Dear Guy, > So, your idea of fetching all entries and then parsing them would work > for SRS. I however think that instead of an associated parameter > -scasesensitive it would be better to have in the emboss.default syntax > for DB entries an optional parameter case:. You should be able to handle > the situation where it is appropriate to pass an id to a case sensitive > search method and the situation where it is appropriate to parse the > output of a case-insensitive search method. This can best be decided for > each > databank at EMBOSS site configuartion time, rather than at sequence > retrieval time. What do you think ?
You are right. Excellent idea. I will do it ASAP. It will mean a new attribute stored for sequence database access. For the PDB case, really only the end of the ID is case-sensitive. Do you think the database should be case-sensitive for the whole ID, or does it make sense to check for a pattern as the case-sensitive part? EMBOSS will initially read only one sequence for a seqall ... it does not read in all the sequences and look for duplicates so we have to decide in the emboss.defaults DB definition how to check a single ID (no way to read them all and check for duplicates). regardrs, Peter _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
