I was looking at the unmapped test and we have
s-p�lyer [u/ml] that clearly should be s-pölyer so i wrote a bash command to fix it. I downloaded the new thl mapping file from 2025
https://koodistopalvelu.kanta.fi/codeserver/pages/classification-view-page.xhtml?classificationKey=88&versionKey=120
and ran
pete@pete-VirtualBox:/media/sf_Dropbox/Projects/kanta_lab_preprocessing/finngen_qc/data$ iconv -f ISO-8859-1 -t UTF-8 120_1387444168447.txt | tr -d '\r' | awk -F';' 'NR==1{print "CodeId\tAbbreviation"} NR>1{abbr=$2; gsub(/ /,"",abbr); print $1"\t"tolower(abbr)}' | grep 7154
7154 s-pölyer
pete@pete-VirtualBox:/media/sf_Dropbox/Projects/kanta_lab_preprocessing/finngen_qc/data$ cat thl_lab_id_abbrv_map.tsv | grep 7154
7154 s-p�lyer
but then i was looking at the changes and there's more changes that also affect our data. with ~500 changes. fortunately if we look at mapped values
| OLD_TEST |
OMOP_ID |
COUNT |
NEW_TEST |
IS_IN_USAGI |
| pt-ekg-12 |
3044889 |
1163408 |
ekg-12 |
true |
| pt-ekg-atk |
3013512 |
299923 |
ekg-atk |
true |
| pt-fvspido |
4010399 |
50607 |
fvspido |
false |
| pt-fvspird |
3000492 |
38360 |
fvspird |
false |
| pt-klr-tje |
4094501 |
13035 |
klr-tje |
false |
| pt-fvspiro |
3000492 |
11757 |
fvspiro |
false |
| pt-fvspio |
3000492 |
10517 |
fvspio |
false |
| -pncanho |
3009595 |
5301 |
-pnjinho |
false |
| s-d-1 |
3011391 |
4661 |
s-d-1,25 |
false |
| pt-ekg-15 |
3004451 |
3021 |
ekg-15 |
false |
| pt-spirom |
4133840 |
1441 |
spirom |
false |
| s-hasphe |
3011951 |
633 |
s-haspähe |
true |
| s-vehne |
3027231 |
528 |
s-vehnäe |
true |
| s-plyry |
3023351 |
251 |
s-pölyry |
true |
| p-kupari |
3001186 |
148 |
p-cu |
true |
Some of them are already in the usagi file, others would need to be introduced
I was looking at the unmapped test and we have
s-p�lyer [u/ml]that clearly should bes-pölyerso i wrote a bash command to fix it. I downloaded the new thl mapping file from 2025https://koodistopalvelu.kanta.fi/codeserver/pages/classification-view-page.xhtml?classificationKey=88&versionKey=120
and ran
but then i was looking at the changes and there's more changes that also affect our data. with ~500 changes. fortunately if we look at mapped values
Some of them are already in the usagi file, others would need to be introduced