ó LAêIc@sedZdZddlZddlZddlZy eZWn!ek r]ddlmZnXddl Z ddl m Z ddl m Z m Z ddlmZd„Zee ƒZee ƒZd efd „ƒYZd efd „ƒYZd efd„ƒYZd„Zd„Zdedd„Zdded„Zd„Zd„ZedkraeƒndS(sProvides objects to represent biological sequences with alphabets. See also U{http://biopython.org/wiki/Seq} and the chapter in our tutorial: - U{http://biopython.org/DIST/docs/tutorial/Tutorial.html} - U{http://biopython.org/DIST/docs/tutorial/Tutorial.pdf} s epytext eniÿÿÿÿN(tSet(tIUPAC(tambiguous_dna_complementtambiguous_rna_complement(t CodonTablecCsZdj|jƒƒ}dj|jƒƒ}||jƒ}||jƒ}tj||ƒS(s¶Makes a python string translation table (PRIVATE). Arguments: - complement_mapping - a dictionary such as ambiguous_dna_complement and ambiguous_rna_complement from Data.IUPACData. Returns a translation table (a string of length 256) for use with the python string's translate method to use in a (reverse) complement. Compatible with lower case and upper case sequences. For internal use only. t(tjointkeystvaluestlowertstringt maketrans(tcomplement_mappingtbeforetafter((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt _maketranss tSeqcBsgeZdZejd„Zd„Zedd„deddƒZd„Z d „Z d „Z d „Z d „Z d „Zd„Zd„Zd„Zdejd„Zdejd„Zdejd„Zdejd„Zdejd„Zd$dd„Zd$dd„Zd$d„Zd$d„Zd$d„Zd„Zd„Z d„Z!d „Z"d!d"e#d#„Z$RS(%syA read-only sequence object (essentially a string with an alphabet). Like normal python strings, our basic sequence object is immutable. This prevents you from doing my_seq[5] = "A" for example, but does allow Seq objects to be used as dictionary keys. The Seq object provides a number of string like methods (such as count, find, split and strip), which are alphabet aware where appropriate. The Seq object also provides some biological methods, such as complement, reverse_complement, transcribe, back_transcribe and translate (which are not applicable to sequences with a protein alphabet). cCsLt|ƒtdƒks6t|ƒtdƒks6t‚||_||_dS(s'Create a Seq object. Arguments: - seq - Sequence, required (string) - alphabet - Optional argument, an Alphabet object from Bio.Alphabet You will typically use Bio.SeqIO to read in sequences from files as SeqRecord objects, whose sequence will be exposed as a Seq object via the seq property. However, will often want to create your own Seq objects directly: >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF", ... IUPAC.protein) >>> my_seq Seq('MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF', IUPACProtein()) >>> print my_seq MKQHKAMIVALIVICITAVVAALVTRKDLCEVHIRTGQTEVAVF RuN(ttypetAssertionErrort_datatalphabet(tselftdataR((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt__init__Ds cCs)ddl}|jdtƒ||_dS(Niÿÿÿÿs8Writing to the Seq object's .data propery is deprecated.(twarningstwarntDeprecationWarningR(RtvalueR((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt _set_dataas  tfgetcCs t|ƒS(N(tstr(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pythstfsettdocs!Sequence as a string (DEPRECATED)cCsvt|ƒdkrId|jjt|ƒd t|ƒdt|jƒfSd|jjt|jƒt|jƒfSdS(sCReturns a (truncated) representation of the sequence for debugging.i<s%s('%s...%s', %s)i6iýÿÿÿs %s(%s, %s)N(tlent __class__t__name__RtreprRR(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt__repr__ls   cCs|jS(sUReturns the full sequence as a python string. Note that Biopython 1.44 and earlier would give a truncated version of repr(my_seq) for str(my_seq). If you are writing code which need to be backwards compatible with old Biopython, you should continue to use my_seq.tostring() rather than str(my_seq). (R(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt__str__yscCs t|jƒS(N(R"R(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt__len__–scCs5t|tƒr|j|St|j||jƒSdS(N(t isinstancetintRRR(Rtindex((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt __getitem__˜s cCsÆt|dƒrtj|j|jgƒsUtdt|jƒt|jƒfƒ‚ntj|j|jgƒ}|jt|ƒt|ƒ|ƒSt |t ƒr¼|jt|ƒ||jƒSt‚dS(s0Add another sequence or string to this sequence.Rs Incompatable alphabets %s and %sN( thasattrtAlphabett_check_type_compatibleRt TypeErrorR%t_consensus_alphabetR#RR)t basestring(Rtotherta((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt__add__£s % cCsÆt|dƒrtj|j|jgƒsUtdt|jƒt|jƒfƒ‚ntj|j|jgƒ}|jt|ƒt|ƒ|ƒSt |t ƒr¼|j|t|ƒ|jƒSt‚dS(NRs Incompatable alphabets %s and %s( R-R.R/RR0R%R1R#RR)R2(RR3R4((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt__radd__´s % cCs t|ƒS(s¨Returns the full sequence as a python string. Although not formally deprecated, you are now encouraged to use str(my_seq) instead of my_seq.tostring().(R(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyttostringÄscCstt|ƒ|jƒS(s»Returns the full sequence as a MutableSeq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> my_seq = Seq("MKQHKAMIVALIVICITAVVAAL", ... IUPAC.protein) >>> my_seq Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein()) >>> my_seq.tomutable() MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein()) Note that the alphabet is preserved. (t MutableSeqRR(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt tomutableËscCsly |j}Wntk r!|SXtj|j|gƒsbtdt|jƒt|ƒfƒ‚nt|ƒS(sstring/Seq/MutableSeq to string, checking alphabet (PRIVATE). For a string argument, returns the string. For a Seq or MutableSeq, it checks the alphabet is compatible (raising an exception if it isn't), and then returns a string. s Incompatable alphabets %s and %s(RtAttributeErrorR.R/R0R%R(Rtother_sequencet other_alpha((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt_get_seq_str_and_check_alphabetÛs  "icCs(|j|ƒ}t|ƒj|||ƒS(s¶Non-overlapping count method, like that of a python string. This behaves like the python string method of the same name, which does a non-overlapping count! Returns an integer, the number of occurrences of substring argument sub in the (sub)sequence given by [start:end]. Optional arguments start and end are interpreted as in slice notation. Arguments: - sub - a string or another Seq object to look for - start - optional integer, slice start - end - optional integer, slice end e.g. >>> from Bio.Seq import Seq >>> my_seq = Seq("AAAATGA") >>> print my_seq.count("A") 5 >>> print my_seq.count("ATG") 1 >>> print my_seq.count(Seq("AT")) 1 >>> print my_seq.count("AT", 2, -1) 1 HOWEVER, please note because python strings and Seq objects (and MutableSeq objects) do a non-overlapping search, this may not give the answer you expect: >>> "AAAA".count("AA") 2 >>> print Seq("AAAA").count("AA") 2 A non-overlapping search would give the answer as three! (R=Rtcount(Rtsubtstarttendtsub_str((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR>ðs)cCs(|j|ƒ}t|ƒj|||ƒS(sÏFind method, like that of a python string. This behaves like the python string method of the same name. Returns an integer, the index of the first occurrence of substring argument sub in the (sub)sequence given by [start:end]. Arguments: - sub - a string or another Seq object to look for - start - optional integer, slice start - end - optional integer, slice end Returns -1 if the subsequence is NOT found. e.g. Locating the first typical start codon, AUG, in an RNA sequence: >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_rna.find("AUG") 3 (R=Rtfind(RR?R@RARB((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRCscCs(|j|ƒ}t|ƒj|||ƒS(sçFind from right method, like that of a python string. This behaves like the python string method of the same name. Returns an integer, the index of the last (right most) occurrence of substring argument sub in the (sub)sequence given by [start:end]. Arguments: - sub - a string or another Seq object to look for - start - optional integer, slice start - end - optional integer, slice end Returns -1 if the subsequence is NOT found. e.g. Locating the last typical start codon, AUG, in an RNA sequence: >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_rna.rfind("AUG") 15 (R=Rtrfind(RR?R@RARB((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRD6scCs‘t|tƒreg|D]}|j|ƒ^q}x-|D]%}t|ƒj|||ƒr8tSq8WtS|j|ƒ}t|ƒj|||ƒSdS(s)Does the Seq start with the given prefix? Returns True/False. This behaves like the python string method of the same name. Return True if the sequence starts with the specified prefix (a string or another Seq object), False otherwise. With optional start, test sequence beginning at that position. With optional end, stop comparing sequence at that position. prefix can also be a tuple of strings to try. e.g. >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_rna.startswith("GUC") True >>> my_rna.startswith("AUG") False >>> my_rna.startswith("AUG", 3) True >>> my_rna.startswith(("UCC","UCA","UCG"),1) True N(R)ttupleR=Rt startswithtTruetFalse(RtprefixR@RAtptprefix_stringst prefix_str((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRFPs cCs‘t|tƒreg|D]}|j|ƒ^q}x-|D]%}t|ƒj|||ƒr8tSq8WtS|j|ƒ}t|ƒj|||ƒSdS(sDoes the Seq end with the given suffix? Returns True/False. This behaves like the python string method of the same name. Return True if the sequence ends with the specified suffix (a string or another Seq object), False otherwise. With optional start, test sequence beginning at that position. With optional end, stop comparing sequence at that position. suffix can also be a tuple of strings to try. e.g. >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_rna.endswith("UUG") True >>> my_rna.endswith("AUG") False >>> my_rna.endswith("AUG", 0, 18) True >>> my_rna.endswith(("UCC","UCA","UUG")) True N(R)RER=RtendswithRGRH(RtsuffixR@RARJtsuffix_stringst suffix_str((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRMus iÿÿÿÿcCsD|j|ƒ}gt|ƒj||ƒD]}t||jƒ^q(S(sPSplit method, like that of a python string. This behaves like the python string method of the same name. Return a list of the 'words' in the string (as Seq objects), using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done. If maxsplit is ommited, all splits are made. Following the python string method, sep will by default be any white space (tabs, spaces, newlines) but this is unlikely to apply to biological sequences. e.g. >>> from Bio.Seq import Seq >>> my_rna = Seq("GUCAUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAGUUG") >>> my_aa = my_rna.translate() >>> my_aa Seq('VMAIVMGR*KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*')) >>> my_aa.split("*") [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))] >>> my_aa.split("*",1) [Seq('VMAIVMGR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('KGAR*L', HasStopCodon(ExtendedIUPACProtein(), '*'))] See also the rsplit method: >>> my_aa.rsplit("*",1) [Seq('VMAIVMGR*KGAR', HasStopCodon(ExtendedIUPACProtein(), '*')), Seq('L', HasStopCodon(ExtendedIUPACProtein(), '*'))] (R=RtsplitRR(Rtseptmaxsplittsep_strtpart((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRQ›s cCsÉ|j|ƒ}y9gt|ƒj||ƒD]}t||jƒ^q+SWnztk rÄgt|ƒddd…j|ddd…|ƒD]%}t|ddd…|jƒ^q‹}|jƒ|SXdS(sˆRight split method, like that of a python string. This behaves like the python string method of the same name. Return a list of the 'words' in the string (as Seq objects), using sep as the delimiter string. If maxsplit is given, at most maxsplit splits are done COUNTING FROM THE RIGHT. If maxsplit is ommited, all splits are made. Following the python string method, sep will by default be any white space (tabs, spaces, newlines) but this is unlikely to apply to biological sequences. e.g. print my_seq.rsplit("*",1) See also the split method. Niÿÿÿÿ(R=RtrsplitRRR:RQtreverse(RRRRSRTRUtwordtwords((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRVÁs6 [ cCs.|j|ƒ}tt|ƒj|ƒ|jƒS(s´Returns a new Seq object with leading and trailing ends stripped. This behaves like the python string method of the same name. Optional argument chars defines which characters to remove. If ommitted or None (default) then as for the python string method, this defaults to removing any white space. e.g. print my_seq.strip("-") See also the lstrip and rstrip methods. (R=RRtstripR(Rtcharst strip_str((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRZáscCs.|j|ƒ}tt|ƒj|ƒ|jƒS(s­Returns a new Seq object with leading (left) end stripped. This behaves like the python string method of the same name. Optional argument chars defines which characters to remove. If ommitted or None (default) then as for the python string method, this defaults to removing any white space. e.g. print my_seq.lstrip("-") See also the strip and rstrip methods. (R=RRtlstripR(RR[R\((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR]òscCs.|j|ƒ}tt|ƒj|ƒ|jƒS(s%Returns a new Seq object with trailing (right) end stripped. This behaves like the python string method of the same name. Optional argument chars defines which characters to remove. If ommitted or None (default) then as for the python string method, this defaults to removing any white space. e.g. Removing a nucleotide sequence's polyadenylation (poly-A tail): >>> from Bio.Alphabet import IUPAC >>> from Bio.Seq import Seq >>> my_seq = Seq("CGGTACGCTTATGTCACGTAGAAAAAA", IUPAC.unambiguous_dna) >>> my_seq Seq('CGGTACGCTTATGTCACGTAGAAAAAA', IUPACUnambiguousDNA()) >>> my_seq.rstrip("A") Seq('CGGTACGCTTATGTCACGTAG', IUPACUnambiguousDNA()) See also the strip and lstrip methods. (R=RRtrstripR(RR[R\((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR^scCstj|jƒ}t|tjƒr3tdƒ‚nt|tjƒrNt}n“t|tjƒrit }nxd|j ks‡d|j kr´d|j ks¥d|j kr´tdƒ‚n-d|j ksÒd|j krÛt }nt}t t |ƒj |ƒ|jƒS(s=Returns the complement sequence. New Seq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> my_dna = Seq("CCCCCGATAG", IUPAC.unambiguous_dna) >>> my_dna Seq('CCCCCGATAG', IUPACUnambiguousDNA()) >>> my_dna.complement() Seq('GGGGGCTATC', IUPACUnambiguousDNA()) You can of course used mixed case sequences, >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_dna >>> my_dna = Seq("CCCCCgatA-GD", generic_dna) >>> my_dna Seq('CCCCCgatA-GD', DNAAlphabet()) >>> my_dna.complement() Seq('GGGGGctaT-CH', DNAAlphabet()) Note in the above example, ambiguous character D denotes G, A or T so its complement is H (for C, T or A). Trying to complement a protein sequence raises an exception. >>> my_protein = Seq("MAIVMGR", IUPAC.protein) >>> my_protein.complement() Traceback (most recent call last): ... ValueError: Proteins do not have complements! s!Proteins do not have complements!tUtutTttsMixed RNA/DNA found(R.t_get_base_alphabetRR)tProteinAlphabett ValueErrort DNAAlphabett_dna_complement_tablet RNAAlphabett_rna_complement_tableRRRt translate(Rtbasetttable((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt complements    cCs|jƒddd…S(sAReturns the reverse complement sequence. New Seq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> my_dna = Seq("CCCCCGATAGNR", IUPAC.ambiguous_dna) >>> my_dna Seq('CCCCCGATAGNR', IUPACAmbiguousDNA()) >>> my_dna.reverse_complement() Seq('YNCTATCGGGGG', IUPACAmbiguousDNA()) Note in the above example, since R = G or A, its complement is Y (which denotes C or T). You can of course used mixed case sequences, >>> from Bio.Seq import Seq >>> from Bio.Alphabet import generic_dna >>> my_dna = Seq("CCCCCgatA-G", generic_dna) >>> my_dna Seq('CCCCCgatA-G', DNAAlphabet()) >>> my_dna.reverse_complement() Seq('C-TatcGGGGG', DNAAlphabet()) Trying to complement a protein sequence raises an exception: >>> my_protein = Seq("MAIVMGR", IUPAC.protein) >>> my_protein.reverse_complement() Traceback (most recent call last): ... ValueError: Proteins do not have complements! Niÿÿÿÿ(Rm(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pytreverse_complementOs!cCsÄtj|jƒ}t|tjƒr3tdƒ‚nt|tjƒrTtdƒ‚n|jtjkrrtj }n'|jtj krtj }n tj }t t|ƒjddƒjddƒ|ƒS(sReturns the RNA sequence from a DNA sequence. New Seq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> coding_dna = Seq("ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG", ... IUPAC.unambiguous_dna) >>> coding_dna Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA()) >>> coding_dna.transcribe() Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA()) Trying to transcribe a protein or RNA sequence raises an exception: >>> my_protein = Seq("MAIVMGR", IUPAC.protein) >>> my_protein.transcribe() Traceback (most recent call last): ... ValueError: Proteins cannot be transcribed! sProteins cannot be transcribed!sRNA cannot be transcribed!RaR_RbR`(R.RcRR)RdReRhRtunambiguous_dnatunambiguous_rnat ambiguous_dnat ambiguous_rnat generic_rnaRRtreplace(RRkR((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt transcribers   cCsÄtj|jƒ}t|tjƒr3tdƒ‚nt|tjƒrTtdƒ‚n|jtjkrrtj }n'|jtj krtj }n tj }t t|ƒjddƒjddƒ|ƒS(s)Returns the DNA sequence from an RNA sequence. New Seq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> messenger_rna = Seq("AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG", ... IUPAC.unambiguous_rna) >>> messenger_rna Seq('AUGGCCAUUGUAAUGGGCCGCUGAAAGGGUGCCCGAUAG', IUPACUnambiguousRNA()) >>> messenger_rna.back_transcribe() Seq('ATGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG', IUPACUnambiguousDNA()) Trying to back-transcribe a protein or DNA sequence raises an exception: >>> my_protein = Seq("MAIVMGR", IUPAC.protein) >>> my_protein.back_transcribe() Traceback (most recent call last): ... ValueError: Proteins cannot be back transcribed! s$Proteins cannot be back transcribed!sDNA cannot be back transcribed!R_RaR`Rb(R.RcRR)RdReRfRRpRoRrRqt generic_dnaRRRt(RRkR((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pytback_transcribe”s   tStandardt*cCsyt|ƒ}Wntk r)d}nXt|tƒrft|ƒdkrftddddƒ‚nttj|jƒtj ƒr“tdƒ‚n|jt j krÑ|dkrÁt j |}q8t j|}ng|jt jkr|dkrÿt j|}q8t j|}n)|dkr+t j|}n t j|}tt|ƒ|||ƒ}||krztj|jd|ƒ}n |j}t||ƒS( sª Turns a nucleotide sequence into a protein sequence. New Seq object. This method will translate DNA or RNA sequences, and those with a nucleotide or generic alphabet. Trying to translate a protein sequence raises an exception. Arguments: - table - Which codon table to use? This can be either a name (string) or an NCBI identifier (integer). This defaults to the "Standard" table. - stop_symbol - Single character string, what to use for terminators. This defaults to the asterisk, "*". - to_stop - Boolean, defaults to False meaning do a full translation continuing on past any stop codons (translated as the specified stop_symbol). If True, translation is terminated at the first in frame stop codon (and the stop_symbol is not appended to the returned protein sequence). e.g. Using the standard table: >>> coding_dna = Seq("GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG") >>> coding_dna.translate() Seq('VAIVMGR*KGAR*', HasStopCodon(ExtendedIUPACProtein(), '*')) >>> coding_dna.translate(stop_symbol="@") Seq('VAIVMGR@KGAR@', HasStopCodon(ExtendedIUPACProtein(), '@')) >>> coding_dna.translate(to_stop=True) Seq('VAIVMGR', ExtendedIUPACProtein()) Now using NCBI table 2, where TGA is not a stop codon: >>> coding_dna.translate(table=2) Seq('VAIVMGRWKGAR*', HasStopCodon(ExtendedIUPACProtein(), '*')) >>> coding_dna.translate(table=2, to_stop=True) Seq('VAIVMGRWKGAR', ExtendedIUPACProtein()) If the sequence has no in-frame stop codon, then the to_stop argument has no effect: >>> coding_dna2 = Seq("TTGGCCATTGTAATGGGCCGC") >>> coding_dna2.translate() Seq('LAIVMGR', ExtendedIUPACProtein()) >>> coding_dna2.translate(to_stop=True) Seq('LAIVMGR', ExtendedIUPACProtein()) NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid or a stop codon. These are translated as "X". Any invalid codon (e.g. "TA?" or "T-A") will throw a TranslationError. NOTE - Does NOT support gapped sequences. NOTE - This does NOT behave like the python string's translate method. For that use str(my_seq).translate(...) instead. is.The Seq object translate method DOES NOT take s*a 256 character string mapping table like s-the python string object's translate method. s'Use str(my_seq).translate(...) instead.sProteins cannot be translated!t stop_symbolN(R*RetNoneR)RR"R.RcRRdRRoRtunambiguous_dna_by_nametunambiguous_dna_by_idRptunambiguous_rna_by_nametunambiguous_rna_by_idtambiguous_generic_by_nametambiguous_generic_by_idt_translate_strt HasStopCodontprotein_alphabetR(RttableRztto_stopttable_idt codon_tabletproteinR((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRj·s67  !        N(%R$t __module__t__doc__R.tgeneric_alphabetRRtpropertyRR&R'R(R,R5R6R7R9R=tsystmaxintR>RCRDRFRMR{RQRVRZR]R^RmRnRuRwRHRj(((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR6s<          ,%&&    3 # " #t UnknownSeqcBs•eZdZejdd„Zd„Zd„Zd„Z d„Z d„Z d„Z de jd „Zd „Zd „Zd „Zd „Zd„ZRS(s£A read-only sequence object of known length but unknown contents. If you have an unknown sequence, you can represent this with a normal Seq object, for example: >>> my_seq = Seq("N"*5) >>> my_seq Seq('NNNNN', Alphabet()) >>> len(my_seq) 5 >>> print my_seq NNNNN However, this is rather wasteful of memory (especially for large sequences), which is where this class is most usefull: >>> unk_five = UnknownSeq(5) >>> unk_five UnknownSeq(5, alphabet = Alphabet(), character = '?') >>> len(unk_five) 5 >>> print(unk_five) ????? You can add unknown sequence together, provided their alphabets and characters are compatible, and get another memory saving UnknownSeq: >>> unk_four = UnknownSeq(4) >>> unk_four UnknownSeq(4, alphabet = Alphabet(), character = '?') >>> unk_four + unk_five UnknownSeq(9, alphabet = Alphabet(), character = '?') If the alphabet or characters don't match up, the addition gives an ordinary Seq object: >>> unk_nnnn = UnknownSeq(4, character = "N") >>> unk_nnnn UnknownSeq(4, alphabet = Alphabet(), character = 'N') >>> unk_nnnn + unk_four Seq('NNNN????', Alphabet()) Combining with a real Seq gives a new Seq object: >>> known_seq = Seq("ACGT") >>> unk_four + known_seq Seq('????ACGT', Alphabet()) >>> known_seq + unk_four Seq('ACGT????', Alphabet()) cCsÁt|ƒ|_|jdkr-tdƒ‚n||_|rit|ƒdkr]tdƒ‚n||_nTtj|ƒ}t|tj ƒr–d|_n't|tj ƒr´d|_n d|_dS( s®Create a new UnknownSeq object. If character is ommited, it is determed from the alphabet, "N" for nucleotides, "X" for proteins, and "?" otherwise. isLength must not be negative.is4character argument should be a single letter string.tNtXt?N( R*t_lengthReRR"t _characterR.RcR)tNucleotideAlphabetRd(RtlengthRt characterRk((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRSs    cCs|jS(s2Returns the stated length of the unknown sequence.(R”(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR(mscCs|j|jS(s@Returns the unknown sequence as full string of the given length.(R•R”(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR'qscCs&d|jt|jƒt|jƒfS(Ns-UnknownSeq(%i, alphabet = %s, character = %s)(R”R%RR•(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR&uscCsat|tƒrG|j|jkrGtt|ƒt|ƒ|j|jƒStt|ƒ|jƒ|S(N(R)RR•R"RRR(RR3((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR5ys cCsat|tƒrG|j|jkrGtt|ƒt|ƒ|j|jƒS|tt|ƒ|jƒS(N(R)RR•R"RRR(RR3((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR6‚s cCsHt|tƒrt|ƒ|Sttd|j|ƒ|j|jƒSdS(Nt#(R)R*RRR"R”RR•(RR+((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR,‹sicCsæ|j|ƒ}t|ƒdkr{t|ƒ|jkrt|dkrX||jkrX|jSt|ƒj|||ƒSqâdSngt|ƒt|jƒkrÞ|dkrÂ||jkrÂ|jt|ƒSt|ƒj|||ƒSndSdS(sžNon-overlapping count method, like that of a python string. This behaves like the python string (and Seq object) method of the same name, which does a non-overlapping count! Returns an integer, the number of occurrences of substring argument sub in the (sub)sequence given by [start:end]. Optional arguments start and end are interpreted as in slice notation. Arguments: - sub - a string or another Seq object to look for - start - optional integer, slice start - end - optional integer, slice end >>> "NNNN".count("N") 4 >>> Seq("NNNN").count("N") 4 >>> UnknownSeq(4, character="N").count("N") 4 >>> UnknownSeq(4, character="N").count("A") 0 >>> UnknownSeq(4, character="N").count("AA") 0 HOWEVER, please note because that python strings and Seq objects (and MutableSeq objects) do a non-overlapping search, this may not give the answer you expect: >>> UnknownSeq(4, character="N").count("NN") 2 >>> UnknownSeq(4, character="N").count("NNN") 1 iiN(R=R"RR•R”R>tset(RR?R@RARB((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR>”s$cCs1ttj|jƒtjƒr-tdƒ‚n|S(ssThe complement of an unknown nucleotide equals itself. >>> my_nuc = UnknownSeq(8) >>> my_nuc UnknownSeq(8, alphabet = Alphabet(), character = '?') >>> print my_nuc ???????? >>> my_nuc.complement() UnknownSeq(8, alphabet = Alphabet(), character = '?') >>> print my_nuc.complement() ???????? s!Proteins do not have complements!(R)R.RcRRdRe(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRmÌs  cCs1ttj|jƒtjƒr-tdƒ‚n|S(s’The reverse complement of an unknown nucleotide equals itself. >>> my_nuc = UnknownSeq(10) >>> my_nuc UnknownSeq(10, alphabet = Alphabet(), character = '?') >>> print my_nuc ?????????? >>> my_nuc.reverse_complement() UnknownSeq(10, alphabet = Alphabet(), character = '?') >>> print my_nuc.reverse_complement() ?????????? s!Proteins do not have complements!(R)R.RcRRdRe(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRnÞs  cCs4t|j|jƒjƒ}t|j|j|jƒS(sŸReturns unknown RNA sequence from an unknown DNA sequence. >>> my_dna = UnknownSeq(10, character="N") >>> my_dna UnknownSeq(10, alphabet = Alphabet(), character = 'N') >>> print my_dna NNNNNNNNNN >>> my_rna = my_dna.transcribe() >>> my_rna UnknownSeq(10, alphabet = RNAAlphabet(), character = 'N') >>> print my_rna NNNNNNNNNN (RR•RRuRR”(Rts((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRuðscCs4t|j|jƒjƒ}t|j|j|jƒS(s¸Returns unknown DNA sequence from an unknown RNA sequence. >>> my_rna = UnknownSeq(20, character="N") >>> my_rna UnknownSeq(20, alphabet = Alphabet(), character = 'N') >>> print my_rna NNNNNNNNNNNNNNNNNNNN >>> my_dna = my_rna.back_transcribe() >>> my_dna UnknownSeq(20, alphabet = DNAAlphabet(), character = 'N') >>> print my_dna NNNNNNNNNNNNNNNNNNNN (RR•RRwRR”(RR›((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRwscKsGttj|jƒtjƒr-tdƒ‚nt|jdtjdƒS(s‹Translate an unknown nucleotide sequence into an unknown protein. e.g. >>> my_seq = UnknownSeq(11, character="N") >>> print my_seq NNNNNNNNNNN >>> my_protein = my_seq.translate() >>> my_protein UnknownSeq(3, alphabet = ProteinAlphabet(), character = 'X') >>> print my_protein XXX In comparison, using a normal Seq object: >>> my_seq = Seq("NNNNNNNNNNN") >>> print my_seq NNNNNNNNNNN >>> my_protein = my_seq.translate() >>> my_protein Seq('XXX', ExtendedIUPACProtein()) >>> print my_protein XXX sProteins cannot be translated!iR’( R)R.RcRRdReRR”tgeneric_protein(Rtkwargs((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRjs N(R$RŠR‹R.RŒR{RR(R'R&R5R6R,RŽRR>RmRnRuRwRj(((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR s2    8    R8cBsæeZdZejd„Zd„Zd„Zd„Zd„Z d„Z d„Z d„Z d „Z d „Zd „Zd „Zd d„Zd„Zdejd„Zd„Zd„Zd„Zd„Zd„Zd„Zd„ZRS(s]An editable sequence object (with an alphabet). Unlike normal python strings and our basic sequence object (the Seq class) which are immuatable, the MutableSeq lets you edit the sequence in place. However, this means you cannot use a MutableSeq object as a dictionary key. >>> from Bio.Seq import MutableSeq >>> from Bio.Alphabet import generic_dna >>> my_seq = MutableSeq("ACTCGTCGTCG", generic_dna) >>> my_seq MutableSeq('ACTCGTCGTCG', DNAAlphabet()) >>> my_seq[5] 'T' >>> my_seq[5] = "A" >>> my_seq MutableSeq('ACTCGACGTCG', DNAAlphabet()) >>> my_seq[5] 'A' >>> my_seq[5:8] = "NNN" >>> my_seq MutableSeq('ACTCGNNNTCG', DNAAlphabet()) >>> len(my_seq) 11 Note that the MutableSeq object does not support as many string-like or biological methods as the Seq object. cCsFt|ƒtdƒkr0tjd|ƒ|_n ||_||_dS(NRtc(RtarrayRR(RRR((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRPs cCsst|ƒdkrId|jjt|d ƒt|dƒt|jƒfSd|jjt|ƒt|jƒfSdS(sCReturns a (truncated) representation of the sequence for debugging.i<s%s('%s...%s', %s)i6iýÿÿÿs %s('%s', %s)N(R"R#R$RR%R(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR&Ws   cCsdj|jƒS(sVReturns the full sequence as a python string. Note that Biopython 1.44 and earlier would give a truncated version of repr(my_seq) for str(my_seq). If you are writing code which needs to be backwards compatible with old Biopython, you should continue to use my_seq.tostring() rather than str(my_seq). R(RR(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR'es cCs¿t|dƒr“tj|j|jgƒsUtdt|jƒt|jƒfƒ‚nt|tƒrwt|j |j ƒStt |ƒt |ƒƒSn(t|t ƒrµtt |ƒ|ƒSt‚dS(smCompare the sequence for to another sequence or a string. If compared to another sequence the alphabets must be compatible. Comparing DNA to RNA, or Nucleotide to Protein will raise an exception. Otherwise only the sequence itself is compared, not the precise alphabet. This method indirectly supports ==, < , etc.Rs Incompatable alphabets %s and %sN( R-R.R/RR0R%R)R8tcmpRRR2(RR3((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt__cmp__ps  %cCs t|jƒS(N(R"R(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR(scCs5t|tƒr|j|St|j||jƒSdS(N(R)R*RR8R(RR+((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR,s cCsŒt|tƒr||j|tt|jƒƒD]'}|j||kr|j|=dSqWtdƒ‚dS(Ns#MutableSeq.remove(x): x not in list(trangeR"RRe(RtitemR¦((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pytremoveês  icCsµy|jƒ}Wntk r)|}nXt|tƒsHtdƒ‚nt|ƒdkr˜d}x1|j||!D]}||krq|d7}qqqqW|S|jƒj|||ƒSdS(sàNon-overlapping count method, like that of a python string. This behaves like the python string method of the same name, which does a non-overlapping count! Returns an integer, the number of occurrences of substring argument sub in the (sub)sequence given by [start:end]. Optional arguments start and end are interpreted as in slice notation. Arguments: - sub - a string or another Seq object to look for - start - optional integer, slice start - end - optional integer, slice end e.g. >>> from Bio.Seq import MutableSeq >>> my_mseq = MutableSeq("AAAATGA") >>> print my_mseq.count("A") 5 >>> print my_mseq.count("ATG") 1 >>> print my_mseq.count(Seq("AT")) 1 >>> print my_mseq.count("AT", 2, -1) 1 HOWEVER, please note because that python strings, Seq objects and MutableSeq objects do a non-overlapping search, this may not give the answer you expect: >>> "AAAA".count("AA") 2 >>> print MutableSeq("AAAA").count("AA") 2 A non-overlapping search would give the answer as three! s$expected a string, Seq or MutableSeqiiN(R7R:R)R2R0R"RR>(RR?R@RAtsearchR>Rž((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR>ñs(   cCsGx4tt|jƒƒD]}|j||kr|SqWtdƒ‚dS(Ns"MutableSeq.index(x): x not in list(R¨R"RRe(RR©R¦((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR+,scCs|jjƒdS(sQModify the mutable sequence to reverse itself. No return value. N(RRW(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRW2scsDttj|jƒtjƒr-tdƒ‚n|jtjtjfkrQt ‰no|jtj tj fkrut ‰nKd|j kr¢d|j kr¢tdƒ‚nd|j krºt ‰nt ‰tgˆjƒD]$\}}|jƒ|jƒf^qЃ}ˆj|ƒt‡fd†|j ƒ|_ tjd|j ƒ|_ dS(sŸModify the mutable sequence to take on its complement. Trying to complement a protein sequence raises an exception. No return value. s!Proteins do not have complements!R_RasMixed RNA/DNA foundcsˆ|S(N((Rž(td(sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRPsRžN(R)R.RcRRdReRRqRoRRrRpRRtdictt iteritemsR tupdatetmapRŸ(RtxtyRž((R¬sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRm9s     = cCs|jƒ|jjƒdS(s¯Modify the mutable sequence to take on its reverse complement. Trying to reverse complement a protein sequence raises an exception. No return value. N(RmRRW(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRnSs cCs[t|tƒr6xE|jD]}|jj|ƒqWn!x|D]}|jj|ƒq=WdS(N(R)R8RR¤(RR3Rž((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pytextend`s  cCsdj|jƒS(s Returns the full sequence as a python string. Although not formally deprecated, you are now encouraged to use str(my_seq) instead of my_seq.tostring(). Because str(my_seq) will give you the full sequence as a python string, there is often no need to make an explicit conversion. For example, print "ID={%s}, sequence={%s}" % (my_name, my_seq) On Biopython 1.44 or older you would have to have done this: print "ID={%s}, sequence={%s}" % (my_name, my_seq.tostring()) R(RR(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR7hscCstdj|jƒ|jƒS(sÐReturns the full sequence as a new immutable Seq object. >>> from Bio.Seq import Seq >>> from Bio.Alphabet import IUPAC >>> my_mseq = MutableSeq("MKQHKAMIVALIVICITAVVAAL", IUPAC.protein) >>> my_mseq MutableSeq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein()) >>> my_mseq.toseq() Seq('MKQHKAMIVALIVICITAVVAAL', IUPACProtein()) Note that the alphabet is preserved. R(RRRR(R((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyttoseqys(R$RŠR‹R.RŒRR&R'R¡R(R,R¢R£R5R6R¤R¥R§RªRŽRR>R+RWRmRnR³R7R´(((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR84s.           ;     cCsXt|tƒr|jƒSt|tƒr8|jƒjƒS|jddƒjddƒSdS(s-Transcribes a DNA sequence into RNA. If given a string, returns a new string object. Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet. Trying to transcribe a protein or RNA sequence raises an exception. e.g. >>> transcribe("ACTGN") 'ACUGN' RaR_RbR`N(R)RRuR8R´Rt(tdna((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRus  cCsXt|tƒr|jƒSt|tƒr8|jƒjƒS|jddƒjddƒSdS(s8Back-transcribes an RNA sequence into DNA. If given a string, returns a new string object. Given a Seq or MutableSeq, returns a new Seq object with an RNA alphabet. Trying to transcribe a protein or DNA sequence raises an exception. e.g. >>> back_transcribe("ACUGN") 'ACTGN' R_RaR`RbN(R)RRwR8R´Rt(trna((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRw¢s  RyR’c Cs[|jƒ}g}|j}|j}|jjdk rQt|jjjƒƒ}n(ttjjjƒtj jjƒƒ}t |ƒ} xÆt d| | ddƒD]ª} || | d!} y|j || ƒWq t tjfk rI| |jkr|rþPn|j |ƒqJ|jt| ƒƒr3|j |ƒqJtjd| ƒ‚q Xq Wdj|ƒS(sHelper function to translate a nucleotide string (PRIVATE). Arguments: - sequence - a string - table - a CodonTable object (NOT a table name or id number) - stop_symbol - a single character string, what to use for terminators. - to_stop - boolean, should translation terminate at the first in frame stop codon? If there is no in-frame stop codon then translation continues to the end. - pos_stop - a single character string for a possible stop codon (e.g. TAN or NNN) Returns a string. e.g. >>> from Bio.Data import CodonTable >>> table = CodonTable.ambiguous_dna_by_id[1] >>> _translate_str("AAA", table) 'K' >>> _translate_str("TAR", table) '*' >>> _translate_str("TAN", table) 'X' >>> _translate_str("TAN", table, pos_stop="@") '@' >>> _translate_str("TA?", table) Traceback (most recent call last): ... TranslationError: Codon 'TA?' is invalid iisCodon '%s' is invalidRN(tuppert forward_tablet stop_codonstnucleotide_alphabettlettersR{RšRRqRrR"txrangeR¤tKeyErrorRtTranslationErrort issupersetR( tsequenceR…RzR†tpos_stopt amino_acidsR¸R¹t valid_letterstnR¦tcodon((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyR‚·s.!    !RxcCs™t|tƒr"|j|||ƒSt|tƒrJ|jƒj|||ƒSytjt|ƒ}Wntk rtj |}nXt ||||ƒSdS(s£Translate a nucleotide sequence into amino acids. If given a string, returns a new string object. Given a Seq or MutableSeq, returns a Seq object with a protein alphabet. Arguments: - table - Which codon table to use? This can be either a name (string) or an NCBI identifier (integer). Defaults to the "Standard" table. - stop_symbol - Single character string, what to use for any terminators, defaults to the asterisk, "*". - to_stop - Boolean, defaults to False meaning do a full translation continuing on past any stop codons (translated as the specified stop_symbol). If True, translation is terminated at the first in frame stop codon (and the stop_symbol is not appended to the returned protein sequence). A simple string example using the default (standard) genetic code: >>> coding_dna = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG" >>> translate(coding_dna) 'VAIVMGR*KGAR*' >>> translate(coding_dna, stop_symbol="@") 'VAIVMGR@KGAR@' >>> translate(coding_dna, to_stop=True) 'VAIVMGR' Now using NCBI table 2, where TGA is not a stop codon: >>> translate(coding_dna, table=2) 'VAIVMGRWKGAR*' >>> translate(coding_dna, table=2, to_stop=True) 'VAIVMGRWKGAR' Note that if the sequence has no in-frame stop codon, then the to_stop argument has no effect: >>> coding_dna2 = "GTGGCCATTGTAATGGGCCGC" >>> translate(coding_dna2) 'VAIVMGR' >>> translate(coding_dna2, to_stop=True) 'VAIVMGR' NOTE - Ambiguous codons like "TAN" or "NNN" could be an amino acid or a stop codon. These are translated as "X". Any invalid codon (e.g. "TA?" or "T-A") will throw a TranslationError. NOTE - Does NOT support gapped sequences. It will however translate either DNA or RNA. N( R)RRjR8R´RRR*ReR€R‚(RÀR…RzR†Rˆ((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRjõs5 cCs¸t|tƒr|jƒSt|tƒr8|jƒjƒSd|ksPd|krwd|kshd|krwtdƒ‚n'd|ksd|kr˜t}nt}|j|ƒddd…S(sHReturns the reverse complement sequence of a nucleotide string. If given a string, returns a new string object. Given a Seq or a MutableSeq, returns a new Seq object with the same alphabet. Supports unambiguous and ambiguous nucleotide sequences. e.g. >>> reverse_complement("ACTG-NH") 'DN-CAGT' R_R`RaRbsMixed RNA/DNA foundNiÿÿÿÿ( R)RRnR8R´ReRiRgRj(RÀRl((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyRn7s   cCs$dGHddl}|jƒdGHdS(s"Run the Bio.Seq module's doctests.sRuning doctests...iÿÿÿÿNtDone(tdoctestttestmod(RÇ((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt_testYs  t__main__(R‹t __docformat__R RŸRŽRšt NameErrortsetsRR.RtData.IUPACDataRRtBio.DataRRRgRitobjectRRR8RuRwRHR‚RjRnRÉR$(((sz/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Seq.pyt s>         ÿÿìÿÿZ  =B "