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Precompute mapping input data

GN relies on precomputed mapping scores for search and other functionality. Here we prepare for a new generation of functionality that introduces LMMs for compute and multiple significant scores for queries.

Tasks

[ ] Start using GEMMA for precomputed values as a background pipeline on a different machine
[ ] Update the table values using GEMMA output (single highest score)

Above is the quick win for plugging in GEMMA value. We will make sure not to recompute the values that are already up to date.

[ ] Track metadata of computed datasets in RDF
[ ] Store all GEMMA values efficiently
[ ] Compute significance with GEMMA or other LMM (bulkLMM?)
[ ] Store signficance and significant values for processing
[ ] Update search & correlations to use these
[ ] Further optimize computations so they can run continuously in the background

Info

Original qtlreaper version

The original reaper precompute lives in

https://github.com/genenetwork/genenetwork2/blob/testing/scripts/maintenance/QTL_Reaper_v6.py

This script first fetches inbredsets

MariaDB [db_webqtl]> select Id, Name from InbredSet limit 5;
+----+----------+
| Id | Name     |
+----+----------+
|  1 | BXD      |
|  2 | B6D2F2   |
|  4 | AXBXA    |
|  5 | AKXD     |
|  6 | B6BTBRF2 |
+----+----------+

and expands them to a .geno file, e.g. BXD.geno. Note that the script does not compute with the many variations of .geno files we have today. Next it sets the Id for ProbeSetFreeze which is the same as the InbredSet Id. So, ProbeSetFreeze.Id == IndbredSet.Id.

Next for this Id we fetch, known as `ProbeSetXRefInfos`:

MariaDB [db_webqtl]> select ProbeSetId, Locus, DataId from ProbeSetXRef where ProbeSetFreezeId=1 limit 5;
+------------+----------------+--------+
| ProbeSetId | Locus          | DataId |
+------------+----------------+--------+
|          1 | rs13480619     |      1 |
|          2 | rs29535974     |      2 |
|          3 | rs49742109     |      3 |
|          4 | rsm10000002321 |      4 |
|          5 | rsm10000019445 |      5 |
+------------+----------------+--------+

Then we fetch the trait values:

MariaDB [db_webqtl]> select Strain.Name, ProbeSetData.value from Strain, ProbeSetData where Strain.Id = ProbeSetData.StrainId and ProbeSetData.Id = 1 limit 5;
+----------+-------+
| Name     | value |
+----------+-------+
| B6D2F1   | 5.742 |
| C57BL/6J | 5.006 |
| DBA/2J   | 6.079 |
| BXD1     | 6.414 |
| BXD2     | 4.885 |
+----------+-------+

with genotypes and these phenotypes qtlreaper is started and next we update the values for

select * from ProbeSetXRef where ProbeSetId=1 and ProbeSetFreezeId=1 limit 5;
+------------------+------------+--------+------------+------------------+------------+------------------+---------------------+------------+-----------------+--------+-------------+------+
| ProbeSetFreezeId | ProbeSetId | DataId | Locus_old  | LRS_old          | pValue_old | mean             |
se                  | Locus      | LRS             | pValue | additive    | h2   |
+------------------+------------+--------+------------+------------------+------------+------------------+---------------------+------------+-----------------+--------+-------------+------+
|                1 |          1 |      1 | 10.095.400 | 13.3971627898894 |      0.163 | 5.48794285714286 |
0.08525787814808819 | rs13480619 | 12.590069931048 |  0.269 | -0.28515625 | NULL |
+------------------+------------+--------+------------+------------------+------------+------------------+---------------------+------------+-----------------+--------+-------------+------+

the actual update is

update ProbeSetXRef set Locus=%s, LRS=%s, additive=%s where ProbeSetId=%s and ProbeSetFreezeId=%s

so Locus, LRS and additive fields are updated.

From this exercise we can conclude:

Existing precomputed values are by linear regression (old QTLreaper)
Only one highest score is stored
Every time the script is run *all* datasets are recomputed
The '_old' named values in the table are not touched by the script
h2 and mean are not updated
No significance score is computed (needs permutations)

Rob voiced a wish to retain all scores (at least those above 1.0). This is not feasible in mariadb, but we can retain GEMMA output if stored efficiently.

Notes on ProbeSetXRef

ProbeSetXRef is pretty small, currently @5.6Gb and 48,307,650 rows, so we could decide to add columns to track different mappers. Something funny

select count(LRS) from ProbeSetXRef;
+------------+
| count(LRS) |
+------------+
|   28335955 |
+------------+

half the fields are used. What to think of

MariaDB [db_webqtl]> select * from ProbeSetXRef where LRS=0 limit 5;
+------------------+------------+----------+-----------+---------+------------+------+------+----------------+------+--------+----------+------+
| ProbeSetFreezeId | ProbeSetId | DataId   | Locus_old | LRS_old | pValue_old | mean | se   | Locus          | LRS  | pValue | additive | h2   |
+------------------+------------+----------+-----------+---------+------------+------+------+----------------+------+--------+----------+------+
|              589 |    8599010 | 70606737 | NULL      |    NULL |       NULL |    0 | NULL | rsm10000000001 |    0 |   NULL |        0 | NULL |
|              589 |    8593710 | 70606738 | NULL      |    NULL |       NULL |    0 | NULL | rsm10000000001 |    0 |   NULL |        0 | NULL |
|              589 |    8607637 | 70606739 | NULL      |    NULL |       NULL |    0 | NULL | rsm10000000001 |    0 |   NULL |        0 | NULL |
|              589 |    8594490 | 70606740 | NULL      |    NULL |       NULL |    0 | NULL | rsm10000000001 |    0 |   NULL |        0 | NULL |
|              589 |    8591994 | 70606741 | NULL      |    NULL |       NULL |    0 | NULL | rsm10000000001 |    0 |   NULL |        0 | NULL |
+------------------+------------+----------+-----------+---------+------------+------+------+----------------+------+--------+----------+------+

MariaDB [db_webqtl]> select count(*) from ProbeSetXRef where LRS=0 and Locus="rsm10000000001";
+----------+
| count(*) |
+----------+
|   291447 |
+----------+

There is obviously more. I think this table can use some cleaning up?

Preparing for GEMMA

A good dataset to take apart is

http://genenetwork.org/show_trait?trait_id=1436869_at&dataset=HC_M2_0606_P