> On Dec 17, 2017, at 7:57 PM, Robert Haas <robertmh...@gmail.com> wrote: > > On Fri, Dec 15, 2017 at 2:49 PM, Gene Selkov <selko...@gmail.com> wrote: >> I need a data type to represent genomic positions, which will consist of a >> string and a pair of integers with interval logic and access methods. Sort >> of like my seg type, but more straightforward. > > Have you thought about just using a composite type?
Yes, I have. That is sort of what I have been doing; a composite type certainly gets the job done but I don’t feel it reduces query complexity, at least from the user’s point of view. Maybe I don’t know enough. Here’s an example of how I imagine a composite genomic locus (conventionally represented as text ‘:’ integer ‘-‘ integer): CREATE TYPE locus AS (contig text, coord int4range); CREATE TABLE test_locus ( pos locus, ref text, alt text, id text ); CREATE INDEX test_locus_coord_ix ON test_locus (((pos).coord)); \copy test_locus from test_locus.tab Where test_locus.tab has stuff like: (chr3,"[178916937,178916940]") GAA CHP2_PIK3CA_2 (chr3,"[178916939,178916948]") AGAAAAGAT CHP2_PIK3CA_2 (chr3,"[178916940,178916941]") G A CHP2_PIK3CA_2 (chr3,"[178916943,178916944]") A G CHP2_PIK3CA_2 (chr3,"[178916943,178916946]") AAG CHP2_PIK3CA_2 (chr3,"[178916943,178916952]") AAGATCCTC CHP2_PIK3CA_2 (chr3,"[178916944,178916945]") A G CHP2_PIK3CA_2 (chr3,"[178916945,178916946]") G C CHP2_PIK3CA_2 (chr3,"[178916945,178916946]") G T CHP2_PIK3CA_2 (chr3,"[178916945,178916948]") GAT CHP2_PIK3CA_2 When the table is loaded, I can pull the subset shown above with this query: SELECT * FROM test_locus WHERE (pos).contig = 'chr3' AND (pos).coord && '[178916937, 178916948]’; pos | ref | alt | id --------------------------------+-----------+-----+--------------- (chr3,"[178916937,178916941)") | GAA | | CHP2_PIK3CA_2 (chr3,"[178916939,178916949)") | AGAAAAGAT | | CHP2_PIK3CA_2 . . . . So far so good. It gets the job done. However, it is only a small step towards a fully encapsulated, monolithic type I want it to be. The above query It is marginally better than its atomic-type equivalent: SELECT * FROM test WHERE contig = 'chr3' AND greatest(start, 178916937) <= least(stop, 178916948); contig | start | stop | ref | alt | id --------+-----------+-----------+-----------+-----+--------------- chr3 | 178916937 | 178916940 | GAA | | CHP2_PIK3CA_2 chr3 | 178916939 | 178916948 | AGAAAAGAT | | CHP2_PIK3CA_2 . . . . and it requires addition syntax transformations steps to go from conventional locus representation 'chr3:178916937-178916940' to composite '(chr3,"[178916937,178916940]”)’ and back. Of course, the relative benefits of partial encapsulation I achieve by bundling text with int4range accumulate, compared to (text, int4, int4), as queries grow more complex. But because the elements of a composite type still require a separate query term for each of them (unless there is some magic I am not aware of), the complexity of a typical query I need to run exceeds my feeble sight-reading capacity. I want things that are conceptually simple to be expressed in simple terms, if possible. Like so: CREATE EXTENSION locus; CREATE TABLE test_locus ( pos locus, ref text, alt text, id text ); \copy test_locus from data/oncomine.hotspot.tab SELECT * FROM test_locus WHERE pos && 'chr3:178916937-178916948'; pos | ref | alt | id --------------------------+-----------+-----+--------------- chr3:178916937-178916940 | GAA | | CHP2_PIK3CA_2 chr3:178916939-178916948 | AGAAAAGAT | | CHP2_PIK3CA_2 chr3:178916940-178916941 | G | A | CHP2_PIK3CA_2 chr3:178916943-178916944 | A | G | CHP2_PIK3CA_2 chr3:178916943-178916946 | AAG | | CHP2_PIK3CA_2 chr3:178916943-178916952 | AAGATCCTC | | CHP2_PIK3CA_2 chr3:178916944-178916945 | A | G | CHP2_PIK3CA_2 chr3:178916945-178916946 | G | C | CHP2_PIK3CA_2 chr3:178916945-178916946 | G | T | CHP2_PIK3CA_2 chr3:178916945-178916948 | GAT | | CHP2_PIK3CA_2 (10 rows) I have encountered some pesky geometry / indexing problems while building this extension (https://github.com/selkovjr/locus <https://github.com/selkovjr/locus>), but I hope I can solve them at least at the level afforded by the composite type, while keeping the clean interface of a monolithic type. I understand I could probably achieve the same cleanliness by defining functions and operators over the complex type, but by the time I’m done with that, will I have coded about the same amount of stuff as required to build an extended type? Regards, —Gene