Closed rcdilorenzo closed 3 years ago
Example from fake data:
phc.GenomicShortVariant.get_data_frame( patient_id="2c8660b4-1e63-403e-b52b-55c290072a66", chromosome=[phc.Option.Chromosome.CHR_19], gene_class=[phc.Option.GeneClass.PROTEIN_CODING], zygosity=[phc.Option.Zygosity.HETEROZYGOUS], rs_id=["rs11324363", "rs36247", "rs77134098"], min_allele_frequency="0.2-1", log=True, all_results=True )
Log output:
{ "path": "genomics/projects/6f37463d-60b5-4c67-b06e-ffc87c8d780f/tests", "method": "GET", "params": { "patientId": "2c8660b4-1e63-403e-b52b-55c290072a66", "status": "ACTIVE", "type": "shortVariant" } } [CACHE] Loading from "/home/jovyan/Downloads/phc/api-cache/genomics_projects_tests_711a406c.csv" { "path": "genomics/variants", "method": "GET", "params": { "variantSetIds": "2293c69b-78a5-4012-8080-e1c20d6934d3,60775dcc-c15a-4f0b-8cb9-264838848be4,de80dbe0-4ae9-4baa-ae95-8f785b958893", "include": "vcf", "rsid": "rs11324363,rs36247,rs77134098", "chromosome": "chr19", "biotype": "protein coding,nonsense mediated decay", "minAlleleFrequency": "0.2-1", "zygosity": "heterozygous" } } 100% 2/2 [00:00<00:00, 29.60it/s] Loading data frame from "/home/jovyan/Downloads/phc/api-cache/genomics_variants_fe0333c5.csv"
Result (frame info):
<class 'pandas.core.frame.DataFrame'> RangeIndex: 2 entries, 0 to 1 Data columns (total 77 columns): # Column Non-Null Count Dtype --- ------ -------------- ----- 0 id 2 non-null object 1 variant_set_id 2 non-null object 2 chromosome 2 non-null object 3 reference 2 non-null object 4 alternate 2 non-null object 5 position 2 non-null int64 6 minimumAlleleFrequency 2 non-null float64 7 maximumAlleleFrequency 2 non-null float64 8 gnomadAlleleFrequency 2 non-null float64 9 gnomadHomozygous 2 non-null int64 10 exacAlleleFrequency 2 non-null float64 11 exacHomozygous 2 non-null int64 12 rsid 2 non-null object 13 zygosity 2 non-null object 14 clinvar.nearVariant 2 non-null int64 15 cosmic.cosmicId 2 non-null object 16 cosmic.status 2 non-null object 17 cosmic.histology 2 non-null object 18 cosmic.tumorSite 2 non-null object 19 cosmic.sampleCount 2 non-null int64 20 cosmic.nearVariant 2 non-null int64 21 ensemblCanon.class 2 non-null object 22 ensemblCanon.group 2 non-null object 23 ensemblCanon.impact 2 non-null object 24 ensemblCanon.gene 2 non-null object 25 ensemblCanon.geneId 2 non-null object 26 ensemblCanon.transcriptId 2 non-null object 27 ensemblCanon.biotype 2 non-null object 28 ensemblCanon.exonIntronRank 2 non-null object 29 ensemblCanon.nucleotideChange 2 non-null object 30 ensemblCanon.aminoAcidChange 1 non-null object 31 ensemblCanon.hgvsAminoAcidChange 1 non-null object 32 dbnsfp.siftPred 0 non-null float64 33 dbnsfp.mutationTasterPred 0 non-null float64 34 dbnsfp.fathmmPred 0 non-null float64 35 vcf.quality 2 non-null float64 36 vcf.filter 2 non-null object 37 vcf.variantAllelicFrequency 2 non-null float64 38 vcf.coverage 2 non-null object 39 gene 2 non-null object 40 status 2 non-null object 41 sequenceType 2 non-null object 42 setType 2 non-null object 43 fileId 2 non-null object 44 sequenceId 2 non-null object 45 name 2 non-null object 46 tasks 2 non-null object 47 id.test 2 non-null object 48 datasetId 2 non-null object 49 name.test 2 non-null object 50 reportFileId 2 non-null object 51 indexedDate 2 non-null object 52 testType 2 non-null object 53 referenceSetId 2 non-null object 54 status.test 2 non-null object 55 createdDate 2 non-null datetime64[ns, UTC] 56 sourceFileId 2 non-null object 57 sourceFile.id 2 non-null object 58 sourceFile.name 2 non-null object 59 sourceFile.datasetId 2 non-null object 60 sourceFile.size 2 non-null int64 61 sourceFile.contentType 2 non-null object 62 sourceFile.lastModified 2 non-null datetime64[ns, UTC] 63 sourceFile.userId 2 non-null object 64 sourceFile.lrn 2 non-null object 65 patientId 2 non-null object 66 patient.name_text 2 non-null object 67 patient.name_family 2 non-null object 68 patient.name_given 2 non-null object 69 patient.identifier_system__urn:oid:1.3.6.1.4.1.12009.1.2.1__type_coding_system__hl7.org/fhir/v2/0203__code 2 non-null object 70 patient.identifier_system__urn:oid:1.3.6.1.4.1.12009.1.2.1__value 2 non-null int64 71 patient.identifier_system__lifeomic.com/unknown/genomics/subject-id__type_coding_system__hl7.org/fhir/v2/0203__code 2 non-null object 72 patient.identifier_system__lifeomic.com/unknown/genomics/subject-id__value 2 non-null int64 73 patient.id 2 non-null object 74 patient.resourceType 2 non-null object 75 bodySite.system__lifeomic.com/fhir__code 2 non-null object 76 bodySite.system__lifeomic.com/fhir__display 2 non-null object dtypes: datetime64[ns, UTC](2), float64(9), int64(9), object(57) memory usage: 1.3+ KB
Example from fake data:
Log output:
Result (frame info):