ó ÒÚ0Ic@sddlZddlZddlmZmZejddƒZd„Zd„Zdejfd„ƒYZ e ƒZ d „Z d dd „ƒYZ d dd „ƒYZ ddd„ƒYZd„Zej dejƒZd„Zej dejƒZd„Zd„ZdS(iÿÿÿÿN(tSeqtAlphabets abcdefghijklmnopqrstuvwxyzX}()<>s ABCDEFGHIJKLMNOPQRSTUVW.YZ.]{}^$cCsï|d dk}|jddƒ}|jtdƒ}|rm|jdƒ}d|d|!d||d }n|d d kr¬|jd ƒ}|| d ||d !d}n?|ddkrë|jd ƒ}|| d ||d!d}n|S(s1convert a valid Prosite pattern into an re stringis[s$  cCsQ|d dk}|jddƒ}|jtdƒ}|rm|jdƒ}d|d|!d||d }n|d d kr¬|jd ƒ}|| d ||d !d}n|ddkrë|jd ƒ}|| d ||d!d}n|d dkr d|d }n d|}|ddkr7|d d}n |d}|jddƒS(sDconvert a valid Prosite pattern into an re with groups for each termis[(tbase_strRDRERC(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/Prosite/Pattern.pyR'Ís   cCsÃ|jrd}nd}|jr9|d|jd}n†t|jƒdkrr|j rr|j rr||j}nM|d}|jr’|d}n||j}|jrµ|d}n|d}|S( Nt(R RNR8R<((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyR!÷s     cCsdt|ƒS(Ns(tid(R ((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyR$scCs t|jƒS(N(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/Prosite/Pattern.pyR'scCs t|jƒS(N(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/Prosite/Pattern.pyR)scCs |j|S(N(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/Prosite/Pattern.pyR*scCs8t|dƒ}t|dƒ}t|j||!|jƒS(Ni(R+RRR>(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/Prosite/Pattern.pyR- scCsˆg}d}|jdƒ}yUxN|jj|dƒ}x'||kr`|j|ƒ|d}q:W|d}q!WWntk rƒnX|S(sreturn a list of numbers mapping to items of the original pattern For example, if the Prosite pattern is "[AP](2)-D." matched against "PAD", then the mapping is [1, 1, 2], meaning the first character of the match ("P") is from the first Prosite group ("[AP]"), as is the second letter ("A"). The 3rd letter ("D") is mapped to group 2 of the pattern. ii(tstartR<tendtappendt IndexError(R tvalsR RQRR((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pytmapping s   cCst|j|jƒƒS(süreturns the specific Prosite pattern used to find this sequence >>> p = Prosite.compile("[AP](2,3)-D.") >>> m = p.search(Seq.Seq("PAD")) >>> mapping = m.mapping() >>> mapped = m.mapped_pattern() >>> print str(m[1]), str(p[mapping[1]]), str(mapped[1]) P [AP](2,3) [AP] >>> print str(mapped) [AP]-[AP]-D. >>> Note that the original term includes the count, while the mapped pattern does the expansion. (tpattern_mappingRNRV(R ((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pytmapped_pattern%sicCs|jj|ƒS(N(R<RQ(R tg((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyRQ8scCs|jj|ƒS(N(R<RR(R RY((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyRR:scCs|jj|ƒS(N(R<tspan(R RY((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyRZ<scCsOg}|j}x3|jj|ƒD]}|jtj||ƒƒq"Wt|ƒS(N(R>R<tgroupsRSRttuple(R tdefaulttresultR>RY((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyR[>s  cGs„|jj|Œ}|dkr"|St|ƒdkrGtj||jƒSg}x*|D]"}|jtj||jƒƒqTWt|ƒS(Ni((R<ROR(RR>RSR\(R R[R^tretvaltx((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyRODs   N(RRR!R$R'R)R*R-RVRXRQRRRZRR[RO(((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyR7ös           cCsQg}x;|D]3}||jƒ}d|_|_|j|ƒq Wtd|ƒS(NiR(RHRDRERSR(RNRVRR R`((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyRWOs  s (?: ([ABCDEFGHIKLMNPQRSTVWXYZx])| # a character OR \[(?)\]| # something in []s OR \{([ABCDEFGHIKLMNPQRSTVWXYZ]+)\} # something in {}s )(?:\((\d+)(,\d+)?\))? # optional count of the form "(i,j)", ",j" optional $ c Cs¦|ddkrtdƒ‚n|d }|jdƒ}g}d}x[|D]S}d}}|d dkr~|d}d}nd}|ddkr§|d }d}nd}tj|ƒ} | dkrátd t|ƒƒ‚n| jdƒdk rd} | jdƒ} nô| jd ƒdk r¿d} | jd ƒ} | jd ƒrud}|dkrutd t|ƒƒ‚qun| jd ƒrd}|t|ƒdkr¼tdt|ƒƒ‚q¼qnC| jdƒdk rìd} | jdƒ} ntdt|ƒƒ‚| jdƒdk r/t| jdƒƒ} nd} | jdƒdk rft| jdƒdƒ} n| } |j t | | ||| | ||ƒƒ|d}qKW|S(NiÿÿÿÿRs)not a prosite pattern - needs a final '.'RiiRKRIsnot a Prosite term (%s)iis$[<] only allowed for first term (%s)is#[>] only allowed for last term (%s)isnot a prosite term (%s)ii( Rtsplittprosite_term_reR<RR"ROR(tintRSR?(R ttermsR^R ttermRFRGRBRCR<RAR@RDRE((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyR0bsd           sõ ^?\])| # something in []s OR \{[ABCDEFGHIKLMNPQRSTVWXYZ]+\} # something in {}s )(\(\d+(,\d+)?\))? # optional count of the form "(i,j)" (",j" is optional) (- # new terms seperated by a '-' ( [ABCDEFGHIKLMNPQRSTVWXYZx]| # a character OR \[[ABCDEFGHIKLMNPQRSTVWXYZ]+>?\]| # something in []s OR \{[ABCDEFGHIKLMNPQRSTVWXYZ]+\} # something in {}s )(\(\d+(,\d+)?\))? # optional count )* # repeat until done >? # pattern ends with an optional ">" \.$ # description ends with a required "." cCshtj|ƒ}|dkrdS|jddƒdkr;dS|jddt|ƒdƒdkrddSdS(sAreturns 1 if the Prosite pattern is syntactically correct, else 0is[]iN(t prosite_reR<RtfindR((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/Prosite/Pattern.pyRÁs %cCsd}xõ|jƒ}|sPn|d dkr5q n||dd!}|ddkr yxdd GH|GHt|ƒ}t|ƒGHt|jƒGHt|ƒGHt|jƒGHt|ƒ}||krÍd G|G|GHnWn tk rð}d G|G|GHnXd}q q Wd S( s.verify the patterns from a Prosite file handleRLitPAiiÿÿÿÿiþÿÿÿRt*i<tDIFFERtPROBLEMN( treadlineRRR"R.RR/R#R(tinfileR tlinetpRdtmsg((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyt _verify_testÍs.       ((((tstringR.tBioRRt maketransRRRRR=RRR?R7RWtVERBOSERbR0RfRRq(((s†/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Prosite/Pattern.pyt3s&    !  B8Y  L