[EMBOSS] Escaping query terms in a USA

Hamish McWilliam hpm at ebi.ac.uk
Fri Aug 23 09:24:36 UTC 2013

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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