ó ‘Ic@sOdZddlZddlZddlTddlmZyddlmZdZWn+e k rej j ddƒd ZnXd dd „ƒYZ d dd „ƒYZ de fd„ƒYZddd„ƒYZerñdejfd„ƒYZnd„Zd„Zd„Zd„Zdddddd„Zd d„Zd„Zd„ZdS(s„Code to support writing parsers. Classes: AbstractParser Base class for parsers. AbstractConsumer Base class of all Consumers. TaggingConsumer Consumer that tags output with its event. For debugging SGMLStrippingConsumer Consumer that strips SGML tags from output. EventGenerator Generate Biopython Events from Martel XML output (note that Martel is now DEPRECATED) Functions: safe_readline Read a line from a handle, with check for EOF. safe_peekline Peek at next line, with check for EOF. read_and_call Read a line from a handle and pass it to a method. read_and_call_while Read many lines, as long as a condition is met. read_and_call_until Read many lines, until a condition is met. attempt_read_and_call Like read_and_call, but forgiving of errors. is_blank_line Test whether a line is blank. iÿÿÿÿN(t*(tFile(thandleris4Warning: Could not import SAX for dealing with XML. s5This causes problems with some ParserSupport modules itAbstractParsercBs)eZdZd„Zd„Zd„ZRS(s#Base class for other parsers. cCstdƒ‚dS(Ns#Please implement in a derived class(tNotImplementedError(tselfthandle((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pytparse0scCs|jtj|ƒƒS(N(RRt StringHandle(Rtstring((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt parse_str3scCs1t|ƒ}z|j|ƒ}Wd|jƒX|S(N(topenRtclose(Rtfilenamethtretval((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt parse_file6s   (t__name__t __module__t__doc__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/ParserSupport.pyR,s  tAbstractConsumercBs)eZdZd„Zd„Zd„ZRS(sžBase class for other Consumers. Derive Consumers from this class and implement appropriate methods for each event that you want to receive. cCsdS(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/ParserSupport.pyt_unhandled_sectionEscCsdS(N((Rtdata((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt _unhandledGscCs9|d dks |d dkr,|j}n |j}|S(Nitstart_itend_(RR(Rtattrtmethod((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt __getattr__Is   (RRRRRR(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyR>s  tTaggingConsumercBsGeZdZdddd„Zd„Zd„Zdd„Zd„ZRS( soA Consumer that tags the data stream with the event and prints it to a handle. Useful for debugging. iiPcCs7|dkrtj}n||_||_||_dS(s<TaggingConsumer(handle=sys.stdout, colwidth=15, maxwidth=80)N(tNonetsyststdoutt_handlet _colwidtht _maxwidth(RRtcolwidthtmaxwidth((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt__init__Us     cCs|jdƒdS(Ntunhandled_section(t _print_name(R((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyR'bscCs|jd|ƒdS(Nt unhandled(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/ParserSupport.pyR)escCss|dkr0|jjdd|j|fƒn?|jjd|j||j ||j|jd jƒfƒdS(Ns%s %s Rs %-*s: %s i(RR!twriteR"R#trstrip(RtnameR((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyR(hs  $ cCsE|d dks |d dkr2||d„}n||d„}|S(NiRiRcSs |j|ƒS(N(R((tats((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyttscSs|j||ƒS(N(R((txR-R.((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyR/vs((RRR((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyRrs N( RRRRR&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/ParserSupport.pyRPs    tSGMLStrippingConsumercBs)eZdZd„Zd„Zd„ZRS(smA consumer that strips off SGML tags. This is meant to be used as a decorator for other consumers. cCsFt|ƒtk r!tdƒ‚n||_d|_tjƒ|_dS(Nsconsumer should be an instance( ttypet InstanceTypet ValueErrort _consumerRt _prev_attrRt SGMLStrippert _stripper(Rtconsumer((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyR&s   cCs#|jj|ƒ}|j|ƒdS(N(R8tstripR6(RRtclean((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt_apply_clean_data†scCsu|dkrt||ƒSt|j|ƒ}t|ƒtk rA|S|d dksa|d dkre|S||_|jS(NR6R8iRiR(R6R8(tgetattrR5R2t MethodTypeR6R<(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/ParserSupport.pyRŠs    (RRRR&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/ParserSupport.pyR1ys  tEventGeneratorcBsJeZdZdgd„Zd„Zd„Zd„Zd„Zd„Z RS(sdHandler to generate events associated with a Martel parsed file. This acts like a normal SAX handler, and accepts XML generated by Martel during parsing. These events are then converted into 'Biopython events', which can then be caught by a standard biopython consumer. Note that Martel is now DEPRECATED. cCsm||_||_||_||_i|_x|jD]}g|j|Spam More Spam In this case the list of information would be: ['Spam', 'More Spam'] This list of lines will be passed to the callback finalizer if it is present. Otherwise the consumer will be called with the list of content information. o exempt_tags - A listing of particular tags that are exempt from being processed by the callback_finalizer. This allows you to use a finalizer to deal with most tags, but leave those you don't want touched. tiN(R5t interest_tagst _finalizert _exempt_tagstinfot _previous_tagt _cur_contentt_collect_characters(RR9RAtcallback_finalizert exempt_tagsttag((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyR&¤s       cCs||jkrd|_ndS(sEDetermine if we should collect characters from this tag. iN(RARG(RR,tattrs((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt startElementÛscCs |jr|jj|ƒndS(s@Extract the information if we are interested in it. N(RGRFtappend(Rtcontent((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt charactersás cCsv|jrr|j|jdj|jƒƒg|_d|_|jrf|j|krf|j|jƒn||_ndS(s“Send the information to the consumer. Once we've got the end element we've collected up all of the character information we need, and we need to send this on to the consumer to do something with it. We have a delay of one tag on doing this, so that we can collect all of the info from multiple calls to the same element at once. R@iN(RGRDRMtjoinRFREt_make_callback(RR,((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt endElementçs    cCsqt|j|ƒ}|jdk rI||jkrI|j|j|ƒ}n |j|}||ƒg|j| number of lines Read a line from uhandle and pass it to the method as long as some condition is true. Returns the number of lines that were read. See the docstring for read_and_call for a description of the parameters. ii(RVRWtsaveline(RXRRYtnlinesRZ((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pytread_and_call_while1s    cKsTd}xGt|ƒ}t|f|Žs8|j|ƒPn||ƒ|d}q W|S(sLread_and_call_until(uhandle, method, start=None, end=None, contains=None, blank=None) -> number of lines Read a line from uhandle and pass it to the method until some condition is true. Returns the number of lines that were read. See the docstring for read_and_call for a description of the parameters. ii(RVRWR](RXRRYR^RZ((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pytread_and_call_untilEs    cKsCt|ƒ}t|f|Ž }|r2||ƒn |j|ƒ|S(sattempt_read_and_call(uhandle, method, **keywds) -> boolean Similar to read_and_call, but returns a boolean specifying whether the line has passed the checks. Does not raise exceptions. See docs for read_and_call for a description of the function arguments. 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A true value signifies that a line containing whitespaces as well as end-of-line characters should be considered blank. iR@is s (R+(RZt allow_spaces((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyRe…s cCs%|jƒ}|s!tdƒ‚n|S(sšsafe_readline(handle) -> line Read a line from an UndoHandle and return it. If there are no more lines to read, I will raise a ValueError. sUnexpected end of stream.(treadlineR4(RRZ((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyRV”s cCs%|jƒ}|s!tdƒ‚n|S(s¦safe_peekline(handle) -> line Peek at the next line in an UndoHandle and return it. If there are no more lines to peek, I will raise a ValueError. sUnexpected end of stream.(tpeeklineR4(RRZ((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyt safe_peekline s ((((RRt tracebackttypestBioRtxml.saxRt xml_supportt ImportErrortstderrR*RRRR1tContentHandlerR?R\R_R`RbRRWReRVRp(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ParserSupport.pyts4       ) ‚