ó ¶GæIc@sCddlmZddlmZddlTddlmZddlZddlmZddl Z ddl m Z de fd „ƒYZ d ejfd „ƒYZ d dd „ƒYZdefd„ƒYZddd„ƒYZddd„ƒYZddd„ƒYZdefd„ƒYZdd d„ƒYZdd!d„ƒYZdS("iÿÿÿÿ(tIUPAC(tFile(t*(tSeqN(tsqrt(tMotift MEMEMotifcBsJeZdZd„Zd„Zd„Zdddddd „Zd „ZRS( sA subclass of Motif used in parsing MEME (and MAST) output. This sublcass defines functions and data specific to MEME motifs. This includes the evalue for a motif and the PSSM of the motif. Methods: add_instance_from_values (name = 'default', pvalue = 1, sequence = 'ATA', start = 0, strand = +): create a new instance of the motif with the specified values. add_to_pssm (position): add a new position to the pssm. The position should be a list of nucleotide/amino acid frequencies add_to_logodds (position): add a new position to the log odds matrix. The position should be a tuple of log odds values for the nucleotide/amino acid at that position. compare_motifs (other_motif): returns the maximum correlation between this motif and other_motif cCstj|ƒd|_dS(Ng(Rt__init__tevalue(tself((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRs cCs7t|ƒtkr||_nt|ƒ}||_dS(N(ttypetinttnum_occurrences(R tnumber((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyt_numoccurrences s  cCs+x$|jD]}|j|kr |Sq WdS(N(t instancest sequence_nametNone(R tnameti((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pytget_instance_by_name'stdefaultitATAit+cCst||jƒ}|j|ƒ|j|ƒ|j|ƒ|j|ƒ|jrb|j|jƒn|jr~|j |jƒn|j |ƒdS(N( t MEMEInstancetalphabett_pvaluet_seqnamet_startt_strandtlengtht_lengthRt _motifnamet add_instance(R Rtpvaluetsequencetstarttstrandtinst((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pytadd_instance_from_values-s      cCs7t|ƒtkr||_nt|ƒ}||_dS(N(R tfloatR(R R((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyt_evalue9s  (t__name__t __module__t__doc__RRRR'R)(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRs      RcBsVeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z RS( sMA class describing the instances of a MEME motif, and the data thereof. cOsPtjj|||Žd|_d|_d|_d|_d|_d|_dS(Ntigð?(RRRR$R"R%Rt motif_name(R targstkwds((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRDs     cCs ||_dS(N(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/Motif/Parsers/MEME.pyRNscCs ||_dS(N(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/Motif/Parsers/MEME.pyR QscCst|ƒ}||_dS(N(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/Motif/Parsers/MEME.pyRTs cCst|ƒ}||_dS(N(R(R"(R tpval((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRXs cCst|ƒ}||_dS(N(R(tscore(R R2((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyt_score\s cCs ||_dS(N(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/Motif/Parsers/MEME.pyR`scCs ||_dS(N(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/Motif/Parsers/MEME.pyRcs( R*R+R,RRR RRR3RR(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRAs      t MEMERecordcBs eZdZd„Zd„ZRS(s²A class for holding the results of a MEME run. A MEMERecord is an object that holds the results from running MEME. It implements no methods of its own. cCs:g|_d|_d|_d|_d|_g|_dS(s__init__ (self)R-N(tmotifstversiontdatafiletcommandRRtsequence_names(R ((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRns      cCs+x$|jD]}|j|kr |Sq WdS(N(R5R(R Rtm((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pytget_motif_by_namews(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/Motif/Parsers/MEME.pyR4gs t MEMEParsercBs eZdZd„Zd„ZRS(sA parser for the text output of the MEME program. Parses the output into an object of the MEMERecord class. Methods: parse (handle): parses the contents of the file handle passed to it. Example: >>>f = open("meme.output.txt") >>>parser = MEMEParser() >>>meme_record = parser.parse(f) >>>for motif in meme_record.motifs: ... for instance in motif.instances: ... print instance.motif_name, instance.sequence_name, instance.strand, instance.pvalue cCstƒ|_tƒ|_dS(s__init__ (self)N(t _MEMEScannert_scannert _MEMEConsumert _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/Motif/Parsers/MEME.pyRs cCs |jj||jƒ|jjS(sparse (self, handle)(R>tfeedR@tdata(R thandle((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pytparse’s(R*R+R,RRD(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR<|s R=cBs)eZdZd„Zd„Zd„ZRS(sBScanner for MEME output. Methods: feed cCsNt|tjƒr|}ntj|ƒ}|j||ƒ|j||ƒdS(sµ Feeds in MEME output for scanning. handle should implement the readline method. consumer is a Consumer object that can receive the salient events. N(t isinstanceRt UndoHandlet _scan_headert _scan_motifs(R RCtconsumertuhandle((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRA¡s  cCsFyt||jddƒWntk r9tdƒ‚nXt||jddƒt||jddƒt||jddƒt||jddƒt||jddƒt||jddƒt||jdd ƒt||jdd ƒt||jdd ƒt||jdd ƒt||jdd ƒt||jdd ƒdS(Ntcontainss MEME versionsFImproper input file. File should contain a line starting MEME version.R$s TRAINING SETs****tDATAFILEtALPHABETs Sequence names----s***scommand:sMOTIF 1( tread_and_call_untiltnoeventt ValueErrort read_and_callt_versiont _datafilet _alphabett_sequence_namet _commandline(R RJRI((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRG¯s  cCsÆx¿t||jddƒt||jddƒt||jddƒt||jddƒt||jddƒt||jddƒt||jddƒt||jddƒt||jƒt||jddƒt||jddƒt||jddƒt||jddƒt||jdd ƒt||jdd ƒt||jd d ƒt||jdd ƒt||jd d ƒt||jdd ƒt |ƒ}|j d ƒrPqqWdS(NR$tMOTIFRKssorted by position p-values---s Sequence nameslog-odds matrixsletter-probability matrixtTimetblankis***sSUMMARY OF MOTIFS( RQt_add_motif_with_infoRNROR.R!tadd_to_logoddst add_to_pssmtread_and_call_whilet safe_peeklinet startswith(R RJRItline((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRHÁs. (R*R+R,RARGRH(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR=™s  R?cBszeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z d „Z d „Z d „ZRS( s’ Consumer that can receive events from MEME Scanner. This is the Consumer object that should be passed to the MEME Scanner. cCs"d|_g|_tƒ|_dS(N(Rt current_motifR9R4RB(R ((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRäs  cCs,|jƒ}|jƒ}|d|j_dS(Ni(tstriptsplitRBR6(R R`tls((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRRés  cCs.|jƒ}|jddƒ}||j_dS(Ns DATAFILE= R-(RbtreplaceRBR7(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/Motif/Parsers/MEME.pyRSîs cCsO|jƒ}|jddƒ}|dkr6tj}n tj}||j_dS(Ns ALPHABET= R-tACGT(RbReRtunambiguous_dnatproteinRBR(R R`tal((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRTós     cCs_|jƒ}|jƒ}|jjj|dƒt|ƒdkr[|jjj|dƒndS(Niii(RbRcRBR9tappendtlen(R R`Rd((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRUüs   cCs.|jƒ}|jddƒ}||j_dS(Ns command: R-(RbReRBR8(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/Motif/Parsers/MEME.pyRVs cCsr|jƒ}|jƒ}tƒ}|j|dƒ|j|dƒ|jj|_|jjj|ƒ||_ dS(Nii ( RbRcRRR)RBRR5RjRa(R R`Rdtmotif((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRZs   cCs>|jƒ}|jƒ}dj|dd!ƒ}||j_dS(Nt ii(RbRctjoinRaR(R R`RdR((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR.s  c Cs®|jƒ}|jƒ}|jjjdƒdkru|jjd|dd|dd|dd |d d |d ƒn5|jjd|dd|d d|d d |dƒdS(NtrevcompiÿÿÿÿRiR#iR$iR"iR%ii(RbRcRBR8tfindRaR'(R R`Rd((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR!s   BcCsdS(N((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/Motif/Parsers/MEME.pyR\#scCsdS(N((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/Motif/Parsers/MEME.pyR[&scCsdS(N((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/Motif/Parsers/MEME.pyRO)s(R*R+R,RRRRSRTRURVRZR.R!R\R[RO(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR?Üs        t _MASTConsumercBsŒeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z d „Z d „Z d „Zd „Zd„ZRS(sÌ Consumer that can receive events from _MASTScanner. A _MASTConsumer parses lines from a mast text output file. The motif match diagrams are parsed using line buffering. Each of the buffering functions have a dummy variable that is required for testing using the Bio.ParserSupport.TaggingConsumer. If this variable isn't there, the TaggingConsumer barfs. In the _MASTScanner, None is passed in the place of this variable. cCs4tƒ|_d|_g|_d|_d|_dS(NR-i(t MASTRecordRBt _current_seqt _line_buffert _buffer_sizet_buffered_seq_start(R ((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR9s     cCs0|jƒ}|jƒ}|jj|dƒdS(Ni(RbRcRBRR(R R`Rd((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRR@s  cCs{|jƒ}|jƒ}|jj|dƒd}|ddkr^tj}|jj|ƒntj}|jj|ƒdS(NiR-is (nucleotide)(RbRcRBt _databaseRRgRTRh(R R`RdRi((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRwEs    cCsu|jƒ}|jƒ}tƒ}|jj|_|d|_|d}||_|j|dƒ|jj|ƒdS(Niii( RbRcRRBRRRR!t _add_motif(R R`RdR:R((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRxQs      c Csd|jƒ}|jƒ}|jj|d|jƒ|djdƒ}d}d}x tdt|ƒƒD]õ}||jdƒdksŸ||jdƒdkrHtƒ}|j |jƒ|j |ƒt j dƒ}|j ||ƒd}||jdƒdkrd|_n d |_|jj|ƒ} | j|ƒ|| j7}qg|t||ƒ7}qgWdS( Nit_it[iÿÿÿÿt Parser for MAST text output. HTML output cannot be parsed, yet. Returns a MASTRecord A MASTParser takes a file handle for a MAST text output file and returns a MASTRecord, containing the hits between motifs and sequences. The parser does some unusual line buffering to parse out match diagrams. Really complex diagrams often lead to an error message and p-values not being parsed for a given line. Methods: parse (handle): parses the data from the file handle passed to it. Example: >>>f = open("mast_file.txt") >>>parser = MASTParser() >>>mast_record = parser.parse(f) >>>for motif in mast_record.motifs: >>> for instance in motif.instances: >>> print instance.motif_name, instance.sequence_name, instance.strand, instance.pvalue cCstƒ|_tƒ|_dS(N(RqR@t _MASTScannerR>(R ((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR-s cCs |jj||jƒ|jjS(N(R>RAR@RB(R RC((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRD1s(R*R+R,RRD(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR«s R¬cBs2eZdZd„Zd„Zd„Zd„ZRS(s1 Scanner for MAST text output. cCs^t|tjƒr|}ntj|ƒ}|j||ƒ|j||ƒ|j||ƒdS(N(RERRFRGt _scan_matchest_scan_annotated_matches(R RCRIRJ((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRA<s  cCsyt||jddƒWntk r9tdƒ‚nXt||jddƒt||jddƒt||jddƒt||jddƒt||jddƒt||jddƒt||jdd ƒt||jdd ƒt||jd d ƒt||jdd ƒdS(NRKs MAST versionsCImproper input file. Does not begin with a line with 'MAST version'R$sDATABASE AND MOTIFStDATABASEs****s MOTIF WIDTHRWs----RYis SECTION II:(RNRORPRQRRRwRx(R RJRI((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRGFs cCsrt||jddƒt||jddƒt||jddƒt||jddƒt||jddƒdS(NR$s SEQUENCE NAMEs---RYi(RNRORQ(R RJRI((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR­Vs cCst||jddƒt||jddƒt||jddƒt||jddƒt||jddƒt||jƒt||jddƒd}x~|dkr|jrá|jdkrÑ|jdƒn|jdƒnt||j ƒt||jddƒt||j ddƒ|j dƒ|jdƒt||jddƒxÇt |ƒ}|j dƒr‚|jdƒd}Pnt||j ddƒt||jddƒ|jdƒt||jddƒr×PqPt||jddƒrP|jdƒ|jdƒd}PqPqPWqWdS( NR$s SECTION III:s****s*****RYiis DIAGRAM(RNRORQR]RsRuR¤RR¥RRŽRŠR^R_R©tattempt_read_and_call(R RJRIt readMatchesR`((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR®^sF        (R*R+R,RARGR­R®(((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR¬7s   RrcBsqeZdZd„Zd„Zd„Zd„Zd„Zd„Zd„Z d„Z d „Z d „Z d „Z RS( svThe class for holding the results from a MAST run. A MASTRecord holds data about matches between motifs and sequences. The motifs held by the MASTRecord are objects of the class MEMEMotif. Methods: get_motif_matches_for_sequence(sequence_name): returns all of the motif matches within a given sequence. The matches are objects of the class MEMEInstance get_motif_matches (motif_name): returns all of the matches for a motif in the sequences searched. The matches returned are of class MEMEInstance get_motif_by_name (motif_name): returns a MEMEMotif with the given name. cCsCg|_d|_g|_d|_i|_d|_g|_dS(NR-(R‹R6tmatchestdatabasetdiagramsRRR5(R ((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyR•s      cCs ||_dS(N(R6(R R6((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRRžscCsA|tjks-|tjks-|tjkr9||_ndSdS(Niÿÿÿÿ(RRht ambiguous_dnaRgR(R R((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRT¡s- cCs ||_dS(N(R³(R R³((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyRw§scCsag}xD|jD]9}x0|jD]%}|j|kr |j|ƒq q WqW|jd„ƒ|S(NcSst|j|jƒS(N(tcmpR$(txty((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pyt°s(R5RRRjtsort(R tseqR˜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/Motif/Parsers/MEME.pyR‘ªscCs|j|jƒ}|jS(N(R;RR(R RlR:((s‰/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Motif/Parsers/MEME.pytget_motif_matches³scCs||j|s"   1&CRé N