[EMBOSS] Escaping query terms in a USA

[David Bauer]

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,
David.

-----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:

A*02:364

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,

Hamish
-- 
============================================================
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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