‘Hc@s=dZddlZddlZy eZWn!ek rKddlmZnXddlmZm Z ddl m Z ddl m ZmZmZddlTddlmZdd lmZid d 6d d 6dd6dd6dd6dd6dd6dd6dd6dd6dd6d d!6d"d#6d$d%6d&d'6ZeZd(efd)YZd*efd+YZd,efd-YZd.efd/YZd0efd1YZd2efd3YZ d4efd5YZ!d6efd7YZ"d8efd9YZ#d:efd;YZ$d<efd=YZ%d>efd?YZ&d@efdAYZ'dBefdCYZ(dDefdEYZ)dFefdGYZ*dHefdIYZ+dJefdKYZ,dLefdMYZ-dNefdOYZ.dPe.efdQYZ/e.Z0e.Z1xej2D]\Z3\Z4Z5e6ge4D]Z7e8e7^q9Z4ej9ed*e4iZ:xMe5D]EZ;e:e;e4ee;Z<e<j=re0j>e<n e1j>e<qsWqWe0e1BZ?ge?D]Z7e@e7^qZAeBjCeDeEeFeAe?d(dPdNdRdSdTgeAZG[;[7[5[3[4[AdS(Us, Notes about the diverses class of the restriction enzyme implementation. RestrictionType is the type of all restriction enzymes. ---------------------------------------------------------------------------- AbstractCut implements some methods that are common to all enzymes. ---------------------------------------------------------------------------- NoCut, OneCut,TwoCuts represent the number of double strand cuts produced by the enzyme. they correspond to the 4th field of the rebase record emboss_e.NNN. 0->NoCut : the enzyme is not characterised. 2->OneCut : the enzyme produce one double strand cut. 4->TwoCuts : two double strand cuts. ---------------------------------------------------------------------------- Meth_Dep, Meth_Undep represent the methylation susceptibility to the enzyme. Not implemented yet. ---------------------------------------------------------------------------- Palindromic, if the site is palindromic or not. NotPalindromic allow some optimisations of the code. No need to check the reverse strand with palindromic sites. ---------------------------------------------------------------------------- Unknown, Blunt, represent the overhang. Ov5, Ov3 Unknown is here for symetry reasons and correspond to enzymes that are not characterised in rebase. ---------------------------------------------------------------------------- Defined, Ambiguous, represent the sequence of the overhang. NotDefined NotDefined is for enzymes not characterised in rebase. Defined correspond to enzymes that display a constant overhang whatever the sequence. ex : EcoRI. G^AATTC -> overhang :AATT CTTAA^G Ambiguous : the overhang varies with the sequence restricted. Typically enzymes which cut outside their restriction site or (but not always) inside an ambiguous site. ex : AcuI CTGAAG(22/20) -> overhang : NN AasI GACNNN^NNNGTC -> overhang : NN CTGN^NNNNNCAG note : these 3 classes refers to the overhang not the site. So the enzyme ApoI (RAATTY) is defined even if its restriction site is ambiguous. ApoI R^AATTY -> overhang : AATT -> Defined YTTAA^R Accordingly, blunt enzymes are always Defined even when they cut outside their restriction site. ---------------------------------------------------------------------------- Not_available, as found in rebase file emboss_r.NNN files. Commercially_available allow the selection of the enzymes according to their suppliers to reduce the quantity of results. Also will allow the implementation of buffer compatibility tables. Not implemented yet. the list of suppliers is extracted from emboss_s.NNN ---------------------------------------------------------------------------- iN(tSet(tSeqt MutableSeq(tIUPAC(t rest_dictttypedictt suppliers(t*(t PrintFormat(t check_basestARWMHVDNtAtCYSMHBVNtCtGRSKBVDNtGtTYWKHBDNtTt ABDGHKMNSRWVtRt CBDHKMNSTWVYtYt ABDHKMNRTWVYtWt CBDGHKMNSRVYtSt ACBDHMNSRWVYtMt BDGHKNSRTWVYtKtACBDHKMNSRTWVYtHtCBDGHKMNSRTWVYtBtACBDGHKMNSRWVYtVtABDGHKMNSRTWVYtDtACBDGHKMNSRTWVYtNt FormattedSeqcBsteZdZedZdZdZdZdZdZ dZ dZ d Z d Z d ZRS( sFormattedSeq(seq, [linear=True])-> new FormattedSeq. Translate a Bio.Seq into a formatted sequence to be used with Restriction. Roughly : remove anything which is not IUPAC alphabet and then add a space in front of the sequence to get a biological index instead of a python index (i.e. index of the first base is 1 not 0). Retains information about the shape of the molecule linear (default) or circular. Restriction sites are search over the edges of circular sequence.cCst|tst|trl|j}|j|_t||_||_|j |_ |j |_ ndt|t r|j|_|j|_|j|_|j |_ |j |_ nt dt|dS(sFormattedSeq(seq, [linear=True])-> new FormattedSeq. seq is either a Bio.Seq, Bio.MutableSeq or a FormattedSeq. if seq is a FormattedSeq, linear will have no effect on the shape of the sequence.s"expected Seq or MutableSeq, got %sN(t isinstanceRRttostringtislowertlowerR tdatatlineart __class__tklasstalphabetR(t TypeErrorttype(tselftseqR.tstringy((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__init__|s       cCst|jdS(Ni(tlenR-(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__len__scCs!dt|dt|jfS(NsFormattedSeq(%s, linear=%s)i(treprR.(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__repr__scCs6t|tr2t|t|kr+tStSntS(N(R)R(R:tTruetFalse(R4tother((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__eq__s cCs t|_dS(s"FS.circularise() -> circularise FSN(R=R.(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt circularises cCs t|_dS(sFS.linearise() -> linearise FSN(R<R.(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt linearises cCs|j|}t|_|S(s(FS.to_linear() -> new linear FS instance(R/R<R.(R4tnew((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt to_linears cCs|j|}t|_|S(s,FS.to_circular() -> new circular FS instance(R/R=R.(R4RB((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt to_circulars cCs|jS(sYFS.is_linear() -> bool. True if the sequence will analysed as a linear sequence.(R.(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt is_linearscCse|jr|j}n|j|jd|d!}gtj||D]}|j|jf^qFS(s~FS.finditer(pattern, size) -> list. return a list of pattern into the sequence. the list is made of tuple (location, pattern.group). the latter is used with non palindromic sites. pattern is the regular expression pattern corresponding to the enzyme restriction site. size is the size of the restriction enzyme recognition-site size.i(RER-tretfinditertstarttgroup(R4tpatterntsizeR-ti((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRGs  cCsC|jr)|j|j|j|jS|j|j||jS(N(R,R0R-R1(R4RL((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt __getitem__s  (t__name__t __module__t__doc__R<R7R9R;R?R@RARCRDRERGRM(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR(ns           tRestrictionTypecBseZdZddidZdZdZdZdZdZdZ d Z d Z d Z d Z d ZdZdZdZdZdZdZdZRS(saRestrictionType. Type from which derives all enzyme classes. Implement the operator methods.tcCs8tt|j||||tj|j|_dS(sRE(name, bases, dct) -> RestrictionType instance. Not intended to be used in normal operation. The enzymes are instantiated when importing the module. see below.N(tsuperRQR7RFtcompiletcompsite(tclstnametbasestdct((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR7scCsEt|trt||gSt|tr;|j|StdS(sRE.__add__(other) -> RestrictionBatch(). if other is an enzyme returns a batch of the two enzymes. if other is already a RestrictionBatch add enzyme to it.N(R)RQtRestrictionBatcht add_nocheckR2(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__add__s  cCs |j|S(sNRE.__div__(other) -> list. RE/other returns RE.search(other).(tsearch(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__div__scCs |j|S(sORE.__rdiv__(other) -> list. other/RE returns RE.search(other).(R](RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__rdiv__scCs |j|S(sRRE.__truediv__(other) -> list. RE/other returns RE.search(other).(R](RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt __truediv__scCs |j|S(sSRE.__rtruediv__(other) -> list. other/RE returns RE.search(other).(R](RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt __rtruediv__scCs |j|S(sVRE.__floordiv__(other) -> list. RE//other returns RE.catalyse(other).(tcatalyse(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt __floordiv__scCs |j|S(sWRE.__rfloordiv__(other) -> list. other//RE returns RE.catalyse(other).(Rb(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt __rfloordiv__scCs|jS(s<RE.__str__() -> str. return the name of the enzyme.(RN(RV((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__str__scCs d|jS(sRRE.__repr__() -> str. used with eval or exec will instantiate the enzyme.s%s(RN(RV((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR;scCs|jS(s=RE.__len__() -> int. length of the recognition site.(RK(RV((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR9"scCs ||kS(sFRE == other -> bool True if RE and other are the same enzyme.((RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR?(scCs1t|tstS|j|jkr)tStSdS(sRE != other -> bool. isoschizomer strict, same recognition site, same restriction -> False all the other-> TrueN(R)RQR<tcharacR=(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__ne__.s cCsCt|tstS|j|jkr;|j|jkr;tStSdS(sRE >> other -> bool. neoschizomer : same recognition site, different restriction. -> True all the others : -> FalseN(R)RQR=tsiteRfR<(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt __rshift__9s $cCs5t|ts(tdt|n|j|S(sxa % b -> bool. Test compatibility of the overhang of a and b. True if a and b have compatible overhang.s(expected RestrictionType, got %s instead(R)RQR2R3t_mod1(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__mod__EscCsgt|tstnt|t|kr4tS|jt|kr_|j|jkr_tStSdS(sa >= b -> bool. a is greater or equal than b if the a site is longer than b site. if their site have the same length sort by alphabetical order of their names.N(R)RQtNotImplementedErrorR8R<RKRNR=(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__ge__Os 'cCsgt|tstnt|t|kr4tS|jt|kr_|j|jkr_tStSdS(sa > b -> bool. sorting order : 1. size of the recognition site. 2. if equal size, alphabetical order of the names.N(R)RQRlR8R<RKRNR=(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__gt__^s 'cCsjt|tstnNt|t|kr4tSt|t|krb|j|jkrbtStSdS(sa <= b -> bool. sorting order : 1. size of the recognition site. 2. if equal size, alphabetical order of the names.N(R)RQRlR8R<RNR=(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__le__ms *cCsjt|tstnNt|t|kr4tSt|t|krb|j|jkrbtStSdS(sa < b -> bool. sorting order : 1. size of the recognition site. 2. if equal size, alphabetical order of the names.N(R)RQRlR8R<RNR=(RVR>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__lt__|s *((RNRORPR7R\R^R_R`RaRcRdReR;R9R?RgRiRkRmRnRoRp(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRQs(             t AbstractCutcBseZdZedZeeZdZeeZdZeeZdZeeZdZ ee Z d dZ ee Z d dZ ee Z d dZ ee Z d ZeeZRS( sImplement the methods that are common to all restriction enzymes. All the methods are classmethod. For internal use only. Not meant to be instantiate.cCsBt|tr"||_|jSt|||_|jSdS(sRE.search(dna, linear=True) -> list. return a list of all the site of RE in dna. Compensate for circular sequences and so on. dna must be a Bio.Seq.Seq instance or a Bio.Seq.MutableSeq instance. if linear is False, the restriction sites than span over the boundaries will be included. The positions are the first base of the 3' fragment, i.e. the first base after the position the enzyme will cut. N(R)R(tdnat_search(RVRrR.((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR]s   cCs?gtjD]}|d^q }|jdj|GHdS(s0RE.all_suppliers -> print all the suppliers of Ris, N(tsuppliers_dictt itervaluestsorttjoin(R4txtsupply((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt all_supplierss# cCs ||k S(sRE.is_equischizomers(other) -> bool. True if other is an isoschizomer of RE. False else. equischizomer <=> same site, same position of restriction.((R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytis_equischizomerscCs||?S(sRE.is_neoschizomers(other) -> bool. True if other is an isoschizomer of RE. False else. neoschizomer <=> same site, different position of restriction.((R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytis_neoschizomerscCs||k p||?S(sRE.is_isoschizomers(other) -> bool. True if other is an isoschizomer of RE. False else. isoschizomer <=> same site.((R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytis_isoschizomerscCsX|st}ng|D]}||ks|^q}|j|}||=|j|S(sRE.equischizomers([batch]) -> list. return a tuple of all the isoschizomers of RE. if batch is supplied it is used instead of the default AllEnzymes. equischizomer <=> same site, same position of restriction.(t AllEnzymestindexRv(R4tbatchRxtrRL((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytequischizomerss % cCs@|st}ng|D]}||?r|^q}|j|S(sRE.neoschizomers([batch]) -> list. return a tuple of all the neoschizomers of RE. if batch is supplied it is used instead of the default AllEnzymes. neoschizomer <=> same site, different position of restriction.(R~Rv(R4RRxR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt neoschizomerss  # cCsc|st}ng|D]#}||?s3||k r|^q}|j|}||=|j|S(sRE.isoschizomers([batch]) -> list. return a tuple of all the equischizomers and neoschizomers of RE. if batch is supplied it is used instead of the default AllEnzymes.(R~RRv(R4RRxRRL((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt isoschizomerss 0 cCs|jS(s6RE.frequency() -> int. frequency of the site.(tfreq(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt frequencysN(RNRORPR<R]t classmethodRzR{R|R}tNoneRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRqs&              tNoCutcBsweZdZdZeeZdZeeZdZeeZdZeeZdZeeZRS(s`Implement the methods specific to the enzymes that do not cut. These enzymes are generally enzymes that have been only partially characterised and the way they cut the DNA is unknow or enzymes for which the pattern of cut is to complex to be recorded in Rebase (ncuts values of 0 in emboss_e.###). When using search() with these enzymes the values returned are at the start of the restriction site. Their catalyse() method returns a TypeError. Unknown and NotDefined are also part of the base classes of these enzymes. Internal use only. Not meant to be instantiated.cCstS(s\RE.cut_once() -> bool. True if the enzyme cut the sequence one time on each strand.(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytcut_oncescCstS(sZRE.cut_twice() -> bool. True if the enzyme cut the sequence twice on each strand.(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt cut_twicesccs |VdS(sRE._modify(location) -> int. for internal use only. location is an integer corresponding to the location of the match for the enzyme pattern in the sequence. _modify returns the real place where the enzyme will cut. example : EcoRI pattern : GAATTC EcoRI will cut after the G. so in the sequence : ______ GAATACACGGAATTCGA | 10 dna.finditer(GAATTC, 6) will return 10 as G is the 10th base EcoRI cut after the G so : EcoRI._modify(10) -> 11. if the enzyme cut twice _modify will returns two integer corresponding to each cutting site. N((R4tlocation((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt_modify%sccs |VdS(sRE._rev_modify(location) -> generator of int. for internal use only. as _modify for site situated on the antiparallel strand when the enzyme is not palindromic N((R4R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt _rev_modify@scCsdddd|jfS(sgRE.characteristic() -> tuple. the tuple contains the attributes : fst5 -> first 5' cut ((current strand) or None fst3 -> first 3' cut (complementary strand) or None scd5 -> second 5' cut (current strand) or None scd5 -> second 3' cut (complementary strand) or None site -> recognition site.N(RRh(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytcharacteristicKs ( RNRORPRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs        tOneCutcBsweZdZdZeeZdZeeZdZeeZdZeeZdZeeZRS(sImplement the methods specific to the enzymes that cut the DNA only once Correspond to ncuts values of 2 in emboss_e.### Internal use only. Not meant to be instantiated.cCstS(s\RE.cut_once() -> bool. True if the enzyme cut the sequence one time on each strand.(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR^scCstS(sZRE.cut_twice() -> bool. True if the enzyme cut the sequence twice on each strand.(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyResccs||jVdS(sRE._modify(location) -> int. for internal use only. location is an integer corresponding to the location of the match for the enzyme pattern in the sequence. _modify returns the real place where the enzyme will cut. example : EcoRI pattern : GAATTC EcoRI will cut after the G. so in the sequence : ______ GAATACACGGAATTCGA | 10 dna.finditer(GAATTC, 6) will return 10 as G is the 10th base EcoRI cut after the G so : EcoRI._modify(10) -> 11. if the enzyme cut twice _modify will returns two integer corresponding to each cutting site. N(tfst5(R4R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRlsccs||jVdS(sRE._rev_modify(location) -> generator of int. for internal use only. as _modify for site situated on the antiparallel strand when the enzyme is not palindromic N(tfst3(R4R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRscCs|j|jdd|jfS(sgRE.characteristic() -> tuple. the tuple contains the attributes : fst5 -> first 5' cut ((current strand) or None fst3 -> first 3' cut (complementary strand) or None scd5 -> second 5' cut (current strand) or None scd5 -> second 3' cut (complementary strand) or None site -> recognition site.N(RRRRh(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs ( RNRORPRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRWs        tTwoCutscBsweZdZdZeeZdZeeZdZeeZdZeeZdZeeZRS(sImplement the methods specific to the enzymes that cut the DNA twice Correspond to ncuts values of 4 in emboss_e.### Internal use only. Not meant to be instantiated.cCstS(s\RE.cut_once() -> bool. True if the enzyme cut the sequence one time on each strand.(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRscCstS(sZRE.cut_twice() -> bool. True if the enzyme cut the sequence twice on each strand.(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRsccs||jV||jVdS(sRE._modify(location) -> int. for internal use only. location is an integer corresponding to the location of the match for the enzyme pattern in the sequence. _modify returns the real place where the enzyme will cut. example : EcoRI pattern : GAATTC EcoRI will cut after the G. so in the sequence : ______ GAATACACGGAATTCGA | 10 dna.finditer(GAATTC, 6) will return 10 as G is the 10th base EcoRI cut after the G so : EcoRI._modify(10) -> 11. if the enzyme cut twice _modify will returns two integer corresponding to each cutting site. N(Rtscd5(R4R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs ccs||jV||jVdS(sRE._rev_modify(location) -> generator of int. for internal use only. as _modify for site situated on the antiparallel strand when the enzyme is not palindromic N(Rtscd3(R4R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCs"|j|j|j|j|jfS(sgRE.characteristic() -> tuple. the tuple contains the attributes : fst5 -> first 5' cut ((current strand) or None fst3 -> first 3' cut (complementary strand) or None scd5 -> second 5' cut (current strand) or None scd5 -> second 3' cut (complementary strand) or None site -> recognition site.(RRRRRh(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs ( RNRORPRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs        tMeth_DepcBs#eZdZdZeeZRS(skImplement the information about methylation. Enzymes of this class possess a site which is methylable.cCstS(sRRE.is_methylable() -> bool. True if the recognition site is a methylable.(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt is_methylables(RNRORPRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs t Meth_UndepcBs#eZdZdZeeZRS(ssImplement informations about methylation sensitibility. Enzymes of this class are not sensible to methylation.cCstS(sRRE.is_methylable() -> bool. True if the recognition site is a methylable.(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs(RNRORPRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs t PalindromiccBs8eZdZdZeeZdZeeZRS(sImplement the methods specific to the enzymes which are palindromic palindromic means : the recognition site and its reverse complement are identical. Remarks : an enzyme with a site CGNNCG is palindromic even if some of the sites that it will recognise are not. for example here : CGAACG Internal use only. Not meant to be instantiated.cCsp|jj|j|j}g|D](\}}|j|D] }|^q;q"|_|jri|jn|jS(sRE._search() -> list. for internal use only. implement the search method for palindromic and non palindromic enzyme. (RrRGRURKRtresultst_drop(R4tsiteloctstgR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs s 8 cCstS(sRRE.is_palindromic() -> bool. True if the recognition site is a palindrom.(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytis_palindromics(RNRORPRsRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs    tNonPalindromiccBs8eZdZdZeeZdZeeZRS(sImplement the methods specific to the enzymes which are not palindromic palindromic means : the recognition site and its reverse complement are identical. Internal use only. Not meant to be instantiated.cCs|jj|j|j}g|_|j}|j}t|}g|_xs|D]k\}}||r|jg||D] }|^q~7_qR|jg||D] }|^q7_qRW|j|j7_|jr|jj |j n|jS(sRE._search() -> list. for internal use only. implement the search method for palindromic and non palindromic enzyme. ( RrRGRURKRRRtstrton_minusRvR(R4titeratortmodiftrevmodifRRHRIR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs)s      +,   cCstS(sRRE.is_palindromic() -> bool. True if the recognition site is a palindrom.(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRBs(RNRORPRsRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR!s    tUnknowncBseZdZedZeeZZdZeeZdZeeZdZ ee Z dZ ee Z dZ ee Z dZ ee Z RS(sImplement the methods specific to the enzymes for which the overhang is unknown. These enzymes are also NotDefined and NoCut. Internal use only. Not meant to be instantiated.cCstd|jdS(sRE.catalyse(dna, linear=True) -> tuple of DNA. RE.catalyze(dna, linear=True) -> tuple of DNA. return a tuple of dna as will be produced by using RE to restrict the dna. dna must be a Bio.Seq.Seq instance or a Bio.Seq.MutableSeq instance. if linear is False, the sequence is considered to be circular and the output will be modified accordingly.s%s restriction is unknown.N(RlRN(R4RrR.((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRbQs cCstS(sRE.is_blunt() -> bool. True if the enzyme produces blunt end. see also : RE.is_3overhang() RE.is_5overhang() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytis_blunt`s cCstS(sRE.is_5overhang() -> bool. True if the enzyme produces 5' overhang sticky end. see also : RE.is_3overhang() RE.is_blunt() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt is_5overhangls cCstS(sRE.is_3overhang() -> bool. True if the enzyme produces 3' overhang sticky end. see also : RE.is_5overhang() RE.is_blunt() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt is_3overhangxs cCsdS(szRE.overhang() -> str. type of overhang of the enzyme., can be "3' overhang", "5' overhang", "blunt", "unknown" tunknown((R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytoverhangscCsgS(s`RE.compatible_end() -> list. list of all the enzymes that share compatible end with RE.((R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytcompatible_endscCstS(sRE._mod1(other) -> bool. for internal use only test for the compatibility of restriction ending of RE and other.(R=(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRjs( RNRORPR<RbRtcatalyzeRRRRRRj(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRIs         tBluntcBseZdZedZeeZZdZeeZdZeeZdZ ee Z dZ ee Z ddZ ee Z dZ ee Z RS( sImplement the methods specific to the enzymes for which the overhang is blunt. The enzyme cuts the + strand and the - strand of the DNA at the same place. Internal use only. Not meant to be instantiated.cCs1|j||}|j}|s,|dfSg}t|d}|jr|j|d|d!|r|gt|D]}|||||d!^q|7}n|j||dnj|j||d|d|d!|st|S|gt|D]}|||||d!^q7}t|S(sRE.catalyse(dna, linear=True) -> tuple of DNA. RE.catalyze(dna, linear=True) -> tuple of DNA. return a tuple of dna as will be produced by using RE to restrict the dna. dna must be a Bio.Seq.Seq instance or a Bio.Seq.MutableSeq instance. if linear is False, the sequence is considered to be circular and the output will be modified accordingly.iii(R]RrR8REtappendtxrangettuple(R4RrR.Rtdt fragmentstlengthRx((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRbs    9$ 6cCstS(sRE.is_blunt() -> bool. True if the enzyme produces blunt end. see also : RE.is_3overhang() RE.is_5overhang() RE.is_unknown()(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCstS(sRE.is_5overhang() -> bool. True if the enzyme produces 5' overhang sticky end. see also : RE.is_3overhang() RE.is_blunt() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCstS(sRE.is_3overhang() -> bool. True if the enzyme produces 3' overhang sticky end. see also : RE.is_5overhang() RE.is_blunt() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCsdS(szRE.overhang() -> str. type of overhang of the enzyme., can be "3' overhang", "5' overhang", "blunt", "unknown" tblunt((R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRscCsH|st}ngttD]}|jr|^q}|j|S(s`RE.compatible_end() -> list. list of all the enzymes that share compatible end with RE.(R~titerRRv(R4RRxR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs  + cCst|trtStSdS(sRE._mod1(other) -> bool. for internal use only test for the compatibility of restriction ending of RE and other.N(t issubclassRR<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/Restriction/Restriction.pyRjsN(RNRORPR<RbRRRRRRRRRjt staticmethod(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs -        tOv5cBseZdZedZeeZZdZeeZdZeeZdZ ee Z dZ ee Z ddZ ee Z dZ ee Z RS( sImplement the methods specific to the enzymes for which the overhang is recessed in 3'. The enzyme cuts the + strand after the - strand of the DNA. Internal use only. Not meant to be instantiated.cCs1|j||}|j}|s,|dfSt|d}g}|jr|j|d|d!|r|gt|D]}|||||d!^q|7}n|j||dnj|j||d|d|d!|st|S|gt|D]}|||||d!^q7}t|S(sRE.catalyse(dna, linear=True) -> tuple of DNA. RE.catalyze(dna, linear=True) -> tuple of DNA. return a tuple of dna as will be produced by using RE to restrict the dna. dna must be a Bio.Seq.Seq instance or a Bio.Seq.MutableSeq instance. if linear is False, the sequence is considered to be circular and the output will be modified accordingly.iii(R]RrR8RERRR(R4RrR.RRRRRx((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRbs    9$ 6cCstS(sRE.is_blunt() -> bool. True if the enzyme produces blunt end. see also : RE.is_3overhang() RE.is_5overhang() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRIs cCstS(sRE.is_5overhang() -> bool. True if the enzyme produces 5' overhang sticky end. see also : RE.is_3overhang() RE.is_blunt() RE.is_unknown()(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRUs cCstS(sRE.is_3overhang() -> bool. True if the enzyme produces 3' overhang sticky end. see also : RE.is_5overhang() RE.is_blunt() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRas cCsdS(szRE.overhang() -> str. type of overhang of the enzyme., can be "3' overhang", "5' overhang", "blunt", "unknown" s 5' overhang((R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRmscCsR|st}ngttD]"}|jr||r|^q}|j|S(s`RE.compatible_end() -> list. list of all the enzymes that share compatible end with RE.(R~RRRv(R4RRxR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRts  5 cCs$t|tr|j|StSdS(sRE._mod1(other) -> bool. for internal use only test for the compatibility of restriction ending of RE and other.N(RRt_mod2R=(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRj~s N(RNRORPR<RbRRRRRRRRRj(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs -        tOv3cBseZdZedZeeZZdZeeZdZeeZdZ ee Z dZ ee Z ddZ ee Z dZ ee Z RS( sImplement the methods specific to the enzymes for which the overhang is recessed in 5'. The enzyme cuts the - strand after the + strand of the DNA. Internal use only. Not meant to be instantiated.cCs1|j||}|j}|s,|dfSg}t|d}|jr|j|d|d!|r|gt|D]}|||||d!^q|7}n|j||dnj|j||d|d|d!|st|S|gt|D]}|||||d!^q7}t|S(sRE.catalyse(dna, linear=True) -> tuple of DNA. RE.catalyze(dna, linear=True) -> tuple of DNA. return a tuple of dna as will be produced by using RE to restrict the dna. dna must be a Bio.Seq.Seq instance or a Bio.Seq.MutableSeq instance. if linear is False, the sequence is considered to be circular and the output will be modified accordingly.iii(R]RrR8RERRR(R4RrR.RRRRRx((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRbs    9$ 6cCstS(sRE.is_blunt() -> bool. True if the enzyme produces blunt end. see also : RE.is_3overhang() RE.is_5overhang() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCstS(sRE.is_5overhang() -> bool. True if the enzyme produces 5' overhang sticky end. see also : RE.is_3overhang() RE.is_blunt() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCstS(sRE.is_3overhang() -> bool. True if the enzyme produces 3' overhang sticky end. see also : RE.is_5overhang() RE.is_blunt() RE.is_unknown()(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCsdS(szRE.overhang() -> str. type of overhang of the enzyme., can be "3' overhang", "5' overhang", "blunt", "unknown" s 3' overhang((R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRscCsR|st}ngttD]"}|jr||r|^q}|j|S(s`RE.compatible_end() -> list. list of all the enzymes that share compatible end with RE.(R~RRRv(R4RRxR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs  5 cCs$t|tr|j|StSdS(sRE._mod1(other) -> bool. for internal use only test for the compatibility of restriction ending of RE and other.N(RRRR=(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRjs  N(RNRORPR<RbRRRRRRRRRj(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs -        tDefinedcBseZdZdZeeZdZeeZdZeeZdZeeZdZeeZdZ ee Z RS(sImplement the methods specific to the enzymes for which the overhang and the cut are not variable. Typical example : EcoRI -> G^AATT_C The overhang will always be AATT Notes : Blunt enzymes are always defined. even if there site is GGATCCNNN^_N There overhang is always the same : blunt! Internal use only. Not meant to be instantiated.cs+t|jtj}tj}|jjrg|d|jD] }|^qF|_g|fd|jD] }|^qw|_nx@t|jD]/\}}|dkr|j|c7 list. for internal use only. drop the site that are situated outside the sequence in linear sequence. modify the index for site in circular sequences.cSs |dkS(Ni((Rx((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt"scs |kS(N((Rx(R(s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR#siNi(R8Rrt itertoolst dropwhilet takewhileRERt enumerate(R4tdropttakeRxRR((Rs/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs  +4 ) cCstS(sRE.is_defined() -> bool. True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site. see also : RE.is_ambiguous() RE.is_unknown()(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt is_defined2s cCstS(sRE.is_ambiguous() -> bool. True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site. see also : RE.is_defined() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt is_ambiguous?s cCstS(sRE.is_unknown() -> bool. True if the sequence is unknown, i.e. the recognition site has not been characterised yet. see also : RE.is_defined() RE.is_ambiguous()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt is_unknownLs cCs8|j}|j}|j}|jr0d}n|jr||koSdknrld|jd}q4|dkr|| d||d}q4|| d|||!d||}nw|jr|| d||}nR||kodknrd|d }n%|| d|||!d||}|S( sRE.elucidate() -> str return a representation of the site with the cut on the (+) strand represented as '^' and the cut on the (-) strand as '_'. ie : >>> EcoRI.elucidate() # 5' overhang 'G^AATT_C' >>> KpnI.elucidate() # 3' overhang 'G_GTAC^C' >>> EcoRV.elucidate() # blunt 'GAT^_ATC' >>> SnaI.elucidate() # NotDefined, cut profile unknown. '? GTATAC ?' >>> s%cut twice, not yet implemented sorry.isN^t_Nt^t_s^_tN_s^N(RRRhRRR(R4tf5tf3RhRF((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt elucidateXs"      ( %cCs:|j|jkrtSt|tr2|j|StSdS(sRE._mod2(other) -> bool. for internal use only test for the compatibility of restriction ending of RE and other.N(tovhgseqR<Rt AmbiguousRR=(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRxs  ( RNRORPRRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs  !       RcBseZdZdZeeZdZeeZdZeeZdZeeZdZeeZdZ ee Z RS(sImplement the methods specific to the enzymes for which the overhang is variable. Typical example : BstXI -> CCAN_NNNN^NTGG The overhang can be any sequence of 4 bases. Notes : Blunt enzymes are always defined. even if there site is GGATCCNNN^_N There overhang is always the same : blunt! Internal use only. Not meant to be instantiated.cs+t|jtj}tj}|jjrg|d|jD] }|^qF|_g|fd|jD] }|^qw|_nx@t|jD]/\}}|dkr|j|c7 list. for internal use only. drop the site that are situated outside the sequence in linear sequence. modify the index for site in circular sequences.cSs |dkS(Ni((Rx((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRscs |kS(N((Rx(R(s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRsiNi(R8RrRRRRERR(R4RRRxRR((Rs/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs  +4 ) cCstS(sRE.is_defined() -> bool. True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site. see also : RE.is_ambiguous() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCstS(sRE.is_ambiguous() -> bool. True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site. see also : RE.is_defined() RE.is_unknown()(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCstS(sRE.is_unknown() -> bool. True if the sequence is unknown, i.e. the recognition site has not been characterised yet. see also : RE.is_defined() RE.is_ambiguous()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCst|jt|jkr"tS|j}x}|D]u}|dkrGn|dkrndj|jd}n|dkr2dt|d}|j|j|}q2q2Wtj||jrtStSdS(sRE._mod2(other) -> bool. for internal use only test for the compatibility of restriction ending of RE and other.tATCGR't.t RYWMSKHDBVt[t]N( R8RR=RwtsplittmatchingRFtmatchR<(R4R>tsetbasetexpand((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs      cCsX|j}|j}t|}|j}|jr<d}n|jr||ko_dknrud|d}qTd|ko|knrd||ko|knr|| d|||!d||}qTd|ko|knr|| d|||dd}qTd||ko5|knredt|d|| d||}qT||dkrdt|ddt||d|}qT||kr|||dd|||dd}qTdt|d||dd}nN|jrz|dkr9dt|d|}qT||kr^|||dd }qTtd |j |fn|dkr|dkrd |d }qT|d||dd }nd||ko|knr$d|ko|knr$|| d|||!d||}n0d||ko?|knrm|| d||||dd }nd|ko|knrd d|||| d||}n|dkr||dd|||dd }nm|dkr(d t|||ddt|d|}n,d t||d|||dd }|S( sRE.elucidate() -> str return a representation of the site with the cut on the (+) strand represented as '^' and the cut on the (-) strand as '_'. ie : >>> EcoRI.elucidate() # 5' overhang 'G^AATT_C' >>> KpnI.elucidate() # 3' overhang 'G_GTAC^C' >>> EcoRV.elucidate() # blunt 'GAT^_ATC' >>> SnaI.elucidate() # NotDefined, cut profile unknown. '? GTATAC ?' >>> s%cut twice, not yet implemented sorry.isN^RRRR'sN^_s^_Ns%s.easyrepr() : error f5=%iRs^N( RRR8RhRRtabsRt ValueErrorRW(R4RRRRhRF((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRsV      <(% +1 -'     <( )) ) 5,( RNRORPRRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs         =t NotDefinedcBseZdZdZeeZdZeeZdZeeZdZeeZdZeeZdZ ee Z RS(sImplement the methods specific to the enzymes for which the overhang is not characterised. Correspond to NoCut and Unknown. Internal use only. Not meant to be instantiated.cCs|jjrdSt|j}x@t|jD]/\}}|dkr`|j|c|7 list. for internal use only. drop the site that are situated outside the sequence in linear sequence. modify the index for site in circular sequences.Nii(RrRER8RR(R4RRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR;s   cCstS(sRE.is_defined() -> bool. True if the sequence recognised and cut is constant, i.e. the recognition site is not degenerated AND the enzyme cut inside the site. see also : RE.is_ambiguous() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRSs cCstS(sRE.is_ambiguous() -> bool. True if the sequence recognised and cut is ambiguous, i.e. the recognition site is degenerated AND/OR the enzyme cut outside the site. see also : RE.is_defined() RE.is_unknown()(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR`s cCstS(sRE.is_unknown() -> bool. True if the sequence is unknown, i.e. the recognition site has not been characterised yet. see also : RE.is_defined() RE.is_ambiguous()(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRns cCs/tdt|t|t|fdS(sRE._mod2(other) -> bool. for internal use only test for the compatibility of restriction ending of RE and other.s0%s.mod2(%s), %s : NotDefined. pas glop pas glop!N(RR(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRzs cCs d|jS(sRE.elucidate() -> str return a representation of the site with the cut on the (+) strand represented as '^' and the cut on the (-) strand as '_'. ie : >>> EcoRI.elucidate() # 5' overhang 'G^AATT_C' >>> KpnI.elucidate() # 3' overhang 'G_GTAC^C' >>> EcoRV.elucidate() # blunt 'GAT^_ATC' >>> SnaI.elucidate() # NotDefined, cut profile unknown. '? GTATAC ?' >>> s? %s ?(Rh(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs( RNRORPRRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR3s        tCommercially_availablecBsbeZdZdZeeZdZeeZdZeeZdZeeZRS(sImplement the methods specific to the enzymes which are commercially available. Internal use only. Not meant to be instantiated.cCsFtj}x3|D]+\}}||jkr|ddGHqqWdS(s,RE.suppliers() -> print the suppliers of RE.it,N(Rttitemstsuppl(R4Rytktv((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs  cCs6gtjD]%\}}||jkr |d^q S(sGRE.supplier_list() -> list. list of the supplier names for RE.i(RtRR(R4RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt supplier_listscCsdS(s=RE.buffers(supplier) -> string. not implemented yet.N((R4tsupplier((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytbuffersscCstS(s7RE.iscomm() -> bool. True if RE has suppliers.(R<(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytis_comms(RNRORPRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs       t Not_availablecBsbeZdZdZeeZdZeeZdZeeZdZeeZRS(sImplement the methods specific to the enzymes which are not commercially available. Internal use only. Not meant to be instantiated.cCsdS(s,RE.suppliers() -> print the suppliers of RE.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/Restriction/Restriction.pyRscCsgS(sGRE.supplier_list() -> list. list of the supplier names for RE.((R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRscCstddS(s=RE.buffers(supplier) -> string. not implemented yet.s"Enzyme not commercially available.N(R2(R4R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRscCstS(s7RE.iscomm() -> bool. True if RE has suppliers.(R=(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs( RNRORPRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs       RZcBseZggdZdZdZdZdZdZedZ dZ dZ d Z d Z d Zd Zd ZdZdZdZdZdZdZdZeeZdZeeZedZRS(cCsg|D]}|j|^q}|g|D]'}t|dD]}t|^q>q,7}tj||tj||_td|_ dS(s5RestrictionBatch([sequence]) -> new RestrictionBatch.iRRN( tformatRttevaltsetR7tdicttfromkeystmappingtDNAtalready_mapped(R4tfirstRRxtn((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR7s "8cCsbt|dkr%dj|jSdjdj|jd dj|jdfSdS(Nit+s...ii(R8Rwtelements(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRescCsd|jS(NsRestrictionBatch(%s)(R(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR;scCs8y|j|}Wntk r'tSXtj||S(N(RRR=Rt __contains__(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs  cCs |j|S(N(R](R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR^ scCs |j|S(N(R](R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR_ scCsM|j|}||kr|S|r6|j||Std|jdS(sB.get(enzyme[, add]) -> enzyme class. if add is True and enzyme is not in B add enzyme to B. if add is False (which is the default) only return enzyme. if enzyme is not a RestrictionType or can not be evaluated to a RestrictionType, raise a ValueError.s$enzyme %s is not in RestrictionBatchN(RtaddRRN(R4tenzymeRte((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytgets  cCsZgtj||D] }|^q}t}ttd|tgt||_|S(sB.lambdasplit(func) -> RestrictionBatch . the new batch will contains only the enzymes for which func return True.N( RtifilterRZRtmapRR<R8t_data(R4tfuncRxRRB((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt lambdasplit!s% (cCsFt|}|jj|x%|dD]}|jt|q%WdS(sB.add_supplier(letter) -> add a new set of enzyme to B. letter represents the suppliers as defined in the dictionary RestrictionDictionary.suppliers return None. raise a KeyError if letter is not a supplier code.iN(RtRRR[R(R4tletterRRx((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt add_supplier+s  cCs2g|jD]}t|d^q }|j|S(sB.current_suppliers() -> add a new set of enzyme to B. return a sorted list of the suppliers which have been used to create the batch.i(RRtRv(R4Rxt suppl_list((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytcurrent_suppliers8s$ cCs|j||S(s7 b += other -> add other to b, check the type of other.(R(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt__iadd__As cCs |j|}|j||S(s# b + other -> new RestrictionBatch.(R/R(R4R>RB((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR\Fs cCstj||j|S(s=B.remove(other) -> remove other from B if other is a RestrictionType. Safe set.remove method. Verify that other is a RestrictionType or can be evaluated to a RestrictionType. raise a ValueError if other can not be evaluated to a RestrictionType. raise a KeyError if other is not in B.(RtremoveR(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRLscCstj||j|S(s B.add(other) -> add other to B if other is a RestrictionType. Safe set.add method. Verify that other is a RestrictionType or can be evaluated to a RestrictionType. raise a ValueError if other can not be evaluated to a RestrictionType. (RRR(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRUscCstj||S(sKB.add_nocheck(other) -> add other to B. don't check type of other. (RR(R4R>((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR[^scCsmy<t|tr|Sttt|tr;t|SWnttfk rUnXtd|jdS(sB.format(y) -> RestrictionType or raise ValueError. if y is a RestrictionType return y if y can be evaluated to a RestrictionType return eval(y) raise a Value Error in all other case.s%s is not a RestrictionTypeN(R)RQRRt NameErrort SyntaxErrorRR/(R4ty((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRcs cCs(t|tp'ttt|tS(sPB.is_restriction(y) -> bool. True is y or eval(y) is a RestrictionType.(R)RQRR(R4R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytis_restrictionvscslfd}gtj||D] }|^q%}t}ttd|tgt||_|S(sB.split(class, [class.__name__ = True]) -> new RestrictionBatch. it works but it is slow, so it has really an interest when splitting over multiple conditions.csYxRD]J}j|jt}t||rD|r=qqQtSq|rtSqqWtS(N(RRNR<RR=(telementR0tb(tbooltclasses(s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt splittests N( RRRZRRRR<R8R(R4R R R RRRB((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/Restriction/Restriction.pyR}s  % (cCs-g|D]}t|^q}|j|S(s]B.elements() -> tuple. give all the names of the enzymes in B sorted alphabetically.(RRv(R4Rtl((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cCsg|D]}t|^qS(sOB.as_string() -> list. return a list of the name of the elements of B.(R(R4R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt as_stringscCs9tgtjD]\}}||df^q}|S(s>B.suppl_codes() -> dict letter code for the suppliersi(RRtt iteritems(R4RRRy((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt suppl_codess5cCs@g|jjD]}dj|^q}dj|GHdS(s0B.show_codes() -> letter codes for the supplierss = s N(RRRw(R4RLRy((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt show_codess.cCst|tr||f|jkr+|jS||f|_t||}tg|D]}||j|f^qS|_|jSn{t|tr||jf|jkr|jS||jf|_tg|D]}||j|f^q|_|jSntdt |dS(sB.search(dna) -> dict.s3Expected Seq or MutableSeq instance, got %s insteadN( R)RRRR(RR]R.R2R3(R4RrR.tfseqRx((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR]s1 1 (RNROR7ReR;RR^R_R=RRRRRR\RRR[RRRRRRRRR<R](((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRZs2                  tAnalysiscBs7eZeededZdZdZdZdZ dZ ddddZ dZ ed Zdd Zdd Zdd Zdd ZddZddZddZddZddZddZddZddZddZddZddZddZRS(RRcCsQtj||||_||_||_|jrM|j|j|jndS(skAnalysis([restrictionbatch [, sequence] linear=True]) -> New Analysis class. For most of the method of this class if a dictionary is given it will be used as the base to calculate the results. If no dictionary is given a new analysis using the Restriction Batch which has been given when the Analysis class has been instantiated.N(RZR7trbtsequenceR.R](R4trestrictionbatchRR.((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR7s     cCs&dt|jt|j|jfS(NsAnalysis(%s,%s,%s)(R:RRR.(R4((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyR;scCs>tg|jjD]$\}}||kr||f^qS(sA._sub_set(other_set) -> dict. Internal use only. screen the results through wanted set. Keep only the results for which the enzymes is in wanted set. (RRR(R4twantedRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt_sub_setscCst|ts(tdt|nt|tsPtdt|n|dkrr|t|j7}n|dkr|t|j7}n||krn|||k|f|dkr|dkn||kr|||jfS|||jfSdS(sA._boundaries(start, end) -> tuple. Format the boundaries for use with the methods that limit the search to only part of the sequence given to analyse. sexpected int, got %s insteadiN(R)tintR2R3R8Rt _test_normalt _test_reverse(R4RHtend((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt _boundariess       cCs||ko|kSS(sA._test_normal(start, end, site) -> bool. Internal use only Test if site is in between start and end. ((R4RHRRh((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRscCs=||ko t|jknp<d|ko:|kSS(sA._test_reverse(start, end, site) -> bool. Internal use only Test if site is in between end and start (for circular sequences). i(R8R(R4RHRRh((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRscCs)|s|j}nHtj||||S(sA.print_that([dct[, title[, s1]]]) -> print the results from dct. If dct is not given the full dictionary is used. (RRt print_that(R4RYttitlets1((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs cKsHxA|jD]3\}}|d kr^t||||j|j|_|j|j|_q |dkrt|d||j|j|jq |dkrt j |||j|j}q |dkrt|d||j|j|q |dkrt|||q |dkr0t d t q t d t q Wd S(sA.change(**attribute_name) -> Change attribute of Analysis. It is possible to change the width of the shell by setting self.ConsoleWidth to what you want. self.NameWidth refer to the maximal length of the enzyme name. Changing one of these parameters here might not give the results you expect. In which case, you can settle back to a 80 columns shell or try to change self.Cmodulo and self.PrefWidth in PrintFormat until you get it right.t NameWidtht ConsoleWidthRRR.tIndenttMaxsizetCmodulot PrefWidths2To change %s, change NameWidth and/or ConsoleWidthsAnalysis has no attribute %sN(R"R#(R$R%(R&R'( RtsetattrR#R"R&R'R]RR.RR7tAttributeErrorRW(R4twhatRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytchange!s,    !    cCs|jS(sHA.full() -> dict. Full Restriction Map of the sequence.(R(R4R.((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytfullDscCsM|s|j}ntg|jD]$\}}|jr"||f^q"S(scA.blunt([dct]) -> dict. Only the enzymes which have a 3'overhang restriction site.(RRRR(R4RYRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRJs cCsM|s|j}ntg|jD]$\}}|jr"||f^q"S(shA.overhang5([dct]) -> dict. Only the enzymes which have a 5' overhang restriction site.(RRRR(R4RYRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt overhang5Rs cCsM|s|j}ntg|jD]$\}}|jr"||f^q"S(sgA.Overhang3([dct]) -> dict. Only the enzymes which have a 3'overhang restriction site.(RRRR(R4RYRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt overhang3[s cCsM|s|j}ntg|jD]$\}}|jr"||f^q"S(skA.defined([dct]) -> dict. Only the enzymes that have a defined restriction site in Rebase.(RRRR(R4RYRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytdefinedds cCsG|s|j}ntg|jD]\}}|r"||f^q"S(scA.with_sites([dct]) -> dict. Enzymes which have at least one site in the sequence.(RRR(R4RYRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt with_sitesls cCsG|s|j}ntg|jD]\}}|s"||f^q"S(s[A.without_site([dct]) -> dict. Enzymes which have no site in the sequence.(RRR(R4RYRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt without_sitets cCsS|s|j}ntg|jD]*\}}t||kr"||f^q"S(s[A.With_N_Sites(N [, dct]) -> dict. Enzymes which cut N times the sequence.(RRRR8(R4R'RYRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt with_N_sites|s cCsS|s|j}ntg|jD]*\}}t||kr"||f^q"S(N(RRRR8(R4tlistRYRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytwith_number_lists cCsx?t|D]1\}}|tkr dGttGH||=q q W|s^t|j|jStg|D]"}||krh|||f^qhS(soA.with_name(list_of_names [, dct]) -> Limit the search to the enzymes named in list_of_names.sno datas for the enzyme:(RR~RRWRZR]RR(R4tnamesRYRLRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt with_names cCsg|D]}|j|kr|^q}|sDt|j|jStg|jD]$\}}||krT||f^qTS(s{A.with_site_size(site_size [, dct]) -> Limit the search to the enzymes whose site is of size .(RKRZR]RRR(R4t site_sizeRYRWtsitesRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytwith_site_sizes(c Cs|j||\}}}|s-|j}nt|}x^|jD]P\}}|se||=qFnx.|D]&}||||rqlql||=PqlWqFW|S(spA.only_between(start, end[, dct]) -> dict. Enzymes that cut the sequence only in between start and end.(RRRR( R4RHRRYttestRtkeyR8Rh((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt only_betweens    c Cs|j||\}}}i}|s3|j}nxN|jD]@\}}x1|D])}||||rS||| dict. Enzymes that cut the sequence at least in between start and end. They may cut outside as well.(RRR( R4RHRRYR:RR;R8Rh((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytbetweens    cCsg}||krrg|j|||D]A}tg|D](}||koU|knr8|^q8f^q(}nYg|j|||D]=}tg|D]$}||ks||kr|^qf^q}t|S(sA.show_only_between(start, end [, dct]) -> dict. Enzymes that cut the sequence outside of the region in between start and end but do not cut inside.(R=RR(R4RHRRYRRtvv((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytshow_only_betweens ]Vc Cs|j||\}}}|s-|j}nt|}x^|jD]P\}}|se||=qFnx.|D]&}||||rl||=PqlqlqlWqFW|S(sA.only_outside(start, end [, dct]) -> dict. Enzymes that cut the sequence outside of the region in between start and end but do not cut inside.(RRRR( R4RHRRYR:RR;R8Rh((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt only_outsides    c Cs|j||\}}}|s-|j}ni}xN|jD]@\}}x1|D])}||||rqqSqS||| dict. Enzymes that cut outside the region in between start and end. No test is made to know if they cut or not inside this region.(RRR( R4RHRRYR:RR;R8Rh((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytoutsides    cCs>|s|j}n|j}|j|j||||S(soA.do_not_cut(start, end [, dct]) -> dict. Enzymes that do not cut the region in between start and end.(RR1tupdateR@(R4RHRRYR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyt do_not_cuts   N(RNRORZRR<R7R;RRRRRRR+R,RR-R.R/R0R1R2R4R6R9R<R=R?R@RARC(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pyRs4      #            R~tCommOnlytNonComm(HRPRFRRRtsetsRtBio.SeqRRt Bio.AlphabetRt&Bio.Restriction.Restriction_DictionaryRt enzymedictRRRttBio.Restriction.RanaConfigtBio.Restriction.PrintFormatRtBio.Restriction.DNAUtilsR RRtobjectR(R3RQRqRRRRRRRRRRRRRRRRRZRRDRERtTYPERXtenzymesRRxRt__new__RRtnewenzRR[R~RR5tlocalsRBRRRt__all__(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/Restriction.pytOsp     czQHJ   (Rwwzk)(J  %   "