[emboss-dev] number of sequences in a database

Peter Rice pmr at ebi.ac.uk
Mon Jul 25 09:35:08 UTC 2005

C Thomas wrote:

> After I index a database for use with emboss, is there an ajax API  
> call to find the total number of sequences in that database?

There are scripts in the CVS scripts/ directory:

If you CD to the database directory, the dbitest.pl script can report on the 
contents of database files. We use them for debugging.

For example:

~/emboss/scripts/dbitest.pl entrynam.idx | more
File size:        1136
Record count:       44
Record size:        19
Database name: 'EMBL'
Release:       '2.10'

Shows there are 44 records (entries) in the database for the tembl database.

You can find the script on our anonymous CVS server at 

(I hope my mailer wraps that correctly :-)

> I imagine that there's not a general way to get the total number of  
> hits from a seqall object, since it looks like the sequences are  
> discovered with each call to ajSeqallNext().
> Am I right about that?

No general call ... some of the database access methods can easily do this, 
others cannot. Most of them can ... so perhaps we can add a call. For methods 
that have problems .... they can refuse, or read every entry to count them.

Hope that helps,


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