Parsing error (?) messages in 4.8c

Ed Griffiths edgrif at sanger.ac.uk
Tue Apr 3 09:57:14 EST 2001


Keith,

> I've recently added 4.8c to our system and am trying to load some ace
> files.  I've noticed some behaviour which didn't occur when using 4.7l.

OK, 4_8 parsing has been tightened up a lot, there were many places where we
either didn't report errors or reported them incorrectly. You will get some
messages that you didn't see before. If you have an instance where you think the
message is in error then let me know, my intention was that the parse messages
should be as accurate as possible, especially because AcePerl makes use of them
to detect when/where errors occurred.


> Specifically, if I try parsing a simple sequence file such as :
> 
> Sequence EMBL:A75959.1_cds
> CDS
> Gene_product "NADPH CYTOCHROME P450 REDUCTASE"
> Gene_name "ARA B"
> 
> Then I get a message confirmation box appear which reads:
> 
> "Type of ARA B does not check in B object "EMBL:A75959.1_cds".

Sorry, but you are going to have to show me your Sequence class definition
before I can comment further.


> I can't do anything until I click continue. Despite this it does seem to
> be adding the sequences to the database, but this is not very helpful when
> I am trying to load a lot of sequences and am having to confirm each one.
> 
> Any ideas on why this is happening in 4.8c and not in 4.7l???

If you want to do bulk updates you can use the tace interface and use the pparse
command to just keep going when an error occurs...of course whether this is
desireable is up to you to decide !

cheers Ed

 ------------------------------------------------------------------------
| Ed Griffiths, Acedb development, Informatics Group,                    |
|               The Sanger Centre, Wellcome Trust Genome Campus,         |
|               Hinxton, Cambridge CB10 1SA, UK                          |
|                                                                        |
| email: edgrif at sanger.ac.uk  Tel: +44-1223-494780  Fax: +44-1223-494919 |
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