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| -rw-r--r-- | topics/systems/mariadb/precompute-mapping-input-data.gmi | 59 |
1 files changed, 56 insertions, 3 deletions
diff --git a/topics/systems/mariadb/precompute-mapping-input-data.gmi b/topics/systems/mariadb/precompute-mapping-input-data.gmi index 85a11ee..caad794 100644 --- a/topics/systems/mariadb/precompute-mapping-input-data.gmi +++ b/topics/systems/mariadb/precompute-mapping-input-data.gmi @@ -916,9 +916,62 @@ select * from StrainXRef WHERE InbredSetId=1 AND Used_for_mapping="Y" 276 rows ``` -so it looks like we need some extra logic. - - +so it looks like we need some extra logic to fetch the used individuals from the actual genotype file(s). + +## Writing the phenotype file + +For gemma we need to feed a phenotype file that has only the individuals that are in the genotype file (the other 'missing' phenotype values should be NAs). + +The genotype header in GN2 is read from a `BXD.json` file. Code is at +wqflask/wqflask/marker_regression/run_mapping.py:get_genofile_samplelist(dataset) + +Zach writes: + +> The JSON files were basically just a "stopgap" solution to allow for +> multiple genotype files for any given group (which previously wasn't +> possible), and they don't even exist for most groups - the code uses +> them only if they exist for a given group. They contain the +> title/label, filename, and sample lists for situations where the other +> genotype files only contain a subset of the samples from the full +> sample list, but otherwise (and usually) the samplelist is just fetched +> from the .geno file. It's also possible to fetch that subset of samples +> from the other/alternate .geno files, but it's easier to just fetch the +> samples as a list from that .json file than it is to parse it out of +> the other .geno files (and the JSON file would still be used to to get +> the "title" and filenames, so it's already being read in the code). +> Basically the JSON files are just a sort of "genotype file metadata" +> thing to deal with the existence of multiple genotype files for a +> single group and provide the "attributes" of the files in question +> (namely the title and filename - the sample lists were only added later +> once we started to get genotype files that didn't contain the full +> samplelist for the group in question). The "titles" appear in the +> drop-down on the trait page* - in their absence it will just use +> "{group_name}.geno" (for example BXD.geno). So if you deleted BXD.json, +> mapping would still work for BXD, but it would just default to BXD.geno +> and wouldn't give the option of other files. This information could +> probably also be stored somehow in the .geno file, but I'm not sure how +> to easily do so since that's a weird proprietary format and would +> seemingly require some sort of direct parsing in the GN code (while +> JSON is more simple to deal with). + +=> https://genenetwork.org/show_trait?trait_id=1427571_at&dataset=HC_M2_0606_P + +> If you scroll down to mapping and Inspect Element on the +> Genotypes drop-down you'll see how the values are the actual filenames +> while the text is the title from the JSON file + +So this is genotype metadata which could go into virtuoso (where all metadata belongs). +Anyway, we'll get there when the time comes, but for now I can use it to see what genotypes we have in the genotype file and write the phenotype file accordingly. + +I note we also have a GenoData table in mariadb which has allele info. The script + +=> https://github.com/genenetwork/genenetwork2/blob/testing/scripts/maintenance/load_genotypes.py + +loads these from the BXD.geno-type files. As far as I can tell GenoData is not used in GN2+GN3. Other Geno files are basically used to fetch metadata on genotypes. + +Genotype state lives in 4 places. Time to create a 5th one with lmdb ;). At least the BXD.json file lines up with BXD.8.geno and the BIMBAM version with 235 inds. + +Using this information we created our first phenotype file and GEMMA run! ## More complicated datasets |