ó ªIc@sLdZdd d„ƒYZd„Zdd d„ƒYZdd d„ƒYZdS( s‘ Handle the SCOP HIErarchy files, which describe the SCOP hierarchy in terms of SCOP unique identifiers (sunid). The file format is described in the scop "release notes.":http://scop.berkeley.edu/release-notes-1.55.html The latest HIE file can be found "elsewhere at SCOP.":http://scop.mrc-lmb.cam.ac.uk/scop/parse/ "Release 1.55":http://scop.berkeley.edu/parse/dir.hie.scop.txt_1.55 (July 2001) tRecordcBs,eZdZdd„Zd„Zd„ZRS(sÄHolds information for one node in the SCOP hierarchy. sunid -- SCOP unique identifiers of this node parent -- Parents sunid children -- Sequence of childrens sunids cCs5d|_d|_g|_|r1|j|ƒndS(Nt(tsunidtparenttchildrent_process(tselftline((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Hie.pyt__init__s    cCsÚ|jƒ}|jdƒ}t|ƒdkr@td|ƒ‚n|\}}}|dkrgd|_nt|ƒ|_|dkrŽd|_nt|ƒ|_|dkrµd|_n!|jdƒ}tt|ƒ|_dS( s™Parses HIE records. Records consist of 3 tab deliminated fields; node's sunid, parent's sunid, and a list of children's sunids. s is#I don't understand the format of %st-Rt,N(( trstriptsplittlent ValueErrorRtintRRtmap(RRtcolumnsRRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Hie.pyR#s       cCs¼g}|jt|jƒƒ|jr>|jt|jƒƒn,|jdkr]|jdƒn |jdƒ|jržtt|jƒ}|jdj|ƒƒn |jdƒdj|ƒdS(Nit0R R s s (tappendtstrRRRRtjoin(Rtst child_str((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Hie.pyt__str__Fs    N(t__name__t __module__t__doc__tNoneRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Hie.pyRs  #ccs x|D]}t|ƒVqWdS(s‰Iterates over a HIE file, returning a Hie record for each line in the file. Arguments: handle -- file-like object. N(R(thandleR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Hie.pytparse\s tIteratorcBs,eZdZdd„Zd„Zd„ZRS(sIterates over a HIE file. cCs{ddl}|jdtƒddlm}m}t|ƒ|k ret|ƒ|k retdƒ‚n||_||_ dS(s/Create an object that iterates over a HIE file. handle -- file-like object. parser -- 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. iÿÿÿÿNsMBio.SCOP.Hie.Iterator is deprecated. Please use Bio.SCOP.Hie.parse() instead.(tFileTypet InstanceTypes,I expected a file handle or file-like object( twarningstwarntDeprecationWarningttypesR R!ttypet TypeErrort_handlet_parser(RRtparserR"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/SCOP/Hie.pyRks $ cCsWx1|jjƒ}|sdS|ddkrPqqW|jdk rS|jj|ƒS|S(sRetrieve the next HIE record.it#N(R(treadlineRR)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/SCOP/Hie.pytnext}scCst|jdƒS(N(titerR-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/SCOP/Hie.pyt__iter__‡sN(RRRRRR-R/(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Hie.pyRhs  tParsercBseZd„Zd„ZRS(cCs ddl}|jdtƒdS(NiÿÿÿÿsºBio.SCOP.Hie.Parser is deprecated. Instead of parser = Hie.Parser() record = parser.parse(entry) please use record = Hie.Record(entry) (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/SCOP/Hie.pyRŒs  cCs t|ƒS(sReturns a Hie Record (R(Rtentry((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Hie.pyR™s(RRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Hie.pyR0‹s N((((RRRRR0(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SCOP/Hie.pytsI #