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missing OMIM info #1833
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Thank you! I confirm it is missing on this variant and a couple of others in the same case. Several others ok however, both in this case and other recent cases. Note that this is a fairly old case with a recent rerun, so reupload issues can be of interest. |
I'm trying to figure out at which stage and why the omim info gets lost for some genes. For instance we know that correct OMIM data gests parsed for genes such as CDC45 (https://scout.scilifelab.se/genes/1739) but not for PRODH (https://scout.scilifelab.se/genes/9453) Following the gene parsing process looks like this: Line 132 in 63c0193
That is responsible for annotating the omim phenotypes, specifically here: Line 226 in 63c0193
I've been printing debug messages and looks like the gene contains a "phenotype" key with the correct values in this latter function, but then when everything goes back to the Line 154 in 63c0193
I've been spending quite some time on this and now omim locked me out for having done too many requests. I could use some help here! |
@moonso when you have some time could you take a look at this? This weird behavior of PRODH gene is still a mistery to me |
Meh, weird! Mystery is the right word! So far:
There might be something weird with the OMIM entries, esp some confusion with PRODH2; let me check that. One worrying detail is that the gene has two phenotype entries in OMIM, one of which is the one we are looking for and the other an association, a ´{pheno}´ which were not correctly parsed in some waaaay old version. The latter is correctly ditched and not loaded to the db, but I can't shake the feeling that may also be connected. |
No, can't reproduce the PRODH2/PRODH OMIM number thing. Leaving that. |
When the dictionary of aliases is created, it contains these items: 'HSPOX2': {'true': None, 'ids': {9453}}, |
Shouldn't Line 51 in 6961041
assign 'true' rather than 'true_id' then? |
(testing that) |
PR upcoming.. |
https://scout.scilifelab.se/cust003/15041/sv/variants/a74106f85d532d2a7aa97225c1fdbab1
no OMIM info in Scout
the gene is in OMIM
https://www.omim.org/entry/606810
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