[Bioperl-l] Validation of information loaded into bioperl-db

Law, Annie Annie.Law at nrc-cnrc.gc.ca
Mon Jul 19 11:38:59 EDT 2004


I would like to know some things about validation of bioperl-db.  I am near
the point where this bioperl-db can be very helpful for Me (so close)
however I just have some questions about validation and updating the
database once it has already been loaded up.

1. When you use the load_seqdatabase.pl script how can you check if the load
has been successful. I would like to automate this process.  I plan to run a
cron job that would load the datbase but would Like to know an efficient
method to see if the load has been successful.  You can create log files to
read or script the runs but is there something else that can be done.

2. I know that there are scriplets in the same directory as
load_seqdatbase.pl that can be used in conjunction 
With load_seqdatbase.pl when you use the options lookup and mergeobjs.  I
would like to know if the same script can be Used for the load_ontology.pl

3. In both load_seqdatabase.pl and load_ontology.pl there is the option
--remove. I want to remove all old information and refresh with new data.
Do I use --remove in conjunction with 
--lookup and --mergobjs with freshen-annot.pl.   I don't understand the need
for the --remove option if you are 
Already using --lookup and --mergobjs with freshen-annot.pl  It seems that
this would be redundant but perhaps there is something 
I am missing.

4. What is the default behavior if I don't use the options such as lookup
and mergeobjs?  Will all the data just be overwritten When I use
load_ontology.pl and load_seqdatabase.pl?

Thanks very much,

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