old Databases

Introduction

Gap cannot be used with databases created by the sequence assembly programs Dap and Bap. Similarly Bap cannot used Dap database files. People wanting to switch to using gap will need to convert their old databases. The program `convert' is provided for this purpose. Convert is an interactive program for converting sequence assembly data between the various formats. It is possible to convert from:

to any of the following formats

The Conversion Program

The program takes no command line arguments. First, you are prompted for the format, name and version of the database you wish to convert. If the source is an xdap or xbap database, ensure that the name and version are in uppercase. If the source is a text file, the version is prompted for but it is ignored. Second, you are prompted for the format, name and version of the database you wish to create. Ensure that names and versions are in the appropriate case and that the files do already exist.

After this, the programs converts the database. This may take some time. The next message to appear on the terminal is a message to indicate the conversion has successfully completed.

Example

Here is a log of a typical conversion session. User input is shown in bold.

Covert Project Database
Version 1.3, 4th December 1995
Please enter database to convert:

Available types are:
0. Flat file - created with this program
1. xdap database
2. xbap database

Database type? 2
Database name? ZK643
Database version? 0

Please enter database to create:

Available types are:
0. Flat file - created with this program
1. xbap database
2. xgap database

Database type? 2
Database name? ZK643
Database version? 1

Conversion completed

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_144.html