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-boun...@lists.open-bio.org [mailto:emboss-boun...@lists.open-bio.org] Im Auftrag von Hamish McWilliam Gesendet: 23 August 2013 11:25 An: emboss@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/ ============================================================ _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss