U 7gbF_@sddlmZmZddlZddlZddlZzddlmZWn ek rXddlmZYnXe dZ Gddde Z Gddde Z Gd d d e ed ZGd d d eZGdddeZGdddeZGdddeZddZdS))ABCMetaabstractmethodN)Counterz[|/]c@seZdZdZdddddddgZd d Zd d Zd dZddZddZ ddZ e ddZ e ddZ e ddZddZe ddZe dd Ze d!d"Zd#S)$_Callz, A genotype call, a cell entry in a VCF filesitesampledatagt_nums gt_allelescalledploiditycCs||_||_||_t|jdddk rvddt|jjD|_t|j|_ t dd|jD|_ |j rn|jjnd|_ nd|_d|_ d|_ d|_ dS)NGTcSsg|]}|dkr|ndqS).N.0Zalrr(lib/python3.8/site-packages/vcf/model.py sz"_Call.__init__..css|]}|dk VqdSNrrrrr sz!_Call.__init__..) rrrgetattrallele_delimitersplitr r lenr anyr r )selfrrrrrr__init__s z_Call.__init__cCsd|jt|jfS)NzCall(sample=%s, %s))rstrrrrrr__repr__&sz_Call.__repr__cCs6|jt|ddko4|jt|ddko4|jt|ddkS)zt Two _Calls are equal if their _Records are equal and the samples and ``gt_type``s are the same rNrgt_type)rrrr rotherrrr__eq__)s z _Call.__eq__cstfddjDS)Nc3s|]}|t|fVqdSr)r)rattrrrrr2sz%_Call.__getstate__..)dict __slots__rrrr __getstate__1sz_Call.__getstate__cCs"|jD]}t||||qdSr)r&setattrget)rstater$rrr __setstate__4s z_Call.__setstate__cCs|js dSdS)N/|)phasedrrrr gt_phase_char8sz_Call.gt_phase_charcsJjrBz fddjDWStjdYqFXndSdS)zXThe actual genotype alleles. E.g. if VCF genotype is 0/1, return A/G c3s.|]&}t|dk r jjt|ndVqdS)Nr)rrallelesintrXrrrrDsz!_Call.gt_bases..z+Allele number not found in list of alleles N)r r/joinr sysstderrwriterrrrgt_bases;s  z_Call.gt_basescsN|jrF|jtfddddDr@ddkr:dSdSqJdSndSdS)zThe type of genotype. hom_ref = 0 het = 1 hom_alt = 2 (we don;t track _which+ ALT) uncalled = None c3s|]}|dkVqdS)rNrr2r0rrrUsz _Call.gt_type..Nr0)r r allrrr9rr Js  z _Call.gt_typecCs|jdk o|jddkS)z^A boolean indicating whether or not the genotype is phased for this sample Nr-r)r findrrrrr._sz _Call.phasedcCs t|j|S)z' Lookup value, backwards compatibility )rr)rkeyrrr __getitem__fsz_Call.__getitem__cCs|js dS|jdkS)z% Return True if not a reference call Nrr r rrrr is_variantjsz_Call.is_variantcCs|js dS|jdkS)z$ Return True for heterozygous calls Nr:rArrrris_hetqsz _Call.is_hetcCsDz |jj}Wntk r"YdSX|dks8t|dkrd?Z"ed@dAZ#edBdCZ$edDdEZ%edFdGZ&edHdIZ'edJdKZ(edLdMZ)edNdOZ*edPdQZ+dS)T_Recordah A set of calls at a site. Equivalent to a row in a VCF file. The standard VCF fields CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO and FORMAT are available as properties. The list of genotype calls is in the ``samples`` property. Regarding the coordinates associated with each instance: - ``POS``, per VCF specification, is the one-based index (the first base of the contig has an index of 1) of the first base of the ``REF`` sequence. - The ``start`` and ``end`` denote the coordinates of the entire ``REF`` sequence in the zero-based, half-open coordinate system (see http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms), where the first base of the contig has an index of 0, and the interval runs up to, but does not include, the base at the ``end`` index. This indexing scheme is analagous to Python slice notation. - The ``affected_start`` and ``affected_end`` coordinates are also in the zero-based, half-open coordinate system. These coordinates indicate the precise region of the reference genome actually affected by the events denoted in ``ALT`` (i.e., the minimum ``affected_start`` and maximum ``affected_end``). - For SNPs and structural variants, the affected region includes all bases of ``REF``, including the first base (i.e., ``affected_start = start = POS - 1``). - For deletions, the region includes all bases of ``REF`` except the first base, which flanks upstream the actual deletion event, per VCF specification. - For insertions, the ``affected_start`` and ``affected_end`` coordinates represent a 0 bp-length region between the two flanking bases (i.e., ``affected_start`` = ``affected_end``). This is analagous to Python slice notation (see http://stackoverflow.com/a/2947881/38140). Neither the upstream nor downstream flanking bases are included in the region. Nc Cs||_||_||_||_||_||_||_||_| |_|jd|_ |j t |j|_ |jg|_ |j |j| prg|_| |_d|_d|_|dSNr:)CHROMPOSIDREFALTQUALFILTERINFOFORMATstartrendr0extendsamples_sample_indexesaffected_start affected_end_set_start_and_end) rrNrOrPrQrRrSrTrUrVZsample_indexesrZrrrrs$   z_Record.__init__cCs|j|_|_|jD]r}|dkr.|\}}n<|jdkrF|\}}n$|jdkr^|\}}n |\}}t |j||_t |j||_qdS)NSNVMNV) rOr\r]rR!_compute_coordinates_for_none_alttype_compute_coordinates_for_snp_compute_coordinates_for_indel_compute_coordinates_for_svminmax)raltrWrXrrrr^s    z_Record._set_start_and_endcCs |jd}|t|j}||fSrMrOrrQrrWrXrrrras z)_Record._compute_coordinates_for_none_altcCs@t|jdkr(|j}|t|jd}n|jd}|j}||fSrMrrQrOrjrrrrcs  z$_Record._compute_coordinates_for_snpcCs:t|jdkr(|j}|t|jd}n |j}}||fSrMrkrjrrrrds  z&_Record._compute_coordinates_for_indelcCs |jd}|t|j}||fSrMrirjrrrres z#_Record._compute_coordinates_for_svcCs&t|j|jft|ddt|ddfSNrNrO)ZcmprNrOrr!rrr__cmp__sz_Record.__cmp__cCsH|jt|ddkoF|jt|ddkoF|jt|ddkoF|jt|ddkS)zO _Records are equal if they describe the same variant (same position, alleles) rNNrOrQrR)rNrrOrQrRr!rrrr#sz_Record.__eq__cCs$|j|jft|ddt|ddfkSrl)rNrOrr!rrr__lt__ sz_Record.__lt__cCs t|jSr)iterrZrrrr__iter__ sz_Record.__iter__cCs d|jS)Nz>Record(CHROM=%(CHROM)s, POS=%(POS)s, REF=%(REF)s, ALT=%(ALT)s))__dict__rrrr__str__sz_Record.__str__cCs|jd||_dS)N:)rV)rZfmtrrr add_formatsz_Record.add_formatcCs$|jdkr|g|_n |j|dSr)rTappend)rZfltrrr add_filters  z_Record.add_filterTcCs||j|<dSr)rU)rinfovaluerrradd_infosz_Record.add_infocCs|j|j|S)z5 Lookup a ``_Call`` for the sample given in ``name`` )rZr[)rnamerrrgenotypesz_Record.genotypecCstdd|jDS)z The number of called samplescss|]}|jrdVqdS)r:N)r rsrrrr&sz%_Record.num_called..)sumrZrrrr num_called#sz_Record.num_calledcCst|jtt|jS)z6 The fraction of genotypes that were actually called. )floatrrrZrrrr call_rate(sz_Record.call_ratecCstdd|jDS)z2 The number of homozygous for ref allele genotypescSsg|]}|jdkr|qSrr r|rrrr0s z'_Record.num_hom_ref..rrZrrrr num_hom_ref-sz_Record.num_hom_refcCstdd|jDS)z2 The number of homozygous for alt allele genotypescSsg|]}|jdkr|qSr<rr|rrrr5s z'_Record.num_hom_alt..rrrrr num_hom_alt2sz_Record.num_hom_altcCstdd|jDS)z% The number of heterozygous genotypescSsg|]}|jdkr|qSr:rr|rrrr:s z#_Record.num_het..rrrrrnum_het7sz_Record.num_hetcCstdd|jDS)z The number of unknown genotypescSsg|]}|jdkr|qSrrr|rrrr?s z'_Record.num_unknown..rrrrr num_unknown<sz_Record.num_unknowncsddt|jD].}|jdk r|jD]}|gd7q$qfddtdt|jdDS)zz A list of allele frequencies of alternate alleles. NOTE: Denominator calc'ed from _called_ genotypes. gNr:csg|]}t|qSrr)riZ allele_counts num_chromsrrrMsz_Record.aaf..)rrZr r updaterangerrR)rr}arrraafAs     z _Record.aafcCsNt|jdkrdS|jd}d|}td|j}t||dd||S)ak pi_hat (estimation of nucleotide diversity) for the site. This metric can be summed across multiple sites to compute regional nucleotide diversity estimates. For example, pi_hat for all variants in a given gene. Derived from: "Population Genetics: A Concise Guide, 2nd ed., p.45" John Gillespie. r:Nrg?g@)rrRrrr)rpqrrrrnucl_diversityOs  z_Record.nucl_diversitycCs,dt|jg|j}dtdd|DS)a6 Heterozygosity of a site. Heterozygosity gives the probability that two randomly chosen chromosomes from the population have different alleles, giving a measure of the degree of polymorphism in a population. If there are i alleles with frequency p_i, H=1-sum_i(p_i^2) r:cSsg|] }|dqSrr)rxrrrrmsz*_Record.heterozygosity..)r~r)rZ allele_freqsrrrheterozygositycs z_Record.heterozygositycCsdd|jDS)z The list of hom ref genotypescSsg|]}|jdkr|qSrrr|rrrrqs z(_Record.get_hom_refs..rZrrrr get_hom_refsosz_Record.get_hom_refscCsdd|jDS)z The list of hom alt genotypescSsg|]}|jdkr|qSrrr|rrrrus z(_Record.get_hom_alts..rrrrr get_hom_altsssz_Record.get_hom_altscCsdd|jDS)z The list of het genotypescSsg|]}|jdkr|qSrrr|rrrrys z$_Record.get_hets..rrrrrget_hetswsz_Record.get_hetscCsdd|jDS)z The list of unknown genotypescSsg|]}|jdkr|qSrrr|rrrr}s z(_Record.get_unknowns..rrrrr get_unknowns{sz_Record.get_unknownscCsHt|jdkrdS|jD]*}|dks.|jdkr4dS|dkrdSqdS)z, Return whether or not the variant is a SNP r:FNr_)ACGTN*T)rrQrRrb)rrhrrris_snps z_Record.is_snpcCsv|j}t|jdkr|sdS|jD]N}|dkr4dS|jdkrN|jdkrNdSt|t|jkr"|sjdSdSq"dS)z/ Return whether or not the variant is an INDEL r:TNFr_r`)is_svrrQrRrb)rrrhrrris_indels z_Record.is_indelcCs|jddkrdSdS)z; Return whether or not the variant is a structural variant SVTYPENFT)rUr)rrrrrsz _Record.is_svcCs|t|jdkrdS|jrt|jd}|jdkr4|dksj|jdkrF|dksj|jdkrX|dksj|jdkrn|dkrndSdSndSd S) z/ Return whether or not the SNP is a transition r:FrrrrrTN)rrRrrQrZ alt_allelerrr is_transitions( z_Record.is_transitioncCsRt|jdkrdS|jrJ|jd}|dkr.dSt|jt|krDdSdSndSdS)z/ Return whether or not the INDEL is a deletion r:FrNT)rrRrrQrrrr is_deletions z_Record.is_deletioncCs&|jr dS|jrdS|jrdSdSdS)z] Return the type of variant [snp, indel, unknown] TO DO: support SVs ZsnpZindelsvunknownN)rrrrrrrvar_typesz_Record.var_typecCs|jr(|jrdSt|jdkr"dSdSnb|jrP|jr8dSt|jdkrJdSdSn:|jr|jddkrhd S|jrx|jdS|jd j SndSd S) a Return the subtype of variant. - For SNPs and INDELs, yeild one of: [ts, tv, ins, del] - For SVs yield either "complex" or the SV type defined in the ALT fields (removing the brackets). E.g.:: -> DEL -> INS:ME:L1 -> DUP The logic is meant to follow the rules outlined in the following paragraph at: http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41 "For precisely known variants, the REF and ALT fields should contain the full sequences for the alleles, following the usual VCF conventions. For imprecise variants, the REF field may contain a single base and the ALT fields should contain symbolic alleles (e.g. ), described in more detail below. Imprecise variants should also be marked by the presence of an IMPRECISE flag in the INFO field." tsr:ZtvrdelZinsrBNDcomplexrN) rrrrRrrrrU is_sv_preciserbrrrr var_subtypes& z_Record.var_subtypecCs|jr|jdSdS)z$ Return the end position for the SV ZENDN)rrUrrrrsv_ends z_Record.sv_endcCsR|jddkr|jsdS|jddk r4|jr4dS|jddkrN|jrNdSdS)zW Return whether the SV cordinates are mapped to 1 b.p. resolution. Z IMPRECISENFT)rUr)rrrrrrs z_Record.is_sv_precisecCst|jdko|jddkS)z! Return True for reference calls r:rN)rrRrrrris_monomorphic"sz_Record.is_monomorphiccCs&|j}|dkst|dkrdSdSdS)z, Return True if a variant has been filtered NrFT)rTrrErrrrF'sz_Record.is_filtered)N)T),rGrHrIrJrr^rarcrdrermr#rnrprrrtrvryr{rKrrrrrrrrrrrrrrrrrrrrrrrrFrrrrrLsz*                    0   rLcs4eZdZdZfddZeddZddZZS) _AltRecordzTAn alternative allele record: either replacement string, SV placeholder, or breakendc stt|jf|||_dSr)superrrrbrrbkwargs __class__rrr4sz_AltRecord.__init__cCstdSr)NotImplementedErrorrrrrrr9sz_AltRecord.__str__cCs|jt|ddkS)Nrb)rbrr!rrrr#=sz_AltRecord.__eq__) rGrHrIrJrrrrr# __classcell__rrrrr1s   r) metaclasscsDeZdZdZfddZddZddZdd Zfd d ZZ S) _SubstitutionzGA basic ALT record, where a REF sequence is replaced by an ALT sequencec sPt|dkr(tt|jfddi|ntt|jfddi|t||_dS)Nr:rbr_r`)rrrrrsequence)rZ nucleotidesrrrrrDs z_Substitution.__init__cCs|jSr)rrrrrrrLsz_Substitution.__str__cCst|SrrrrrrrOsz_Substitution.__repr__cCs t|jSr)rrrrrr__len__Rsz_Substitution.__len__cs@t|tr|j|kSt||js$dStt||o>|j|jkS)NF) isinstancerrrrrr#r!rrrr#Us    z_Substitution.__eq__) rGrHrIrJrrrrrr#rrrrrrAs  rcs<eZdZdZfddZddZddZfdd ZZS) _BreakendzDA breakend which is paired to a remote location on or off the genomec sjtt|jfddi||dk r.t||_nd|_|dk rHt||_nd|_||_||_||_ ||_ dS)Nrbr) rrrrchrr1posremoteOrientationwithinMainAssembly orientationconnectingSequence)rrrrrrrrrrrr`s  z_Breakend.__init__cCst|Srrrrrrrusz_Breakend.__repr__cCs|jdkrd}nX|jr|j}nd|jd}|jrNd|dt|jd}nd|dt|jd}|jrx||jS|j|SdS)Nr<>[rs])rrrrrrr)rZ remoteTagZ remoteChrrrrrrxs  z_Breakend.__str__cst||jsdStt||o|jt|ddko|jt|ddko|jt|ddko|j t|ddko|j t|ddko|j t|ddkS)NFrrrrrr) rrrrr#rrrrrrrr!rrrr#s z_Breakend.__eq__) rGrHrIrJrrrrr#rrrrrr]s  rcs eZdZdZfddZZS)_SingleBreakendzA single breakendc s"tt|jdd|d|df|dSr)rrr)rrrrrrrrsz_SingleBreakend.__init__)rGrHrIrJrrrrrrrsrcs0eZdZdZfddZddZddZZS)_SVzAn SV placeholderc stt|j|f|dSr)rrrrrrrrsz _SV.__init__cCsd|jdS)Nrr)rbrrrrrrsz _SV.__str__cCst|Srrrrrrrsz _SV.__repr__)rGrHrIrJrrrrrrrrrrs rcs"GfdddtdS)z- Return a namedtuple for a given call format cs4eZdZdZgZgZddZfddZZS)z%make_calldata_tuple..CallDatarcSs(dddt|j|D}d|dS)Nz, cSsg|]\}}d||fqS)z%s=%sr)rryrrrrszAmake_calldata_tuple..CallData.__str__..z CallData())r4zip_fields)rZdatrrrrrs  z-make_calldata_tuple..CallData.__str__cst|}tffSr)r __reduce__make_calldata_tuple)rargs)CallDatarfieldsrrrsz0make_calldata_tuple..CallData.__reduce__) rGrHrIr&Z_typesZ_numsrrrrrrrrrrs rZcalldata) collections namedtuple)rrrrrsr)abcrrrr5rer ImportErrorZcountercompilerobjectrrLrrrrrrrrrrs& x/9