5i6ddlmZddlZddlmZdZdZejjZ dZ ddZ d Z d Z dd Z dd Z dd Zy)) annotationsN)err_exitz#Found following invalid filters: {}z/Too many items given in field {}, maximum is {})refzhet-refhomzhet-althalfno-callc@td|tjy)Nz WARNING: )file)printsysstderr)msgs /home/marpiech/ifpan-abm-pgxpred/analysis/marpiech-gwas-test/venv/lib/python3.12/site-packages/dxpy/dx_extract_utils/input_validation.pywarnrs IcU #**-ct|tsy|D]A}tdk(r$t|trt|tr.yt|trAyy)NFrT) isinstancelistpython_versionstrunicode)objectitems ris_list_of_stringsrsN fd # Q tS)Zg-FdC( rc|j}|dk(rd|vrd|vr tdd|vsd|vs tdd|vr\t|dsttj dt |ddkDrtt j ddd|vrt|dsttj d|dD]%}|dvsttj d't |ddkDrtt j ddd |vry|d d }|d d }|d krttj d |d kDrttj d ||kDrttj d d|vry|dd }|dd }|d krttj d|d kDrttj d||kDrttj dd|vrt |ddkDrtt j dd|dD]}}|j}d|vrd|vrd|vsttj dtt|jr`ttj d|dk(r|j}d|jvs/d|jvsd|jvs tdd|vrd|vsd|vr;tdn/d|vrd|vsd|vr#tdnd|vrd|vsd|vr tdd|vsd|vrd|vrd|vrd|vr td|D]/}t||rttj |1d|vr0t |ddkDrtt j ddd|vr0t |ddkDrtt j ddd|vr0t |ddkDrtt j ddd|vr0t |ddkDrtt j ddd|vr0t |ddkDrtt j dd|dk(rv|j}d|vsd|vs tdd|vrd|vr td d|vr\t|dsttj dt |ddkDrtt j ddd|vrt |ddkDrtt j dd|dD]}|j}d|vrd|vsttj dd|vrttj dtt|jr~ttj dd!|vr\t|d!sttj d!t |d!d"kDrtt j d!d"d#|vrt|d#s!ttj d#d$z|d#D];}|tvs ttj d#d%j |z=t |d#d&kDr tt j d#d'yyyy)(NallelelocationrsidzDlocation and rsid fields cannot both be specified in the same filterz=Either location or rsid must be specified in an allele filterdtype)SNPInsDelMixeddataset_alt_afminmaxr gnomad_alt_af chromosomestarting_positionending_position annotation allele_id gene_namegene_idzBallele_id, gene_name, or gene_id is required in annotation_filterszUOnly one of allele_id, gene_name, and gene_id can be provided in an annotation filter consequencesputative_impact feature_idzvconsequences and putative impact fields may not be specified without at least one of gene_id, gene_name, or feature_idhgvs_chgvs_pgenotypez5allele_id or location is required in genotype filterszRallele_id and location fields cannot both be specified in the same genotype filter sample_idi genotype_typez' genotype type is not a list of stringsz& value {} is not a valid genotype_type) keysrrmalformed_filterformatlenmaxitem_messagervaluesGENOTYPE_TYPES) filter filter_typer<rmin_valmax_valindiv_locationindiv_loc_keyskeys rvalidate_filterrJ(s ;;=Dh $ Vt^ V t#4 T U T>%fVn5)00896&>"S(//<= T>%fVn5)0089v >==-44V<= >6&>"S(//<= t #-.u5G-.u5G{)001ABC{)001ABC )001ABC d "_-e4G_-e4G{)00AB{)00AB )00AB  6*%&,// C@A"("4 B!/!4!4!6"^3,>*n<-44Z@A)$~/D/D/F*GH-44Z@A Bl"{{} FKKM )v{{},V[[]* T  $ t#d):k$ t#)<kD T!{d':k d "(9T(A$& ,!-J  7C%fSk2)0056 7 $ 6+&'#-// SAB $ 6+&'#-// SAB  6)$%+// 3?@ t 6(#$s*//#>? t 6(#$s*//#>?j {{}t#zT'9 L M $ :#5 i j $ %f[&9:)00=>6+&'#-// SAB  6*%&,// C@A"("4 B!/!4!4!6$6;NR`;`-44Z@A$6-44Z@A)$~/D/D/F*GH-44Z@A B $ %f[&9:)00=>6+&'$.// TBC d "%f_&=>)00ADnno/ ~--44_EGpGwGwx|G}}~  6/*+a///CD0 #W!rc2|s|r | tddt|jdt|jdt|j}|r|dur|dur|std||r|r|dur|dustd|yyy)NzThe --infer-ref or --infer-nocall flags can only be used when the undelying assay is of version generalized_assay_model_version 1.0.1/1.1.1 or higher.z:Exclusion parameters set at the ingestion: exclude_nocall=z, exclude_halfref=z, exclude_refdata=FzThe --infer-ref flag can only be used when exclusion parameters at ingestion were set to 'exclude_nocall=false', 'exclude_halfref=false', and 'exclude_refdata=true'. zThe --infer-nocall flag can only be used when exclusion parameters at ingestion were set to 'exclude_nocall=true', 'exclude_halfref=false', and 'exclude_refdata=false'. )rrlower) infer_nocall infer_refexclude_nocallexclude_refdataexclude_halfrefingestion_parameters_strs rvalidate_infer_flagsrSs, \~'= e "\\_`n\o\u\u\w[xyKLOP_L`LfLfLhKii{|@O|P|V|V|X{Y Z e #5( z{SzTU  5(5( }~V}WX ) rc>d|vr|r'|s%d|dvr td|dgk(r td|r'|s%d|dvr td|dgk(r td|r%d|dvr td |dgk(r td |d|dvs |d|dvr td yyyy) Nr9r zFilter requested genotype type 'no-call', genotype entries of this type were not ingested in the provided dataset and the --infer-nocall flag is not set!zNo genotype type requested in the filter. All genotype types will be returned. Genotype entries of type 'no-call' were not ingested in the provided dataset and the --infer-nocall flag is not set!rzFilter requested genotype type 'ref', genotype entries of this type were not ingested in the provided dataset and the --infer-ref flag is not set!zNo genotype type requested in the filter. All genotype types will be returned. Genotype entries of type 'ref' were not ingested in the provided dataset and the --infer-ref flag is not set!rzsFilter requested genotype type 'half', 'half-ref genotype' entries (0/.) were not ingested in the provided dataset!zNo genotype type requested in the filter. All genotype types will be returned. 'half-ref' genotype entries (0/.) were not ingested in the provided dataset!z"ref" and "no-call" genotype types can only be filtered when the undelying assay is of version generalized_assay_model_version 1.0.1/1.1.1 or higher.)rrrMrN filter_dictrOrPrQs r)validate_filter_applicable_genotype_typesrWs +% ,K88p?+r1Z 9 O44i?+r1S _55J?+r1s  #_55%[99 h :&?&rcBt|||||t||||||y)N)rSrWrUs rinference_validationrY:s3i/. r)rr) rMboolrNrZrOrZrPrZrQrZ) rMrZrNrZrVdictrOrZrPrZrQrZ) __future__rr exceptionsrr=r@ version_infomajorrrBrrrJrSrWrYrrras" !9C!!''. }E~   B//// /  /  /d     r