[EMBOSS] Escaping query terms in a USA

David Bauer david.bauer at bayer.com
Fri Aug 23 12:02:31 UTC 2013

Hi Hamish,

it seems the index is OK, just the database query code can not handle the ":" which has special meanings in USAs.
So as workaround you can replace the ":" by a "*".

entret -stdout -auto 'imgthla-key:A*02*364'

will return the entry HLA08011.

But be aware that by this you actually generate a wildcard query, so the * matches any single character at that position.

Kind regards,

-----Ursprüngliche Nachricht-----
Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Hamish McWilliam
Gesendet: 23 August 2013 11:25
An: emboss at lists.open-bio.org
Betreff: [EMBOSS] Escaping query terms in a USA

Hi folks,

In the IMGT/HLA database (http://www.ebi.ac.uk/ipd/imgt/hla/) the 
keywords field in the EMBL-Bank format flat-file contains allele names like:


While I can build an index containing the keywords, it does not appear 
to be possible to search the index with the allele names. For example:

$ entret -stdout -auto 'imgthla-key:Allele'

works as expected, but:

$ entret -stdout -auto 'imgthla-key:A*02:364'

just gives errors:

Error: Failed to open filename 'imgthla-key'
Error: Unable to read sequence 'imgthla-key:A*02:364'
Died: entret terminated: Bad value for '-sequence' with -auto defined

I am guessing that the problem is the '*' and ':' characters in the 
term... so is there some way to escape these or are the terms in the 
index mangles in some way?

All the best,

Mr Hamish McWilliam,
Web Production,
European Bioinformatics Institute (EMBL-EBI),
European Molecular Biology Laboratory,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SD
United Kingdom

URL: http://www.ebi.ac.uk/

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