Re: genomic locus - Mailing list pgsql-hackers

Hmm, would you try to implement separate type for querying? Similar to tsquery, 
lquery (for ltree), jsquery etc.

Gene Selkov wrote:
> 
>> On Dec 17, 2017, at 7:57 PM, Robert Haas <robertmhaas@gmail.com 
>> <mailto:robertmhaas@gmail.com>> wrote:
>>
>> On Fri, Dec 15, 2017 at 2:49 PM, Gene Selkov <selkovjr@gmail.com 
>> <mailto: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]")GAACHP2_PIK3CA_2
> (chr3,"[178916939,178916948]")AGAAAAGATCHP2_PIK3CA_2
> (chr3,"[178916940,178916941]")GACHP2_PIK3CA_2
> (chr3,"[178916943,178916944]")AGCHP2_PIK3CA_2
> (chr3,"[178916943,178916946]")AAGCHP2_PIK3CA_2
> (chr3,"[178916943,178916952]")AAGATCCTCCHP2_PIK3CA_2
> (chr3,"[178916944,178916945]")AGCHP2_PIK3CA_2
> (chr3,"[178916945,178916946]")GCCHP2_PIK3CA_2
> (chr3,"[178916945,178916946]")GTCHP2_PIK3CA_2
> (chr3,"[178916945,178916948]")GATCHP2_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
> 
> 
> 
> 

-- 
Teodor Sigaev                                   E-mail: teodor@sigaev.ru
                                                    WWW: http://www.sigaev.ru/