U 7gb u*@sddlZddlZddlZddlZddlZddlZddlZddlZddlm Z zddlm Z Wn e k r|ddl m Z YnXz ddl Z Wne k rdZ YnXz ddlZWne k rdZYnXddlmZmZmZddlmZmZmZmZddd dd dd ddd d d dddd d d d d dddddddddddddddddddddd )Zdddd ddd dddddddd d dddd ZdZdZd ZdZddZddeDZddeDZ dddgZ!dddddZ"e#dddddd d!d"gZ$e#d#ddgZ%e#d$ddgZ&e#d%ddddd"gZ'e#d&d'd(d)d*gZ(e#d+dd,gZ)Gd-d.d.e*Z+Gd/d0d0e*Z,Gd1d2d2e*Z-d3d4Z.e,Z/e-Z0dS)5N)get_uncompressed_size) OrderedDict)_Call_Recordmake_calldata_tuple) _Substitution _Breakend_SingleBreakend_SVStringIntegerFloatFlag))ZAAZACZAFZANZBQZCIGARZDBDPZENDZH2ZH3MQZMQ0ZNSZSBZSOMATICZ VALIDATEDZ1000GZ IMPRECISEZNOVELZSVTYPEZSVLENZCIPOSZCIENDZHOMLENZHOMSEQZBKPTIDZMEINFOZMETRANSZDGVIDZDBVARIDZDBRIPIDZMATEIDZPARIDZEVENTZCILENZDPADJCNZCNADJZCICNZCICNADJ)GTrFTZGLZGLEZPLZGPZGQZHQZPSZPQZECrrZCNQZCNLZNQZHAPZAHAPcCsttttttd|S)N)r r Z CharacterrZNumericr)INTEGERSTRINGFLOATFLAG)Z field_typer)lib/python3.8/site-packages/vcf/parser.py _encode_typejsrcCsi|]\}}|t|qSrr.0kvrrr usr#cCsi|]\}}|t|qSrrrrrrr#vsZ fileformatZfileDateZ reference).AGRZInfoidnumtypedescsourceversion type_codeZFilterZAltZFormatZ SampleInfosamplesZgt_basesZgt_typesZ gt_phasesZContiglengthcs`eZdZdZfddZddZddZdd Zd d Zd d Z ddZ ddZ ddZ Z S)_vcf_metadata_parserz/Parse the metadata in the header of a VCF file.csntt|tdtj|_tdtj|_tdtj|_tdtj|_ tdtj|_ td|_ dS)Na=\#\#INFO=< ID=(?P[^,]+),\s* Number=(?P-?\d+|\.|[AGR])?,\s* Type=(?PInteger|Float|Flag|Character|String),\s* Description="(?P[^"]*)" (?:,\s*Source="(?P[^"]*)")? (?:,\s*Version="?(?P[^"]*)"?)? >ze\#\#FILTER=< ID=(?P[^,]+),\s* Description="(?P[^"]*)" >zb\#\#ALT=< ID=(?P[^,]+),\s* Description="(?P[^"]*)" >z\#\#FORMAT=< ID=(?P.+),\s* Number=(?P-?\d+|\.|[AGR]),\s* Type=(?P.+),\s* Description="(?P.*)" >zr\#\#contig=< ID=(?P[^>,]+) (,.*length=(?P-?\d+))? .* >z##(?P.+?)=(?P.+)) superr4__init__recompileVERBOSE info_patternfilter_pattern alt_patternformat_patterncontig_pattern meta_patternself __class__rrr6s,  z_vcf_metadata_parser.__init__cCs(|dkr dS|tkrt|St|SdS)z*Cast vcf header numbers to integer or NoneN) field_countsintrAZnum_strrrrvcf_field_counts z$_vcf_metadata_parser.vcf_field_countc Csv|j|}|std|||d}t|d||d|d|d|dt|d}|d|fS)z"Read a meta-information INFO line.z&One of the INFO lines is malformed: %snumberr+r-r.r/r0)r:match SyntaxErrorrGgroup_Infor)rAZ info_stringrIr,inforrr read_infos    z_vcf_metadata_parser.read_infocCs@|j|}|std|t|d|d}|d|fS)z$Read a meta-information FILTER line.z(One of the FILTER lines is malformed: %sr+r.)r;rIrJ_FilterrK)rAZ filter_stringrIfiltrrr read_filters z _vcf_metadata_parser.read_filtercCs@|j|}|std|t|d|d}|d|fS)z Read a meta-information ALTline.z%One of the ALT lines is malformed: %sr+r.)r<rIrJ_AltrK)rAZ alt_stringrIaltrrrread_alts   z_vcf_metadata_parser.read_altc Csf|j|}|std|||d}t|d||d|dt|d}|d|fS)z$Read a meta-information FORMAT line.z(One of the FORMAT lines is malformed: %srHr+r-r.)r=rIrJrGrK_Formatr)rA format_stringrIr,Zformrrr read_formats  z _vcf_metadata_parser.read_formatcCsJ|j|}|std|||d}t|d|}|d|fS)z$Read a meta-contigrmation INFO line.z(One of the contig lines is malformed: %sr3r+)r>rIrJrGrK_Contig)rAZ contig_stringrIr3Zcontigrrr read_contig s z _vcf_metadata_parser.read_contigc Cs|dd}|dd}t}d}d}d}|ddD]}|dkr^|dkrTd}q||7}q:|dkr|dkr|dkr||7}d}q|d kr|||<d}d}d}q||7}q:|dkr:|dkr||7}d}q:||7}q:|dkr|||<||fS) N=rr#z[<>]"r,)splitlstriprstrip) rA meta_stringitemskeyvalstater!r"crrrread_meta_hashs:    z#_vcf_metadata_parser.read_meta_hashcCsHtd|r||S|j|}|s4|ddfS|d|dfS)Nz##.+=~sz"Reader.__init__..)'r5rpr6 ExceptionZ_readerhasattrrrendswithopenfilename _total_bytes _read_bytesgzipZGzipFilesysr0codecs getreaderZ _separatorr7r8 _row_pattern _alt_patternreadermetadatainfosfiltersaltsformatscontigsr2_sample_indexes _header_lines_column_headers_tabix _prepend_chr_parse_metainfo _format_cacheencoding)rAZfsockr} compressedZ prepend_chrZstrict_whitespacerrBrrr6JsR    zReader.__init__cCs d|_|S)Nrrr@rrr__iter__szReader.__iter__cCs|jS)zFReturn read bytes from uncompress data. Usefull to have a progress barrr@rrr read_bytesszReader.read_bytescCs|jdkrt|j|_|jS)zGReturn total bytes from uncompress data. Usefull to have a progress barr)r~rr}r@rrr total_bytess  zReader.total_bytescCsdD]}t||tqt}t|j}|drJ|j||drd||\}}||j |<n|dr| |\}}||j |<n|dr| |\}}||j |<n|dr||\}}||j|<nn|dr||\}}||j|<nJ||\}}|tkr||j|<n&||jkr.g|j|<|j||t|j}q(|j|dd }|d d |_|d d |_td d t|jD|_d S) zParse the information stored in the metainfo of the VCF. The end user shouldn't have to use this. She can access the metainfo directly with ``self.metadata``.)rrrrrrz##z##INFOz##FILTERz##ALTz##FORMATz##contigrN cSsg|]\}}||fqSrr)r ixrrr sz*Reader._parse_metainfo..)setattrrr4nextr startswithrappendrNrrQrrTrrWrrYrrjSINGULAR_METADATArrr_rr2dict enumerater)rAattrparserrwrdreZfieldsrrrrs@                  zReader._parse_metainfor'r\ZNAcsfdd|DS)z"``map``, but make bad values None.cs g|]}|kr|ndqSrvrr rbadfuncrrrszReader._map..r)rAriterablerrrr_mapsz Reader._mapcCs&|dkr dS|dkrgS|dSdS)zParse the FILTER field of a VCF entry into a Python list NOTE: this method has a cython equivalent and care must be taken to keep the two methods equivalent r'NPASS;)r_)rAZfilt_strrrr _parse_filters zReader._parse_filterc Cs|dkr iS|d}i}|D]}|dd}|d}z|j|j}WnLtk rz t|}Wn*tk r|ddrt}nt}YnXYnX|tkr|dd}z|t |}Wn t k r|t |}YnXn~|t kr|dd}|t |}nX|tkrd}nH|tkr^z|dd}|t |}Wntk r\t}d}YnXz(|j|jdkr|tkr|d}Wntk rYnX|||<q|S) zXParse the INFO field of a VCF entry into a dictionary of Python types. r'rrZrrNr^T)r_rr1KeyErrorRESERVED_INFO_CODESrrrrrE ValueErrorfloatrstr IndexErrorr,) rAZinfo_strentriesZretdictentryID entry_typevalsrerrr _parse_infosV           zReader._parse_infoc Cst|d}|jD]x}z|j|j}|j|j}Wn>tk rrd}z t|}Wntk rlt}YnXYnX|j ||j |q|S)z-Parse the format of the calls in this _Record:N) rr__fieldsrr1r,rRESERVED_FORMAT_CODESr_typesr_nums)rAsamp_fmtfmtr entry_numrrr_parse_sample_format$s    zReader._parse_sample_formatc Cs||jkr|||j|<|j|}trBt|j|||j|j|Sg}|j}t|j }t |j|D]\}}dg|} t | dD]H\} } |j | dkr| | | <qn6|j | dkr| | | | <qn| r| dkrd| | <q|j| } |j| } | dkr^| tkr) rsearchr_r7r rr r r) rArrcZ remoteCoordschrZwithinMainAssemblyposZ orientationZremoteOrientationZconnectingSequencerrr _parse_alts:    zReader._parse_altc Cst|j}|jt|7_|j|}|d}|jrBd|}t|d}|ddkrd|d}nd}|d}| |j |dd }zt|d }Wn>t k rzt |d }Wnt k rd}YnXYnX| |d } tdk rt|d |jt} n||d } z |d } Wntk r:d} YnX| dkrJd} t||||||| | | |j } | dk r||dd| | } | | _| S)z#Return the next record in the file.rrrrr'Nrr^r)rrrrrr_rstriprrErrrrrrZ parse_inforrrrrrrr2)rArwrowchromrrrefrSZqualrPrMrrecordr2rrr__next__sZ         zReader.__next__cCslts td|jstd|js4tj|j|jd|_|jrV|dddkrV|dd}|j||||_|S)aOFetches records from a tabix-indexed VCF file and returns an iterable of ``_Record`` instances chrom must be specified. The start and end coordinates are in the zero-based, half-open coordinate system, similar to ``_Record.start`` and ``_Record.end``. The very first base of a chromosome is index 0, and the the region includes bases up to, but not including the base at the end coordinate. For example ``fetch('4', 10, 20)`` would include all variants overlapping a 10 base pair region from the 11th base of through the 20th base (which is at index 19) of chromosome 4. It would not include the 21st base (at index 20). See http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms for more information on the zero-based, half-open coordinate system. If end is omitted, all variants from start until the end of the chromosome chrom will be included. If start and end are omitted, all variants on chrom will be returned. requires pysam z-pysam not available, try "pip install pysam"?z/Please provide a filename (or a "normal" fsock))rNrr) pysamryr}rZ Tabixfilerrfetchr)rArstartendrrrrs z Reader.fetch)NNNFFrq)NN)rkrlrmrnr6rrrrrrrrrrrrrorrrBrrpGs(L 2 :K#2rpc@seZdZdZeddeDZd"ddZddZ d d Z d d Z d dZ ddZ ddZddZddZddZd#ddZd$ddZd%dd Zd!S)&Writerz7VCF Writer. On Windows Python 2, open stream with 'wb'.ccs|]\}}||fVqdSrvrrrrrrxszWriter. c stj|d|dtjd|_|_||_tfddttt t j t |_d}d}|j}jD]l\}}|tkr|g}|D]P} t| trdd d t| D} |d || q|d || qqnj D]"} ||j| d || jdqjD]$} ||j| d|| jdqjD]} ||j| ddiqDjD]} ||j| ddiqljD]0} | jr|dj| n|dj| q|dS)Nrur\)Z delimiterlineterminatorZ quotecharZquotingcs tjSrv)rrrtemplaterrz!Writer.__init__..z###{key}= z9##{key}= r^css|]\}}d||VqdS)z{0}={1}N)format)r rdvaluerrrrx!sz"Writer.__init__..z ##{0}=<{1}> z ##{0}={1} INFO)rdr,FORMATrdFILTERALTz##contig= z##contig= ) csvwriterZ QUOTE_NONErstream collections defaultdictrlistriterrkeys itertoolscount info_order_fix_field_countrrcr isinstancejoinwritervaluesr,rrrrr3 _write_header) rArrrZtwoZfourZ_numrdrrerrwrrrr6sN     "zWriter.__init__cCs*|jdd|jj|jjddS)Nr[rur)rrrrrr2r@rrrr7szWriter._write_headercstjjjjgjjp,d j  j g}j rX|j fddjD}j||dS)zwrite a record to the filer'csg|]}j|qSr)_format_sampler)r rrrArrrJsz'Writer.write_record..N)rrZCHROMZPOSrZREF _format_altrZQUAL_format_filterr _format_inforrrr2rZwriterow)rArZffsr2rrr write_record?s     zWriter.write_recordcCs(z|jWntk r"YnXdS)zFlush the writerN)rflushAttributeErrorr@rrrrOsz Writer.flushcCs(z|jWntk r"YnXdS)zClose the writerN)rcloserr@rrrrVsz Writer.closecCs||jkr|S|j|SdS)z'Restore header number to original stateN)countsrFrrrr]s zWriter._fix_field_countcCsd|t|S)Nr^)rrr)rArSrrrrdszWriter._format_altcCs|gkr dS|j|dddS)Nrr'rridelim) _stringify)rAZfltrrrrgszWriter._format_filtercsHtrtjSsdSfdd}dfddt|dDS)Nr'csj||fSrv)r)fieldr@rr order_keyssz&Writer._format_info..order_keyrc3s|]}||VqdSrv)_stringify_pair)r frMrArrrxwsz&Writer._format_info..)rd)r format_inforrsorted)rArMr rrrrls  zWriter._format_infocCstrt||St|jdr&|jj}nd|kr2dnd}|r@|gng}|jjD]D}t|j|}|dkrfqL|dkr|||qL|| |qLd |S)Nrz./.r\rr) rZ format_samplerzdatarrgetattrrrr r)rArrgtresultr rrrrr{s     zWriter._format_sampler'r^cCs8t|tgkr$||t||S|dk r4t|S|Srv)r-rrr)rArrir rrrr szWriter._stringifycCs6t|tr|rt|SdSdt||j|||dfS)Nr\z%s=%sr )rboolrr )rAryrir rrrrs zWriter._stringify_paircsfdd|DS)z#``map``, but make None values none.cs g|]}|dk r|nqSrvrrrrirrrszWriter._map..r)rArrrirrrrsz Writer._mapN)r)r'r^)r'r^)r')rkrlrmrnrrDrcrr6rrrrrrrrrr rrrrrrrs 0  rcCs&ddl}ddl}tdd|jdS)Nrz README.rstw)rvcffilerrn)rrrrr__update_readmesr)1rrrrrosr7rZutilsrr ImportErrorZ ordereddictrrZmodelrrrrr r r Z RESERVED_INFOZRESERVED_FORMATrrrrrrcrrrrD namedtuplerLrOrRrUZ _SampleInforXobjectr4rprrZ VCFReaderZ VCFWriterrrrrs     .   7=