Re: genomic locus

> On Dec 22, 2017, at 1:53 AM, Teodor Sigaev <teodor(at)sigaev(dot)ru> wrote:
>
> Hmm, would you try to implement separate type for querying? Similar to tsquery, lquery (for ltree), jsquery etc.

That sounds like a good idea if I want to make an app that will only be accessed through a purpose-built front end. Now I’m messing with lots of data, making numerous small one-off experiments. Since all of that stuff consumes my brain power and keystrokes, I want to minimize all the ancillary stuff or at least make it invisible. But I’ll probably go ahead and add a separate query-friendly type that if nothing else helps.

I think I can wrangle this type into GiST just by tweaking consistent(), union(), and picksplit(), if I manage to express my needs in C without breaking too many things. My first attempt segfaulted.

Here’s my plan of attack. I think that by setting a union of inconsistent loci (those on different contigs) to [0, MAX_INT], I will expose such union to a huge penalty, even without having to do anything with the current penalty(). No query will go there.

The required change to consistent() is obvious: contigs do not match — go away.

The situation with picksplit() may be more tricky; I can’t imagine all possible consequences until I’ve seen how it works. Currently, with simple intervals, it sorts them by center points and splits the sorted list in half. I have already changed the internal sort function, picksplit_item_cmp(), to make sure the data are sorted on the contig first, then by center point (or any other geometric feature). I am thinking about splitting the list at the first inconsistent contig, sending the consistent first part with its well-defined geometry to the left page, and filling the right page with whatever remains. If the right page has inconsistent contigs, its bounding box will be [0, MAX_INT], and it should be again picked for splitting at the next iteration (if I understand the algorithm correctly).

If all goes to plan, I will end up with an index tree partitioned by contig at the top level and geometrically down from there. That will be as close as I can get to an array of config-specific indices, without having to store data in separate tables.

What do you think of that?

~~~~~~~~~~~~~~~~~~~~~~~~~~~~

I have a low-level technical question. Because I can’t anticipate the maximum length of contig names (and do not want to waste space), I have made the new locus type a varlena, like this:

#include "utils/varlena.h"

typedef struct LOCUS
{
int32 l_len_; /* varlena header (do not touch directly!) */
int32 start;
int32 end;
char contig[FLEXIBLE_ARRAY_MEMBER];
} LOCUS;

#define LOCUS_SIZE(str) (offsetof(LOCUS, contig) + sizeof(str))

That flexible array member messes with me every time I need to copy it while deriving a new locus object from an existing one (or from a pair). What I ended up doing is this:

LOCUS *l = PG_GETARG_LOCUS_P(0);
LOCUS *new_locus;
char *contig;
int size;

new_locus = (LOCUS *) palloc0(sizeof(*new_locus));
contig = pstrdup(l->contig); // need this to determine the length of contig name at runtime
size = LOCUS_SIZE(contig);
SET_VARSIZE(new_locus, size);
strcpy(new_locus->contig, contig);

Is there a more direct way to clone a varlena structure (possibly assigning an differently-sized contig to it)? One that is also memory-safe?

Thank you,

—Gene

> Gene Selkov wrote:
>>> On Dec 17, 2017, at 7:57 PM, Robert Haas <robertmhaas(at)gmail(dot)com <mailto:robertmhaas(at)gmail(dot)com> <mailto:robertmhaas(at)gmail(dot)com <mailto:robertmhaas(at)gmail(dot)com>>> wrote:
>>>
>>> On Fri, Dec 15, 2017 at 2:49 PM, Gene Selkov <selkovjr(at)gmail(dot)com <mailto:selkovjr(at)gmail(dot)com> <mailto:selkovjr(at)gmail(dot)com <mailto:selkovjr(at)gmail(dot)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(at)sigaev(dot)ru <mailto:teodor(at)sigaev(dot)ru>
> WWW: http://www.sigaev.ru/ <http://www.sigaev.ru/>