ó W/Ic@søddlmZddlmZddlTddlmZddlmZddlZddd„ƒYZ d e fd „ƒYZ d dd „ƒYZ d dd„ƒYZ ddd„ƒYZde fd„ƒYZddd„ƒYZddd„ƒYZdS(iÿÿÿÿ(tIUPAC(tFile(t*(tSeq(tMotifNt 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)tN(tmotifstversiontdatafiletcommandtNonetalphabettsequence_names(tself((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyt__init__s      cCs+x$|jD]}|j|kr |Sq WdS(N(Rtname(RRtm((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pytget_motif_by_names(t__name__t __module__t__doc__RR(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR s t MEMEParsercBs eZdZd„Zd„ZRS(sõA 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/MEME/Parser.pyR3s cCs |jj||jƒ|jjS(sparse (self, handle)(RtfeedRtdata(Rthandle((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pytparse8s(RRRRR(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR"s RcBs)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(RRtconsumertuhandle((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyRGs  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.tstarts TRAINING SETs****tDATAFILEtALPHABETs Sequence names----s***scommand:sMOTIF 1( tread_and_call_untiltnoeventt ValueErrort read_and_callt_versiont _datafilet _alphabett_sequence_namet _commandline(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/MEME/Parser.pyR!Us  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&tMOTIFR%ssorted by position p-values---s Sequence nameslog-odds matrixsletter-probability matrixtTimetblankis***sSUMMARY OF MOTIFS( R,t_add_motif_with_infoR)R*t motif_namet add_instancetadd_to_logoddst add_to_pssmtread_and_call_whilet safe_peeklinet startswith(RR$R#tline((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR"gs. (RRRRR!R"(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR?s  RcBszeZdZd„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(R t current_motifR 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/MEME/Parser.pyRŠs  cCs,|jƒ}|jƒ}|d|j_dS(Ni(tstriptsplitRR(RR=tls((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR-s  cCs.|jƒ}|jddƒ}||j_dS(Ns DATAFILE= R(R?treplaceRR (RR=((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR.”s cCsO|jƒ}|jddƒ}|dkr6tj}n tj}||j_dS(Ns ALPHABET= RtACGT(R?RBRtunambiguous_dnatproteinRR (RR=tal((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR/™s     cCs_|jƒ}|jƒ}|jjj|dƒt|ƒdkr[|jjj|dƒndS(Niii(R?R@RR tappendtlen(RR=RA((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR0¢s   cCs.|jƒ}|jddƒ}||j_dS(Ns command: R(R?RBRR (RR=((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR1©s cCsŠ|jƒ}|jƒ}tjƒ}|j|dƒ|j|dƒ|j|dƒ|j|jj ƒ|jj j |ƒ||_ dS(Niii ( R?R@Rt MEMEMotift_lengtht_numoccurrencest_evalueR/RR RRGR>(RR=RAtmotif((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR5®s   cCsB|jƒ}|jƒ}dj|dd!ƒ}|jj|ƒdS(Nt ii(R?R@tjoinR>t_name(RR=RAR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR6¹s  c CsÞ|jƒ}|jƒ}|jjjdƒdkrtj|d|jjƒ}|jjd|dd|d|dd |d d |d ƒnMtj|d |jjƒ}|jjd|dd|d|d d |dƒdS(NtrevcompiÿÿÿÿiRitsequenceR&itpvalueitstrandii( R?R@RR tfindRR R>tadd_instance_from_values(RR=RAtseq((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR7¿s  >cCsQ|jƒ}|jƒ}tg|D]}t|ƒ^q"ƒ}|jj|ƒdS(N(R?R@ttupletfloatR>R9(RR=tsltit thisposition((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR9És  %cCsQ|jƒ}|jƒ}tg|D]}t|ƒ^q"ƒ}|jj|ƒdS(N(R?R@RXRYR>R8(RR=RZR[R\((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR8Ïs  %cCsdS(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/MEME/Parser.pyR*Õs(RRRRR-R.R/R0R1R5R6R7R9R8R*(((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR‚s        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(NRi(t MASTRecordRt _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/MEME/Parser.pyRås     cCs0|jƒ}|jƒ}|jj|dƒdS(Ni(R?R@RR-(RR=RA((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR-ìs  cCs{|jƒ}|jƒ}|jj|dƒd}|ddkr^tj}|jj|ƒntj}|jj|ƒdS(NiRis (nucleotide)(R?R@Rt _databaseRRDR/RE(RR=RARF((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyRcñs    cCs„|jƒ}|jƒ}tjƒ}|j|jjƒ|j|dƒ|d}|j|ƒ|j |dƒ|jj |ƒdS(Niii( R?R@RRIR/RR RJRPt _consensust _add_motif(RR=RARR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyReýs     c Csg|jƒ}|jƒ}|jj|d|jƒ|djdƒ}d}d}xtdt|ƒƒD]ø}||jdƒdksŸ||jdƒdkrKtj ƒ}|j |jƒ|j |ƒt j dƒ}|j||ƒd}||jdƒdkrd|_n d |_|jj|ƒ} | j|ƒ|| j7}qg|t||ƒ7}qgWdS( Nit_it[iÿÿÿÿt\s(Rt instancest sequence_nameRGtsort(RRWRRR[((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pyR…VscCs|j|jƒ}|jS(N(RRR¯(RRMR((s‚/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/MEME/Parser.pytget_motif_matches_scCs||j|s  CXé N