Upload Sample - geneyx/geneyx.analysis.api GitHub Wiki

This API call allows a user to upload a VCF file and create a corresponding Sample entry in Geneyx Analysis. Other than the VCF file, additional metadata may be included in the Sample with or without an associated JSON file. Optionally, the Sample entry may be associated with an existing Subject entry (by ID).

To run this code, you will need to navigate to https://github.com/geneyx/geneyx.analysis.api/. There is a green icon for Code. Select the icon and click Download Zip. Extract the files, then navigate to the script directory.

The https://github.com/geneyx/geneyx.analysis.api/tree/main/scripts directory contains:

• ga.config.yml
• ga_uploadSample.py
• ga_uploadSample_json.py
• UnifiedVcf.py

Additionally, the https://github.com/geneyx/geneyx.analysis.api/tree/main/scripts/templates directory contains:

• sample.json

First you will need to modify the ga.config.yml file to reflect your api ID and api key. Once saved, you can then define the parameters which are listed below. The CMD values will be used for the command line. Please see the command line request below, which provides an example of the process.

https://analysis.geneyx.com/api/createSample

https://fa.shanyint.com/api/createSample

Category	Parameter	CMD Values	Description	Required
Auth	ApiUserId	—	The API user Id	Yes
	ApiUserKey	—	The API user key	Yes
	CustomerAccountKey	—	Geneyx Analysis Customer account key (	No
Sample	SampleSerialNumber	sampleId	Sample ID, name given to the VCF file	Yes
	SampleSequenceDate	sampleSequenceDate	Date when sample was sequenced	No
	SampleTakenDate	sampleTakeDate	Date when sample was taken	No
	SampleReceivedDate	sampleRecieveDate	Date when sample was received	No
	SampleSequencingMachineID	seqMachineId	ID of Sequencing Machine entry as defined in customer account.	No
	SampleEnrichmentKitId	kitId	ID of Enrichment Kit entry as defined in account	No
	SampleType	sampleType	May be one of the following: RnaSeq , DnaSeq	No
	SampleTarget	sampleTarget	May be one of the following: WholeGenome, Exome,GenePanel, TargetRegion	Yes
	SampleSource	sampleSource	May be one of the following: Germline, Tumor, Blood, Buccal, Fetal, Saliva, Other	No
	SampleGenomeBuild	genomeBuild	Maybe one of the following: hg19,hg38	No
	SampleRelation	sampleRelation	The sample relation, can be: Self, Mother, Father, Sibling, Twin, MotherRelative, FatherRelative, Other	No
	SampleNotes	sampleNotes	Free text up to 1024 characters	No
	SampleQcData	sampleQcData	JSON structure for QC data	No
	SnvFile	snvBaseName	The name of the SNV file	No
	StructFile	svBaseName	The name of the structural variation file	No
	BamUrl	bamUrl	The URL to the BAM file	No
Subject	SubjectId	patientId	Unique identified for Subject. May be any string. If an existing subject exists. It will be associated.	Yes
	SubjectName	patientName	Name of subject	No
	SubjectGender	patientGender	May be “M” or “F”	No
	SubjectDateOfBirth	patientDateOfBirth	Date of birth of subject	No
	SubjectConsanguinity	patientConsanguinity	The subject consanguinity, option are Unkown (Default), Consanguineous, Non-Consanguineous	No
	SubjectPopulationType	patientPopulationType	Population type	No
	SubjectPaternalAncestry	patientPaternalAncestry	Paternal ancestry	No
	SubjectMaternalAncestry	patientMaternalAncestry	Maternal ancestry	No
	SubjectFamilyHistory	patientFamilyHistory	The family history	No
Assignment	AssignedToUserId	groupAssignmentCode	The user id the sample is assigned to.	No
	AssignedToFullName	groupAssignmentName	The full name of the user the sample is assigned to.	No
	GroupAssignment	GroupAssignment	List of groups the sample is assigned to. Each list item has: Code, Name	No
File	Files	snvVcf, svVcf, cnvVcf	Parameter of type File, must be .vcf or .vcf.gz	No

C:\Dev\geneyx.analysis.api\scripts>python ga_uploadSamples.py --snvVcf "C:\Users\eliws\OneDrive\Desktop\Geneyx\Production\scripts\GeneyxEval.vcf.gz" --sampleId Example3 --sampleSequenceDate 01/02/03 --sampleTakenDate 02/03/04 --sampleReceiveDate 03/18/22 --seqMachineId "NextSeq 2000" --kitId "Default - Exons only" --sampleType DnaSeq --sampleTarget Exome --sampleSource GermLine --genomeBuild hg19 --sampleNotes DemonstrationImport --sampleRelation Self --patientId ExampleImporta --patientName Example12 --patientGender M --patientDateOfBirth 08/04/1969 --patientConsanguinity Unknown

C:\Dev\geneyx.analysis.api\scripts>python ga_uploadSample_json.py --snvVcf "C:\Users\eliws\OneDrive\Desktop\Geneyx\Production\scripts\GeneyxEval.vcf.gz" --data sample.json

Uploading sample(s)
<Response [200]>
b'{"Code":"success","Data":null,"Info":null,"MoreInfo":null,"NeedEval":false}'