Re: genomic locus - Mailing list pgsql-hackers
| From | Gene Selkov |
|---|---|
| Subject | Re: genomic locus |
| Date | |
| Msg-id | F80D911E-EC7B-4BCB-BCC2-8E356D4F7FCB@gmail.com Whole thread Raw |
| In response to | Re: genomic locus (Robert Haas <robertmhaas@gmail.com>) |
| Responses |
Re: genomic locus
|
| List | pgsql-hackers |
On Dec 17, 2017, at 7:57 PM, Robert Haas <robertmhaas@gmail.com> wrote:On Fri, Dec 15, 2017 at 2:49 PM, Gene Selkov <selkovjr@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), 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
pgsql-hackers by date: