Don-Isdale
commented
3 months ago Test
Test Case
This facility is implemented and tested first, to confirm the functionality and performance of the lookup from SNP names to regions, before adding the ability to pass an array of SNP names in the lookup request from the frontend. This will be replaced by actual params from frontend.
The test configuration used the existing request, which requires a region. The region chosen for the request contains the SNP names, so it doesn't impact the test.
Results
Server log extract
Confirming that the correct filter command is used.
+ '[' query = view_query ']'
+ bcftools query 201028_40K_DAS5_samples_XT_exomeIDs/1A.MAF.SNPList.vcf.gz -r 1A:322574-2019320 -S /dev/null -H -f '%ID %POS %REF %ALT %INFO[ %TGT]
' -i ' ID="scaffold38755_1235130" || ID="scaffold38755_1337276" '
dataOutReply lineCount 3 235 0
+ status=0
+ set -x
+ status_0=0
+ '[' -n '' ']'
+ exit 0
child process exited with code 0
cbWrap null #[1]ID [2]POS [3]REF [4]ALT [5](null)
scaffold38755_1235130 1235130 C T F_MISSING=0.0259067;NS=564;AN=1128;MAF=0.150709;AC=170;AC_Het=12
scaffold38755_1337276 1337276 G C F_MISSING=0.0138169;NS=571;AN undefinedAPI Request
http://localhost:3000/api/Blocks/vcfGenotypeLookup?datasetId=201028_40K_DAS5_samples_XT_exomeIDs&scope=1A&preArgs%5Bregion%5D=1A%3A322574-2019320&preArgs%5BrequestInfo%5D=false&preArgs%5BrequestFormat%5D=CATG&nLines=400API Result
{"text":"#[1]ID\t[2]POS\t[3]REF\t[4]ALT\t[5](null)
scaffold38755_1235130\t1235130\tC\tT\tF_MISSING=0.0259067;NS=564;AN=1128;MAF=0.150709;AC=170;AC_Het=12
scaffold38755_1337276\t1337276\tG\tC\tF_MISSING=0.0138169;NS=571;AN=1142;MAF=0.400175;AC=457;AC_Het=1
"}
Part of #383
Observable outcomes :
This enables the User to enter SNP names instead of selecting a chromosome region, and request the lookup of Genotype values for those SNP names.
Measure with :
Perform the script either from the command line, or by adding parameters to a request sent by the application, and confirm from the trace that the correct lookup command is performed, and that the results are correct and apply to the requested SNP names.