o Rŀge@sUdZddlZddlZddlZddlmZddlmZddlm Z ddl m Z dd d d d Z iZ id ddddddddddddddddddd d!d"d#d$d%d&d'd(d)d*d+d,d-d.id/d0d1d2d3d4d5d6d7d8d9d:d;d<d=d>d?d@dAdBdCdDdEdFdGdHdIdJdKdLdMdNdOdPidQdRdSdTdUdVdWdXdYdZd[d\d]d^d_d`dadbdcdddedfdgdhdidjdkdldmdndodpdqdridsdtdudvdwdvdxdvdydvdzd{d|d{d}d{d~d{ddddddddddddddddidddddddddddddddddddddddddddddddddddddde d<ddddddde d<iddddddÓddœddǓddɓdd˓dd͓ddϓddѓddӓddՓddדddٓddۓddݓddߓiddddddddddddddddddddddddddddddddddidddddddd d d d d ddddddddddddddddddd d!d"d#id$d%d&d'd(d)d*d+d,d-d.d/d0d1d2d3d4d5d6d7d8d9d:d;d<d=d>d?d@dAdBdCdDdEidFdGdHdIdJdKdLdMdNdOdPd dQdRdSdTdUdVdWdXdYdZd[d\d]d^d_d`ddadbdcdddeidfdgdhdidjdkdldmdndodpdqdrdsdtdudvdwdxdydzd{d|d}d~d ddddddddddde d<ddie d<idddddddddddddddddddddddddddddddddddddZdZdZgZeeed<e D] Zee7ZqdddZGddde ZddZddZddZddZedkr dSdS(aBio.SeqIO parser for the ABI format. ABI is the format used by Applied Biosystem's sequencing machines to store sequencing results. For more details on the format specification, visit: http://www6.appliedbiosystems.com/support/software_community/ABIF_File_Format.pdf N)basename)Seq) SeqRecord)SequenceIterator sample_welldyepolymer machine_model)TUBE1DySN1GTyp1MODL1APFN2z(Sequencing Analysis parameters file nameAPXV1z$Analysis Protocol XML schema versionAPrN1zAnalysis Protocol settings nameAPrV1z"Analysis Protocol settings versionAPrX1zAnalysis Protocol XML stringCMNT1zSample CommentCTID1z*Container Identifier, a.k.a. plate barcodeCTNM1zAContainer name, usually identical to CTID, but not necessarily soCTTL1z Comment TitleCpEP1z`Capillary type electrophoresis. 1 for a capillary based machine. 0 for a slab gel based machine.DATA1zChannel 1 raw dataDATA2zChannel 2 raw dataDATA3zChannel 3 raw dataDATA4zChannel 4 raw dataDATA5z=Short Array holding measured volts/10 (EP voltage) during runDATA6zDShort Array holding measured milliAmps trace (EP current) during runDATA7zIShort Array holding measured milliWatts trace (Laser EP Power) during runDATA8zTShort Array holding measured oven Temperature (polymer temperature) trace during runDATA9zChannel 9 processed dataDATA10zChannel 10 processed dataDATA11zChannel 11 processed dataDATA12zChannel 12 processed dataDSam1zDownsampling factorr z Dye set namezDye#1zNumber of dyesDyeN1z Dye 1 nameDyeN2z Dye 2 nameDyeN3z Dye 3 nameDyeN4z Dye 4 nameDyeW1zDye 1 wavelengthDyeW2zDye 2 wavelengthDyeW3zDye 3 wavelengthDyeW4zDye 4 wavelengthEPVt1z'Electrophoresis voltage setting (volts)EVNT1zStart Run eventEVNT2zStop Run eventEVNT3zStart Collection eventEVNT4zStop Collection eventFWO_1zLBase Order. Sequencing Analysis Filter wheel order. Fixed for 3500 at "GATC"r zGel or polymer TypeInSc1zInjection time (seconds)InVt1zInjection voltage (volts)LANE1zLane/CapillaryLIMS1zSample tracking IDLNTD1zLength to detectorLsrP1z!Laser Power setting (micro Watts)MCHN1z!Instrument name and serial numberMODF1zData collection module filerz Model numberNAVG1zPixels averaged per laneNLNE1zNumber of capillariesOfSc1zAList of scans that are marked off scale in Collection. (optional)OvrI1zList of scan number indexes that have values greater than 32767 but did not saturate the camera. In Genemapper samples, this can have indexes with values greater than 32000. In sequencing samples, this cannot have indexes with values greater than 32000.OvrI2OvrI3OvrI4OvrV1zList of color data values found at the locations listed in the OvrI tag. There must be exactly as many numbers in this array as in the OvrI array.OvrV2OvrV3OvrV4PDMF1z;Sequencing Analysis Mobility file name chosen in collectionRMXV1zRun Module XML schema versionRMdN1zRun Module name (same as MODF)RMdX1zRun Module XML stringRPrN1zRun Protocol nameRPrV1zRun Protocol versionRUND1zRun Started DateRUND2zRun Stopped DateRUND3zData Collection Started DateRUND4zData Collection Stopped dateRUNT1zRun Started TimeRUNT2zRun Stopped TimeRUNT3zData Collection Started TimeRUNT4zData Collection Stopped TimeRate1z&Scanning Rate. Milliseconds per frame.RunN1zRun NameSCAN1zNumber of scansSMED1zPolymer lot expiration dateSMLt1zPolymer lot numberSMPL1z Sample nameSVER1z Data collection software versionSVER3z Data collection firmware versionSatd1zyArray of longs representing the scan numbers of data points, which are flagged as saturated by data collection (optional)Scal1z Rescaling divisor for color dataScan1z#Number of scans (legacy - use SCAN)zWell IDzRun temperature settingz-Name of user who created the plate (optional))r Tmpr1User1generalzContainer ownerzInstrument ClasszInstrument FamilyzOfficial Instrument NamezInstrument ParameterszRun Module version)CTOw1HCFG1HCFG2HCFG3HCFG4RMdVa1zabi_3130/3130xlAAct1zPrimary Analysis Audit Active indication. True if system auditing was enabled during the last write of this file, false if system auditing was disabled.ABED1zAnode buffer expiration date using ISO 8601 format using the patterns YYYY-MM-DDTHH:MM:SS.ss+/-HH:MM. Hundredths of a second are optional.ABID1z&Anode buffer tray first installed dateABLt1zAnode buffer lot numberABRn1zcNumber of runs (injections) processed with the current Anode Buffer (runs allowed - runs remaining)ABTp1zAnode buffer typeAEPt1z?Analysis Ending scan number for basecalling on initial analysisAEPt2z, CPUBoard=, ArraySize=<# of capillaries>, SerialNumber=.InjN1zInjection nameLAST1zParameter settings informationNOIS1zThe estimate of rms baseline noise (S/N ratio) for each dye for a successfully analyzed sample. Corresponds in order to the raw data in tags DATA 1-4. KB basecaller only.P1AM1zkAmplitude of primary peak, which is not necessarily equal to corresponding signal strength at that positionP1RL1zODeviation of primary peak position from (PLoc,2), times 100, rounded to integerP1WD1zFull-width Half-max of primary peak, times 100, rounded to integer. Corresponding signal intensity is not necessarily equal to one half of primary peak amplitudeP2AM1zmAmplitude of secondary peak, which is not necessarily equal to corresponding signal strength at that positionP2BA1zBase of secondary peakP2RL1zQDeviation of secondary peak position from (PLoc,2), times 100, rounded to integerPBAS1z+Array of sequence characters edited by userPBAS2z4Array of sequence characters as called by BasecallerPCON1z1Array of quality Values (0-255) as edited by userPCON2z7Array of quality values (0-255) as called by BasecallerPDMF2zFMobility file name chosen in most recent analysis (identical to PDMF1)PLOC1z&Array of peak locations edited by userPLOC2z/Array of peak locations as called by BasecallerPRJT1z"SeqScape 2.0 project template namePROJ4zSeqScape 2.0 project namePSZE1z]Plate size. The number of sample positions in the container. Current allowed values: 96, 384.PTYP1z6Plate type. Current allowed values: 96-Well, 384-Well.PuSc1zMedian pupscoreQV201z QV20+ valueQV202QcPa1z QC parametersQcRn1zTrimming and QC codeQcRs1z2QC warnings, a concatenated comma separated stringQcRs2z0QC errors, a concatenated comma separated stringRGOw1zThe name entered as the Owner of a Results Group, in the Results Group Editor. Implemented as the user name from the results group.RInj1zpReinjection number. The reinjection number that this sample belongs to. Not present if there was no reinjection.RNmF1zRaman normalization factorRevC1z.for whether the sequence has been complementedzH4sI2H3Iz>4sI2H4I__global_tag_listingcCs:|dur|Sz|WSty|jtdYSw)zReturn the string value of the given an optional raw bytes tag value. If the bytes value is None, return the given default value. N)encoding)decodeUnicodeDecodeErrorsysgetdefaultencoding)opt_bytes_valuedefaultrC/var/www/html/myenv/lib/python3.10/site-packages/Bio/SeqIO/AbiIO.py_get_string_tagLs  rcs2eZdZdZd fdd ZddZddZZS) AbiIteratorzParser for Abi files.Fcs||_tj|ddddS)z+Return an iterator for the Abi file format.rABI)modefmtN)trimsuper__init__)selfsourcer __class__rrr]szAbiIterator.__init__cCs:|d}|s td|dkrtd|||}|S)z9Start parsing the file, and return a SeqRecord generator.rz Empty file.sABIFzFile should start ABIF, not )read ValueErrorOSErroriterate)rhandlemarkerrecordsrrrparsebs  zAbiIterator.parsec#s:ddddd}tttdgtt}tt|t t}d}id}}t ||D]B\}} } |t | } | | <| dkrG| }q/| dkrUdd| D}q/| d kr^t | }q/| |vrg| || <q/| tvrq| |t| <q/|d d |d |d <|dd |d|d<|d<tfdddD} | rz t|jdd} Wn tyd} Ynwt d|}t dd}ttd|| ||d}n"z t|jdd} Wn tyd} Ynwtt||| d|d}|r||jd<n| s|s|jrtd|jr| st|}d|jd<|VdS)z.Parse the file and generate SeqRecord objects.)rMrNrQrRNz rrcSsg|]}t|qSr)ord).0valrrr sz'AbiIterator.iterate..rZrM rQ run_startrNrR run_finishabif_rawc3s|]}|vVqdSNr)r tnrawrr sz&AbiIterator.iterate..)rrz.fsar7rz)idname description annotationsz.ab1 phred_qualityzGThe 'abi-trim' format can not be used for files without quality values.DNA molecule_type)dictzip_EXTRACTvalueslenstructunpack_HEADFMTrcalcsize_abi_parse_headerstrrrallrrreplaceAttributeErrorgetrrletter_annotationsrr _abi_trimr)rrtimesannotheader sample_idseqqualtag_name tag_numbertag_datakey is_fsa_file file_namerrecordrrrros|           zAbiIterator.iterate)F)__name__ __module__ __qualname____doc__rr r __classcell__rrrrrZs  rcCs t|ddS)z[Return an iterator for the Abi file format that yields trimmed SeqRecord objects (PRIVATE).T)r)r)rrrr_AbiTrimIterators rBccs|d}|d}|d}d}||kr|||}||tt|tt|f}|d7}|d}|t|d7}|d} |d} |d} |d} |d} |d}|d}| dkre|d }|||| }| | t| | |fV||ksd Sd S) z$Return directory contents (PRIVATE).rrrrrrrrrN) seekr$r%_DIRFMTrr'rr)_parse_tag_data)r2rhead_elem_size head_elem_num head_offsetindexstart dir_entryr9r6r7 elem_codeelem_num data_size data_offset tag_offsetdatarrrr(s6      r(c sd}d}d}dt||kr|Sfdd|jdD}dg}tdt|D]}|d ||}|dkr:|dq&|||sE|}d }q&|t|}|||S) aTrims the sequence using Richard Mott's modified trimming algorithm (PRIVATE). Arguments: - seq_record - SeqRecord object to be trimmed. Trimmed bases are determined from their segment score, which is a cumulative sum of each base's score. Base scores are calculated from their quality values. More about the trimming algorithm: http://www.phrap.org/phredphrap/phred.html http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/650/Quality_trimming.html Frrg?csg|] }d|dqS)rg$r)r r5cutoffrrrsz_abi_trim..rrT)r#r.rangeappendrImax) seq_recordrJsegment trim_start score_list cummul_scorerscore trim_finishrrRrr/s*      r/cCs|tvrt|dkr d}nt|}d|t|}t|t|ks"Jt||}|dvr6t|dkr6|d}|dkr<|S|dkrGttj|S|dkrVttj|d d S|d kr^t |S|d krh|dd S|d krr|d dS|Sd S)zReturn single data value (PRIVATE). Arguments: - elem_code - What kind of data - elem_num - How many data points - raw_data - abi file object from which the tags would be unpacked rr >)rrrrrrNrrrrrT) _BYTEFMTr)r#r$r'r%datetimedatetimebool)rLrMraw_datanumrrQrrrrE,s.    rE__main__r)r@rar$ros.pathrBio.Seqr Bio.SeqRecordr Interfacesrr!_INSTRUMENT_SPECIFIC_TAGSr`r&rDrlistr)__annotations__r"tagkeysrrrBr(r/rEr=rrrrs            !"#$'()*+,-./0123456789<@DHLNPRTUVWXYZ[\]^_`abcdefghijklm w        !"#$%&'()*+,-./01234789;<=?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklq         r  ( 3 ,