* ͑:cs?dZdkTdkZdklZdklZdkZ dkZ!dkT"dk Z#dk Z %dfdYZ 6dfdYZ bd fd YZ d eifd YZLed joQMedZNeiieZOeZPeieQeindS(s"Rebase.py This module provides code to work with files from http://rebase.neb.com/rebase/rebase.html Classes: Record Holds rebase sequence data. Iterator Iterates over sequence data in a rebase file. Dictionary Accesses a rebase file using a dictionary interface. RecordParser Parses rebase sequence data into a Record object. _Scanner Scans a rebase-format stream. _RecordConsumer Consumes rebase data to a Record object. Functions: index_file Index a FASTA file for a Dictionary. (s*N(sFile(sIndexsRecordcs%dZ,-dZRS(smHolds information from a Rebase record. Members: seq_5_to_3 The sequence. seq_3_to_5 cs"-23d|_4d|_dS(s7__init__(self ) Create a new Record. sN(sselfs seq_5_to_3s seq_3_to_5(sself((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys__init__-s (s__doc__s__init__(((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pysRecord%s sIteratorcs)6dZ<=edZJdZRS(sReturns one record at a time from a Rebase file. Methods: next Return the next record from the stream, or None. csj=DEt|tj ot|tj oFtdnGtti||_ H||_ 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. 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N( sIndexs indexnamesselfs_indexsopens Dictionarys_Dictionary__filename_keys_handlesparsers_parser(sselfs indexnamesparser((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys__init__hs csvwt|iSdS(N(slensselfs_index(sself((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys__len__vscsyz|i|\}}{|ii|||ii|}}|i t j o ~|i i t i |Sn|SdS(N(sselfs_indexskeysstartslens_handlesseeksreadsdatas_parsersNonesparsesFiles StringHandle(sselfskeyslensdatasstart((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys __getitem__ys  cst|i|SdS(N(sgetattrsselfs_indexsname(sselfsname((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys __getattr__s(s__doc__s_Dictionary__filename_keysNones__init__s__len__s __getitem__s __getattr__(((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys Dictionarybs    s RebaseParsercsdZdZdZdZdZdZdZdZdZd Z d Z d Z d Z d Z dZdZdZ$dZ-dZ2ddZGdZRS(s7Parses Rebase sequence data into a Record object. cstii|d|_ti|_d|_d|_g|id<ti|id<d|_ d|_ d|_ dS(Nsstitlesfactoidssnumber_of_sitesi( ssgmllibs SGMLParsersresetsselfstextsUserDicts enzyme_dicts_states key_waitings_table_nest_levels_table_nest_dirs_factoid(sself((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pysresets     cs.|i|i||iSdS(N(sselfsresetsfeedshandles enzyme_dict(sselfshandle((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pysparses cst|tio |}nti|}d}xydon|i}ti |}t |doPn|d djoPn|d|}qJWt i i ||dS(sfeed(self, handle ) Feed in rebase data for scanning. handle is a file-like object containing rebase data. consumer is a Consumer object that will receive events as the rebase data is scanned. siiiss N(s isinstanceshandlesFiles UndoHandlesuhandlestextsreadlineslinesstringsstrips is_blank_linessgmllibs SGMLParsersfeedsself(sselfshandlesuhandlestextsline((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pysfeeds   cs,ti|}|i||_dS(N(sstringsstripsnewtextsselfstext(sselfsnewtext((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys handle_datascs&|id|_d|_dS(Nis increasing(sselfs_table_nest_levels_table_nest_dir(sselfsattrs((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys start_tablescs|id|_|idjod|idjo|id|_n1|idjo|id|_nnd|_dS(Nis increasingsdetailssnumber_of_sitesscompletes decreasing(sselfs_table_nest_levels_table_nest_dirs_statesextract_detailssextract_number_of_sites(sself((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys end_tables  cs8|idjo|in|idS(Nsdetails(sselfs_statesextract_detailss flush_text(sselfsattrs((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pysstart_bscs|idjo|i}|djo|d djoT|i}|djo#|i|i|<d|_n|d |_n|id||_nndS(Nsdetailssis:s (sselfs_states flush_textstexts key_waitingskeys_factoids enzyme_dict(sselfskeystext((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pysend_bs cs+|idjo|indS(Nsnumber_of_sites(sselfs_statesextract_number_of_sites(sselfsattrs((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pysstart_iscs|idjo|in|idjo|i}|djoq|d djo|d |_nD|idjo0|i}d|_||id|d||fGH?|i|||dqWnu@t|thjoPAxF|i dAr3}Bd||fGHC|i|||dqeWn E|GHdS(Ns iss%s%sis %skey is %s( sindentsrangeslevelsjstypesitemssubitemsselfs print_items isinstancesUserDictskeys(sselfsitemslevelssubitemsjsindent((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys print_item2s,    # #csLGHx?|iidHr)}Id|GHJ|i|i|qWdS(Niskey %s(sselfs enzyme_dictskeysskeys print_item(sselfskey((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys print_tagsGs  (s__doc__sresetsparsesfeeds handle_datas start_tables end_tablesstart_bsend_bsstart_isend_is start_presend_presdo_brs start_fontsend_fontsextract_detailssextract_number_of_sitess flush_texts print_items print_tags(((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys RebaseParsers*             s__main__s bamii.htm(s__doc__stypessstringsBiosFilesIndexsurllibssgmllibsBio.ParserSupportsBio.FilesUserDictsRecordsIterators Dictionarys SGMLParsers RebaseParsers__name__sopenshandles UndoHandles undo_handles rebase_parsersparses print_tags(s rebase_parserssgmllibshandlesFilesRecordsIndexsurllibs RebaseParsersUserDicts undo_handlesIteratorsstrings DictionarysBio((s*/mit/seven/lib/python/Bio/Rebase/Rebase.pys?s&        ,"