ó 4˙Hc@sđdZdd-d„ƒYZdd.d„ƒYZdd/d„ƒYZdd0d„ƒYZd d1d „ƒYZd d2d „ƒYZd d3d„ƒYZdd4d„ƒYZdd5d„ƒYZ dd6d„ƒYZ dd7d„ƒYZ d„Z dd8d„ƒYZ d„ZddlmZddlTdd9d„ƒYZd efd!„ƒYZd"efd#„ƒYZd$d:d%„ƒYZd&efd'„ƒYZed(krěd)GHed*ƒZe eƒZx0eD](ZejGeej ƒGeej!ƒGHqŽWej"ƒd+GHnd,S(;sË Parser for ACE files output by PHRAP. Written by Frank Kauff (fkauff@duke.edu) and Cymon J. Cox (cymon@duke.edu) Uses the Biopython Parser interface: ParserSupport.py Usage: There are two ways of reading an ace file: 1) The function 'read' reads the whole file at once; 2) The function 'parse' reads the file contig after contig. 1) Parse whole ace file at once: from Bio.Sequencing import Ace acefilerecord=Ace.read(open('my_ace_file.ace')) This gives you: acefilerecord.ncontigs (the number of contigs in the ace file) acefilerecord.nreads (the number of reads in the ace file) acefilerecord.contigs[] (one instance of the Contig class for each contig) The Contig class holds the info of the CO tag, CT and WA tags, and all the reads used for this contig in a list of instances of the Read class, e.g.: contig3=acefilerecord.contigs[2] read4=contig3.reads[3] RD_of_read4=read4.rd DS_of_read4=read4.ds CT, WA, RT tags from the end of the file can appear anywhere are automatically sorted into the right place. see _RecordConsumer for details. 2) Or you can iterate over the contigs of an ace file one by one in the ususal way: from Bio.Sequencing import Ace contigs=Ace.parse(open('my_ace_file.ace')) for contig in contigs: print contig.name ... Please note that for memory efficiency, when using the iterator approach, only one contig is kept in memory at once. However, there can be a footer to the ACE file containing WA, CT, RT or WR tags which contain additional meta-data on the contigs. Because the parser doesn't see this data until the final record, it cannot be added to the appropriate records. Instead these tags will be returned with the last contig record. Thus an ace file does not entirerly suit the concept of iterating. If WA, CT, RT, WR tags are needed, the 'read' function rather than the 'parse' function might be more appropriate. trdcBseZdZd„ZRS(s5RD (reads), store a read with its name, sequence etc.cCs1d|_d|_d|_d|_d|_dS(Nt(tnametNonet padded_basest info_itemst read_tagstsequence(tself((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyt__init__>s     (t__name__t __module__t__doc__R (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR<stqacBseZdZdd„ZRS(sIQA (read quality), including which part if any was used as the consensus.cCs~d|_d|_d|_d|_|rztt|jƒdƒ}|d|_|d|_|d|_|d|_ndS(Niiii(Rtqual_clipping_starttqual_clipping_endtalign_clipping_starttalign_clipping_endtmaptevaltsplit(Rtlinetheader((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR Gs       N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR EstdscBseZdZdd„ZRS(s:DS lines, include file name of a read's chromatogram file.c Cs(d|_d|_d|_d|_d|_d|_d|_|r$dddddddg}t|j|ƒ}t t ||ƒƒ}d |kr|d =n|j ƒ}|j ƒxnt ||d t |ƒd gƒD]E\}}t|||jƒ||t ||ƒd |!jƒƒqŘWndS( NRt CHROMAT_FILEtPHD_FILEtTIMEtCHEMtDYEtTEMPLATEt DIRECTIONi˙˙˙˙i(t chromat_filetphd_filettimetchemtdyettemplatet directionRtfindtdicttziptkeystsorttlentsetattrtlowertstrip(RRttagstpossttagpostpstp1tp2((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR Us"           1N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRSstafcBseZdZdd„ZRS(s<AF lines, define the location of the read within the contig.cCsad|_d|_d|_|r]|jƒ}|d|_|d|_t|dƒ|_ndS(NRiii(RRtcorut padded_startRtint(RRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR ks      N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR5istbscBseZdZdd„ZRS(sL"BS (base segment), which read was chosen as the consensus at each position.cCsgd|_d|_d|_|rc|jƒ}t|dƒ|_t|dƒ|_|d|_ndS(NRiii(RRR7t padded_endRR8(RRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR ws    N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR9ustrtcBseZdZdd„ZRS(s<RT (transient read tags), generated by crossmatch and phrap.cCsŠd|_d|_d|_d|_d|_d|_|rĽ|jƒ}|d|_|d|_|d|_t|dƒ|_t|dƒ|_|d|_ndS(NRiiiiii( Rttag_typetprogramRR7R:tdateRR8(RRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR ƒs          N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR;stctcBseZdZdd„ZRS(sCT (consensus tags).cCsćd|_d|_d|_d|_d|_d|_d|_g|_g|_ |râ|j ƒ}|d|_|d|_|d|_t |dƒ|_t |dƒ|_|d|_t |ƒdkrâ|d |_qândS( NRiiiiiiii( RR<R=RR7R:R>tnotranstinfotcommentRR8R+(RRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR •s&              N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR?“stwacBseZdZdd„ZRS(sGWA (whole assembly tag), holds the assembly program name, version, etc.cCsdd|_d|_d|_g|_|r`|jƒ}|d|_|d|_|d|_ndS(NRiii(R<R=R>RAR(RRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR Źs       N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRCŞstwrcBseZdZdd„ZRS(s WR lines.cCsqd|_d|_d|_g|_|rm|jƒ}|d|_|d|_|d|_|d|_ndS(NRiiii(RtalignedR=R>R(RRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR šs        N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRDˇstReadscBseZdZdd„ZRS(s8Holds information about a read supporting an ACE contig.cCs¤d|_d|_d|_d|_d|_|r tƒ|_|jƒ}|d|j_t|dƒ|j_ t|dƒ|j_ t|dƒ|j_ ndS(Niiii( RRR RR;RDRRR8RRR(RRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR Çs       N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRFĹstContigcBseZdZdd„ZRS(s4Holds information about a contig from an ACE record.cCsŘd|_d|_d|_d|_d|_d|_g|_g|_g|_ g|_ d|_ d|_ |rÔ|j ƒ}|d|_t|dƒ|_t|dƒ|_t|dƒ|_|d|_ndS(NRiiiii(RRtnbasestnreadst nsegmentstuorcRtqualityR5R9treadsR?RCRR8(RRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR ×s&              N(R R R RR (((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRGŐsccs t|ƒ}d}xđtry0x)trI|jdƒr:Pn|jƒ}q!WWntk r_dSXt|ƒ}x3|D]+}|jƒ}|sPn|j|7_qsWx|D]}|jƒrŠPqŠqŠW|jdƒsátdƒ‚nx=|D]5}|jƒsţPn|j j t t |j ƒƒƒqčWx|D]}|jƒr(Pq(q(Wxctr§|jdƒs^Pn|jjt|ƒƒy|jƒ}WqEtk rŁtdƒ‚qEXqEWxJtrô|jƒrÁPny|jƒ}WqŤtk rđtdƒ‚qŤXqŤWxctrZ|jd ƒsPn|jjt|ƒƒy|jƒ}Wqřtk rVtd ƒ‚qřXqřWxžtrűy0x)tr’|jd ƒrƒPn|jƒ}qjWWntk rłtd ƒ‚nX|jjt|ƒƒx=|D]5}|jƒ}|síPn|jd jj|7_qŃWx|D]}|jƒrPqqW|jdƒsItdƒ‚nt|ƒ|jd _x|D]}|jƒrfPqfqfWP|jdƒrŻt|ƒ|jd _d}nx3träy-x&tră|jƒrÔPn|jƒ}qžWWntk růPnX|jdƒr…|jd jdkr2g|jd _nxG|D]?}|jƒ}|dkr[Pn|jd jjt|ƒƒq9Wd}q˛|jdƒr|jd jdkr˝g|jd _nxG|D]?}|jƒ}|dkrćPn|jd jjt|ƒƒqÄWd}q˛|jdƒrÍ|jdkr:g|_ny|jƒ}Wntk ritdƒ‚nX|jjt|ƒƒxA|D]9}|jƒ}|dkrŠPn|jd jj|ƒq‡Wd}q˛|jdƒrŕ|jdkr÷g|_ny|jƒ}Wntk r&tdƒ‚nX|jjt|ƒƒx—|D]}|jƒ}|dkrŹxn|D]<}|jƒ}|jdƒrŽPn|jd jj|ƒqiWqD|dkrźPqD|jd jj|ƒqDWd}q˛Pq˛W|jdƒs^Pq^q^W|VqWdS(sGparse(handle) where handle is a file-like object. This function returns an iterator that allows you to iterate over the ACE file record by record: records = parse(handle) for record in records: # do something with the record where each record is a Contig object. RtCONtBQsFailed to find BQ linesAF sUnexpected end of AF blocksUnexpected end of filesBS sFailed to find end of BS blocksRD sFailed to find RD linei˙˙˙˙sQA sFailed to find QA linesDS sRT{t}sWR{sWA{sFailed to read WA blocksCT{sFailed to read CT blocksCOMMENT{sC}tRD(titertTruet startswithtnextt StopIterationRGR.Rt ValueErrorRLtextendRR8RR5tappendR9RMRFRR RR;RRDRCRAR?tendswithRB(thandleRtrecord((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pytparseěs           #                          !    !                t ACEFileRecordcBs eZdZd„Zd„ZRS(sHolds data of an ACE file. cCs(d|_d|_g|_d|_dS(N(RtncontigsRItcontigsRC(R((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR °s   cCsŚg}g}g}xÂtt|jƒƒD]Ť}|j|}|jro|jsYg|_n|jj|jƒn|jrĐg|jD]}|j|jkr‚|^q‚}t|j|jj|ƒ|j|ƒnxtt|j ƒƒD]é}|j |} | j rdg| j D]!} | j| j jkr | ^q } t|j|j |j j| ƒ|j| ƒn| j rćg| j D]!} | j| j jkrw| ^qw} t|j|j |j j| ƒ|j| ƒqćqćWq(WxČtt|jƒƒD]ą}|j|}xc|D][}|j|jkr|j|jdkrHg|j|_n|j|jj|ƒqqW|sr|ríx)tt|j ƒƒD]}|j |} x{|D]s} | j| j jkr˘|j|j |j dkrôg|j|j |_ n|j|j |j j| ƒq˘q˘Wx{|D]s} | j| j jkr |j|j |j dkrrg|j|j |_ n|j|j |j j| ƒq q WqˆWqíqíWdS(sTSorts wr, rt and ct tags into the appropriate contig / read instance, if possible. N(trangeR+R`RCRXR?RRtremoveRMR;RRDRRY(RR?R;RDtitctct_tagtnewctstjtrtrt_tagtnewrtstwr_tagtnewwrs((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR*śsV     .  1! 1!     % (R R R R R*(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR^­s cCs´t|ƒ}tƒ}y|jƒ}Wntk rDtdƒ‚nX|jdƒsctdƒ‚n|jƒ}tt|dd!ƒ\|_ |_ t t |ƒƒ|_ |jƒ|S(s2Parses the full ACE file in list of contigs. sPremature end of filetASsFile does not start with 'AS'.ii(RRR^RURVRWRTRRR8R_RItlistR]R`R*(R[R\Rtwords((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pytreadçs    " i˙˙˙˙(tFile(t*tIteratorcBs,eZdZdd„Zd„Zd„ZRS(s…Iterates over an ACE-file with multiple contigs. Methods: next Return the next record from the stream, or None. cCs;ddl}|jdtƒtj|ƒ|_||_dS(s__init__(self, handle, parser=None) Create a new iterator. handle is a file-like object. parser is an optional Parser object to change the results into another form. If set to None, then the raw contents of the file will be returned. i˙˙˙˙NsmAce.Iterator is deprecated. Instead of Ace.Iterator(handle, Ace.RecordParser()), please use Ace.parse(handle)(twarningstwarntDeprecationWarningRqt UndoHandlet_uhandlet_parser(RR[tparserRt((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR s cCsăg}x>|jjƒ}|s"dS|d dkr |j|ƒPq q WxT|jjƒ}|scPn|r|d dkr|jj|ƒPn|j|ƒqJW|s¨dSdj|ƒ}|jdk rß|jjtj |ƒƒS|S(s{next(self) -> object Return the next contig record from the file. If no more records return None. iRNRN( RxtreadlineRRYtsavelinetjoinRyR]Rqt StringHandle(RtlinesRtdata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRUs, cCst|jdƒS(s+Iterate over the ACE file record by record.N(RRRUR(R((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyt__iter__AsN(R R R RR RUR(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRs s "t RecordParsercBs eZdZd„Zd„ZRS(s*Parses ACE file data into a Record object.cCstƒ|_tƒ|_dS(N(t_Scannert_scannert_RecordConsumert _consumer(R((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR Gs cCsJt|tjƒr|}ntj|ƒ}|jj||jƒ|jjS(N(t isinstanceRqRwR„tfeedR†R€(RR[tuhandle((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR]Ks  (R R R R R](((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR‚Es t ACEParsercBs eZdZd„Zd„ZRS(s.Parses full ACE file in list of contigs. cCs,ddl}|jdtƒtƒ|_dS(Ni˙˙˙˙sbAce.ACEParser is deprecated. Instead of Ace.ACEParser().parse(handle), please use Ace.read(handle)(RtRuRvR^R€(RRt((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR Xs cCs•|jƒ}|d dkr+tdƒ‚nt|jƒdƒ|j_t|jƒdƒ|j_t|ƒ}t|ƒ|j_ |jj ƒ|jS(NiRmsFile does not start with 'AS'.i( R{RWRRR€R_RIR]RnR`R*(RR[t firstlinetrecords((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR]]s   (R R R R R](((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRŠSs RƒcBs;eZdZd„Zd„Zd„Zd„Zd„ZRS(sSScans an ACE-formatted file. Methods: feed - Feed one ACE record. cCsAt|tjƒstdƒ‚|jƒr=|j||ƒndS(säfeed(self, handle, consumer) Feed in ACE data for scanning. handle is a file-like object containing ACE data. consumer is a Consumer object that will receive events as the ACE data is scanned. shandle must be an UndoHandleN(R‡RqRwtAssertionErrortpeeklinet _scan_record(RR[tconsumer((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRˆvs  cCsÉ|jƒt||jddƒ|j|j|ƒƒt||jddƒt||jddƒ|j|j ||ƒƒt||jddƒt||j ddƒt||jddƒt||j ddƒxďt ||jddƒt||j ddƒ|j|j|ƒƒt||jddƒt||jdd ƒy0t||jddƒt||jdd ƒWntk r’|jƒdSXxyt||jddƒWntk rÎ|jƒdSXt||jdd ƒr|j|j|ƒƒq–t||jdd ƒr1|j|j|ƒƒq–t||jdd ƒrb|j|j|ƒƒq–t||jddƒr“|j|j|ƒƒq–t|ƒ}Pq–W|jdƒsÖ|jƒPqÖqÖWdS(NtstartsCO tblankiROsAF sBS sRD sQA sDS tRTtWRtWAtCTRQ(t begin_contigt read_and_callt co_headertco_datat_scan_sequence_datatread_and_call_whiletnoeventt bq_headertbq_datat _scan_bq_dataR5R9tread_and_call_untilt rd_headertrd_dataR tattempt_read_and_callRRWt end_contigtrt_starttrt_datat_scan_bracket_tagstwr_starttwr_datatwa_starttwa_datatct_starttct_datat safe_peeklineRT(RR‰RR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR‚sR       cCsHd}x;|jƒ}t|ƒr2|j|ƒPn|d|7}q W|S(s;Scans multiple lines of quality data and concatenates them.Rt (R{t is_blank_lineR|(RR‰RtqualR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR źs   cCsJd}x=|jƒ}t|ƒr2|j|ƒPn||jƒ7}q W|S(s<Scans multiple lines of sequence data and concatenates them.R(R{RąR|R.(RR‰tseqR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR›Čs   cCsrg}xe|jƒjƒ}|j|ƒ|jdƒr |dd |d<|ddkrf|d }nPq q W|S(s!Reads the data lines of a {} tag.RPi˙˙˙˙R(R{R.RYRZ(RR‰tfulltagR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR¨Ôs  (R R R RˆRR R›R¨(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRƒps  : R…cBsËeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z d „Z d „Z d „Zd „Zd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„ZRS(s%Reads the ace tags into data records.cCs d|_dS(N(RR€(R((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR ĺscCstƒ|_dS(N(RGR€(R((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR—čscCsdS(N((R((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRĽëscCsr|jƒ}|d|j_t|dƒ|j_t|dƒ|j_t|dƒ|j_|d|j_dS(Niiiii(RR€RRRHRIRJRK(RRR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR™îs  cCs||j_dS(N(R€R(RRł((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRšöscCsdS(N((RR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRžůscCstt|jƒƒ|j_dS(N(RRRR€RL(RR˛((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRŸüscCsY|jƒ}tƒ}|d|_|d|_t|dƒ|_|jjj|ƒdS(Niii(RR5RR6RR7R€RY(RRRtafdata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR5˙s     cCs_|jƒ}tƒ}t|dƒ|_t|dƒ|_|d|_|jjj|ƒdS(Niii(RR9RR7R:RR€RY(RRRtbsdata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR9s    cCsˆ|jƒ}|jjjtƒƒtƒ}|d|_t|dƒ|_t|dƒ|_ t|dƒ|_ ||jjd_dS(Niiiii˙˙˙˙( RR€RMRYRFRRRRRR(RRRtrddata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR˘s   cCs||jjdj_dS(Ni˙˙˙˙(R€RMRR(RRł((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRŁscCsmtt|jƒdƒ}tƒ}|d|_|d|_|d|_|d|_||jj d_dS(Niiiii˙˙˙˙( RRRR RRRRR€RM(RRRtqadata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR s     c Csütƒ}dddddddg}t|j|ƒ}tt||ƒƒ}d|kra|d=n|jƒ}|jƒxkt||d t|ƒd gƒD]E\}}t|||j ƒ||t||ƒd |!j ƒƒqœW||j j d_dS( NRRRRRRRi˙˙˙˙i( RRR&R'R(R)R*R+R,R-R.R€RM( RRtdsdataR/R0R1R2R3R4((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR&s     1=cCse|jƒjdƒs$tdƒ‚ntƒ}|jjdkrNg|j_n|jjj|ƒdS(Nt{sCT tag does not start with CT{(R.RZRWR?R€RRY(RRtctdata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR­3s  cCst|ƒdkr!tdƒ‚n|djƒ}|d|jjd_|d|jjd_|d|jjd_t|dƒ|jjd_ t|dƒ|jjd_ |d|jjd_ t|ƒd kró|d |jjd_ n|d|jjd_ dS( NisMissing header line in CT tagii˙˙˙˙iiiiii(R+RWRR€R?RR<R=RR7R:R>R@RA(RttaglinesR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRŽ;scCsz|jƒjdƒs$tdƒ‚ntƒ}|jjdjdkr\g|jjd_n|jjdjj|ƒdS(NRşsRT tag does not start with RT{i˙˙˙˙(R.RZRWR;R€RMRRY(RRtrtdata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRŚIs  cCsőt|ƒdkr!tdƒ‚n|djƒ}|d|jjdjd_|d|jjdjd_|d|jjdjd_t |dƒ|jjdjd_ t |dƒ|jjdjd_ |d|jjdjd_ dS( NisMissing header line in RT tagii˙˙˙˙iiii( R+RWRR€RMR;RR<R=RR7R:R>(RRźR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR§Ss$$cCse|jƒjdƒs$tdƒ‚ntƒ}|jjdkrNg|j_n|jjj|ƒdS(NRşsWA tag does not start with WA{(R.RZRWRCR€RRY(RRtwadata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRŤ^s  cCs‘t|ƒdkr!tdƒ‚n|djƒ}|d|jjd_|d|jjd_|d|jjd_|d|jjd_dS(NisMissing header line in WA tagii˙˙˙˙i( R+RWRR€RCR<R=R>RA(RRźR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRŹfscCsz|jƒjdƒs$tdƒ‚ntƒ}|jjdjdkr\g|jjd_n|jjdjj|ƒdS(NRşsWR tag does not start with WR{i˙˙˙˙(R.RZRWRDR€RMRRY(RRtwrdata((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRŠos  cCs­t|ƒdkr!tdƒ‚n|djƒ}|d|jjdjd_|d|jjdjd_|d|jjdjd_|d|jjdjd_ dS(NisMissing header line in WR tagii˙˙˙˙ii( R+RWRR€RMRDRRER=R>(RRźR((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyRŞws(R R R R R—RĽR™RšRžRŸR5R9R˘RŁR RR­RŽRŚR§RŤRŹRŠRŞ(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyR…âs,              t__main__sQuick self tests../../Tests/Ace/contig1.acetDoneN(((((((((((((((#R RR RR5R9R;R?RCRDRFRGR]R^RptBioRqtBio.ParserSupportRstAbstractParserR‚RŠRƒtAbstractConsumerR…R topenR[R`tcontigRR+RRMtclose(((s…/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Sequencing/Ace.pyt9s:     Á: " 9rž    &