ó ¸¬¼Ic@sxdZd„Zd„Zddd„ƒYZddd„ƒYZd„Zd„Zd „Zd „Zd „Z d „Z d S(s® This module provides code to work with the prosite.doc file from Prosite. http://www.expasy.ch/prosite/ Tested with: Release 15.0, July 1998 Release 16.0, July 1999 Release 20.22, 13 November 2007 Release 20.43, 10 February 2009 Functions: read Read a Prodoc file containing exactly one Prodoc entry. parse Iterates over entries in a Prodoc file. Classes: Record Holds Prodoc data. Reference Holds data from a Prodoc reference. DEPRECATED functions: index_file Index a Prodoc file for a Dictionary. _extract_record Extract Prodoc data from a web page. DEPRECATED classes: Dictionary Accesses a Prodoc file using a dictionary interface. RecordParser Parses a Prodoc record into a Record object. _Scanner Scans Prodoc-formatted data. _RecordConsumer Consumes Prodoc data to a Record object. Iterator Iterates over entries in a Prodoc file. cCs1t|ƒ}|jƒ}|r-tdƒ‚n|S(Ns!More than one Prodoc record found(t__readtreadlinet ValueError(thandletrecordtline((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pytread(s   ccs,x%tr't|ƒ}|sdS|VqWdS(N(tTrueR(RR((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pytparse0s   tRecordcBseZdZd„ZRS(sHolds information from a Prodoc record. Members: accession Accession number of the record. prosite_refs List of tuples (prosite accession, prosite name). text Free format text. references List of reference objects. cCs(d|_g|_d|_g|_dS(Nt(t accessiont prosite_refsttextt references(tself((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pyt__init__As   (t__name__t __module__t__doc__R(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pyR 7s t ReferencecBseZdZd„ZRS(sºHolds information from a Prodoc citation. Members: number Number of the reference. (string) authors Names of the authors. citation Describes the citation. cCsd|_d|_d|_dS(NR (tnumbertauthorstcitation(R((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pyRQs  (RRRR(((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pyRHscCse|jƒ}|ddkr/td|ƒ‚n|dd!jdƒ\}}|jj||fƒdS(Niÿÿÿÿt}s3I don't understand the Prosite reference on line %sis; (trstripRtsplitR tappend(RRtacctname((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pyt__read_prosite_reference_lineXs  cCs|j|7_tS(N(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/ExPASy/Prodoc.pyt__read_text_line_scCsltƒ}|dd!jƒ|_|ddkrE|djƒ|_n|djƒ|_|jj|ƒdS(NiitEi(RtstripRRRRR(RRt reference((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pyt__read_reference_startcs  cCs†|jƒstS|jd}|jdƒrr|jddkr[|j|djƒ7_n|j|d7_tStd|ƒ‚dS(Niÿÿÿÿs t,iis(I don't understand the reference line %s( R!tFalseRt startswithRRRRt Exception(RRR"((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pyt__read_reference_lineos  cCs|jdƒrtStS(Ns+----(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/ExPASy/Prodoc.pyt__read_copyright_line{scCséx8|D],}|jƒ}|r|jdƒ rPqqWdStƒ}|jdƒsftd|ƒ‚n|ddkr‰td|ƒ‚n|dd!|_x:|D]&}|jdƒrÅt||ƒq Pq Wtd ƒ‚|jd ƒsøtd |ƒ‚nt}xØ|D]Ð}|jd ƒrVx5|jD]*}|j jƒ|_ |j jƒ|_ q$W|S|d dkrœ|ddkrœ|ddkrœt ||ƒt }q|jdƒr´t }q|r|||ƒsÕd}qÕqqWtd ƒ‚dS(Ns//s{PDOCs$Line does not start with '{PDOC': %siÿÿÿÿRs$I don't understand accession line %sis{PSsUnexpected end of stream.s{BEGINs%Line does not start with '{BEGIN': %ss{END}it[it]it s+----(RR&tNoneR RR RRRRRR#R(R)(RRRt read_lineR"((s„/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/ExPASy/Prodoc.pyRsD      0   N((( RRRR RRRR#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/ExPASy/Prodoc.pyt%s