diff options
| -rw-r--r-- | topics/systems/mariadb/precompute-mapping-input-data.gmi | 30 |
1 files changed, 27 insertions, 3 deletions
diff --git a/topics/systems/mariadb/precompute-mapping-input-data.gmi b/topics/systems/mariadb/precompute-mapping-input-data.gmi index d44273f..90b0d63 100644 --- a/topics/systems/mariadb/precompute-mapping-input-data.gmi +++ b/topics/systems/mariadb/precompute-mapping-input-data.gmi @@ -38,6 +38,19 @@ The original reaper precompute lives in This script first fetches inbredsets ``` + select Id,InbredSetId,InbredSetName,Name,SpeciesId,FullName,public,MappingMethodId,GeneticType,Family,FamilyOrder,MenuOrderId,InbredSetCode from InbredSet LIMIT 5; ++----+-------------+-------------------+----------+-----------+-------------------+--------+-----------------+-------------+--------------------------------------------------+-------------+-------------+---------------+ +| Id | InbredSetId | InbredSetName | Name | SpeciesId | FullName | public | MappingMethodId | GeneticType | Family | FamilyOrder | MenuOrderId | InbredSetCode | ++----+-------------+-------------------+----------+-----------+-------------------+--------+-----------------+-------------+--------------------------------------------------+-------------+-------------+---------------+ +| 1 | 1 | BXD | BXD | 1 | BXD Family | 2 | 1 | riset | Reference Populations (replicate average, SE, N) | 1 | 0 | BXD | +| 2 | 2 | B6D2F2 OHSU Brain | B6D2F2 | 1 | B6D2F2 OHSU Brain | 2 | 1 | intercross | Crosses, AIL, HS | 3 | 0 | NULL | +| 4 | 4 | AXB/BXA | AXBXA | 1 | AXB/BXA Family | 2 | 1 | NULL | Reference Populations (replicate average, SE, N) | 1 | 0 | AXB | +| 5 | 5 | AKXD | AKXD | 1 | AKXD Family | 2 | 1 | NULL | Reference Populations (replicate average, SE, N) | 1 | 0 | AKD | +| 6 | 6 | B6BTBRF2 | B6BTBRF2 | 1 | B6BTBRF2 | 2 | 1 | intercross | Crosses, AIL, HS | 3 | 0 | BBT | ++----+-------------+-------------------+----------+-----------+-------------------+--------+-----------------+-------------+--------------------------------------------------+-------------+-------------+---------------+ +``` + +``` MariaDB [db_webqtl]> select Id, Name from InbredSet limit 5; +----+----------+ | Id | Name | @@ -732,9 +745,6 @@ update ProbeSetXRef set Locus_old=NULL; SELECT DISTINCT DataId from ProbeSetXRef INNER JOIN ProbeSetData ON ProbeSetXRef.DataId = ProbeSetData.Id where StrainId>45 AND Locus_old is NULL limit 10; - - - ## Preparing for GEMMA Meanwhile I have prepared tux04 and tux05 for the new runs. Next step is to query the DB and run GEMMA. @@ -786,6 +796,20 @@ For development I'll tunnel to the Tux02 database. As we are doing the BXD's first we first fetch a record from ProbeSetXRef that has Locus_old set to NULL AND matches a BXD trait. +First we fetch all BXD strainids. I wrote a function `bxd-strain-id-names` for that. + +Next, using + +=> https://git.genenetwork.org/gn-guile/commit/?id=b1db013cc01c94e27edf982be9b027a2b0bb9712 + +we fetch the first BXD dataset where all strains are members of BXD: + +``` +((Locus . rs13480619) (DataId . 1) (ProbeSetId . 1))1 +WE HAVE OUR FIRST BXD DATASET for precompute!((1 . 5.742) (2 . 5.006) (3 . 6.079) (4 . 6.414) (5 . 4.885) (6 . 4.719) (7 . 5.761) (8 . 5.604) (9 . 5.661) (10 . 5.708) (11 . 5.628) (12 . 6.325) (13 . 5.37) (14 . 6.544) (15 . 5.476) (16 . 5.248) (17 . 5.528) (19 . 5.51) (20 . 5.886) (21 . 5.177) (22 . 5.655) (23 . 5.522) (24 . 5.549) (25 . 4.588) (26 . 5.618) (28 . 6.335) (29 . 5.569) (30 . 4.422) (31 . 5.194) (35 . 4.784) (36 . 5.056) (37 . 5.869) (39 . 5.175) (40 . 5.207) (41 . 5.264)) +``` + +If it is not a match we'll need to iterate to the next one. ## More complicated datasets |