ó > Ic@s•dZddlTddlmZdZddd„ƒYZeƒZd„Zd„Zd „Zd „Z d „Z d „Z d „Z d„Z d„Zd„Zd„Zd„ZdZed„Zdd d„ƒYZdd!d„ƒYZdd"d„ƒYZd„Zd„Zd„ZyddlZWnek r7nZXddlZejeZx=ej j!ƒD],Z"e"j#dƒsaej e"ej e"XX where is either "global" or "local" and XX is a 2 character code indicating the parameters it takes. The first character indicates the parameters for matches (and mismatches), and the second indicates the parameters for gap penalties. The match parameters are CODE DESCRIPTION x No parameters. Identical characters have score of 1, otherwise 0. m A match score is the score of identical chars, otherwise mismatch score. d A dictionary returns the score of any pair of characters. c A callback function returns scores. The gap penalty parameters are CODE DESCRIPTION x No gap penalties. s Same open and extend gap penalties for both sequences. d The sequences have different open and extend gap penalties. c A callback function returns the gap penalties. All the different alignment functions are contained in an object "align". For example: >>> from Bio import pairwise2 >>> alignments = pairwise2.align.globalxx("ACCGT", "ACG") will return a list of the alignments between the two strings. The parameters of the alignment function depends on the function called. Some examples: >>> pairwise2.align.globalxx("ACCGT", "ACG") # Find the best global alignment between the two sequences. # Identical characters are given 1 point. No points are deducted # for mismatches or gaps. >>> pairwise2.align.localxx("ACCGT", "ACG") # Same thing as before, but with a local alignment. >>> pairwise2.align.globalmx("ACCGT", "ACG", 2, -1) # Do a global alignment. Identical characters are given 2 points, # 1 point is deducted for each non-identical character. >>> pairwise2.align.globalms("ACCGT", "ACG", 2, -1, -.5, -.1) # Same as above, except now 0.5 points are deducted when opening a # gap, and 0.1 points are deducted when extending it. To see a description of the parameters for a function, please look at the docstring for the function. >>> print newalign.align.localds.__doc__ localds(sequenceA, sequenceB, match_dict, open, extend) -> alignments iÿÿÿÿ(t*(tlistfnsiètaligncBs*eZdZddd„ƒYZd„ZRS(s1This class provides functions that do alignments.talignment_functioncBsÁeZdZigdfd6ddgdfd6dgdfd 6d gd fd 6Zigdfd6d dgdfd6ddddgdfd 6ddgdfd 6Zd„Zd„Zd„ZRS(sìThis class is callable impersonates an alignment function. The constructor takes the name of the function. This class will decode the name of the function to figure out how to interpret the parameters. ttxtmatchtmismatchshmatch is the score to given to identical characters. mismatch is the score given to non-identical ones.tmt match_dictsmatch_dict is a dictionary where the keys are tuples of pairs of characters and the values are the scores, e.g. ("A", "C") : 2.5.tdtmatch_fns]match_fn is a callback function that takes two characters and returns the score between them.tctopentextendsbopen and extend are the gap penalties when a gap is opened and extended. They should be negative.tstopenAtextendAtopenBtextendBs}openA and extendA are the gap penalties for sequenceA, and openB and extendB for sequeneB. The penalties should be negative.tgap_A_fntgap_B_fnsžgap_A_fn and gap_B_fn are callback functions that takes 1) the index where the gap is opened, and 2) the length of the gap. They should return a gap penalty.c Cs½|jdƒr3t|ƒdkrrtdƒ‚qrn?|jdƒrft|ƒdkrrtdƒ‚qrn t|ƒ‚|d |d|d}}}y|j|\}}Wn#tk rÎ}td |ƒ‚nXy|j|\}} Wn#tk r }td |ƒ‚nXd d g} | j|ƒ| j|ƒ||_||_| |_ |j|_ d |j dj |j ƒf} |r| d|7} n| r¦| d| 7} n| d7} | |_ dS(Ntglobalisfunction should be globalXXtlocalisfunction should be localXXiþÿÿÿiÿÿÿÿsunknown match type %rsunknown penalty type %rt sequenceAt sequenceBs%s(%s) -> alignments s, s %s s  alignments is a list of tuples (seqA, seqB, score, begin, end). seqA and seqB are strings showing the alignment between the sequences. score is the score of the alignment. begin and end are indexes into seqA and seqB that indicate the where the alignment occurs. ( t startswithtlentAttributeErrort match2argstKeyErrort penalty2argsRt function_namet align_typet param_namest__name__tjoint__doc__( tselftnameR!t match_typet penalty_typet match_argst match_docRt penalty_argst penalty_docR"tdoc((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyt__init__Žs@         c OsD|jƒ}t|ƒt|jƒkrUtd|jt|jƒt|ƒfƒ‚nd}x.|t|jƒkr‹|j|dkr¨||||j|<|d7}q^|j|d kr|j|dd ksØt‚||||d}}t||ƒ|d<|d 7}q^|j|d krEt||ƒ|d<|d7}q^|j|d krÙ|j|ddksut‚||||d}}|jddƒ}t |||ƒ|dR Rt_make_score_matrix_fastt_make_score_matrix_generict _find_starttmaxRtrinttabst_recover_alignments(RRR RRR0R1R2R3R5R6R7topen_Atextend_Atopen_Btextend_BRt score_matrixt trace_matrixtstartst best_scoret toleranceRBtscoretpos((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyRGsF      #" c CsUt|ƒt|ƒ} } gg} } x?t| ƒD]1} | jdg| ƒ| jdgg| ƒq3WxUt| ƒD]G} ||| |dƒ}|r®||d| ƒ7}n|| | dt||||ƒ}n%||krct||||ƒ}n||fS(N(Rt_pad(ts1ts2tchartls1tls2((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyt_pad_until_equal¤s   cCsmt|ƒt|ƒ}}||kr>t||||ƒ}n%||krct||||ƒ}n||fS(N(Rt_lpad(R˜R™RšR›Rœ((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyR|­s   cCs |||S(N((RRštn((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyR—·scCs |||S(N((RRšRŸ((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyRž»scCst||dƒS(Ngà?(tint(Rt precision((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyRSÀsR;cBs&eZdZddd„Zd„ZRS(sñidentity_match([match][, mismatch]) -> match_fn Create a match function for use in an alignment. match and mismatch are the scores to give when two residues are equal or unequal. By default, match is 1 and mismatch is 0. iicCs||_||_dS(N(RR(R&RR((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyR/Ës cCs||kr|jS|jS(N(RR(R&tcharAtcharB((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyRHÎs (R#RIR%R/RH(((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyR;ÃsR<cBs#eZdZdd„Zd„ZRS(s¬dictionary_match(score_dict[, symmetric]) -> match_fn Create a match function for use in an alignment. score_dict is a dictionary where the keys are tuples (residue 1, residue 2) and the values are the match scores between those residues. symmetric is a flag that indicates whether the scores are symmetric. If true, then if (res 1, res 2) doesn't exist, I will use the score at (res 2, res 1). icCs||_||_dS(N(t score_dictt symmetric(R&R¤R¥((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyR/Þs cCs?|jr.||f|jkr.||}}n|j||fS(N(R¥R¤(R&R¢R£((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyRHás(R#RIR%R/RH(((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyR<Ós  R>cBs#eZdZdd„Zd„ZRS(s€affine_penalty(open, extend[, penalize_extend_when_opening]) -> gap_fn Create a gap function for use in an alignment. icCsG|dks|dkr'tdƒ‚n|||_|_||_dS(Nis%Gap penalties should be non-positive.(R?R RR0(R&R RR0((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyR/îscCst||j|j|jƒS(N(RkR RR0(R&tindextlength((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyRHós(R#RIR%R/RH(((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyR>ès cCs5|dkrdS|||}|s1||8}n|S(Ni((R§R RR0tpenalty((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyRk÷s   cCsþgtt|dƒƒD] }g^q}x`tt|ƒƒD]L}xCtt||ƒƒD]+}||jtt|||ƒƒƒqYWq<Wtt|ƒ}x\tt|ƒƒD]H}x>tt||ƒƒD]&}||}d||||fGqËWHq®WdS(sLprint_matrix(matrix) Print out a matrix. For debugging purposes. is%*s N(RaRRbtstrtmapRR(tmatrixRtmatrixTRBtjtndigitsRŸ((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pyt print_matrixÿs)- cCsig}|jd|ƒ|jdd|d||fƒ|jd|ƒ|jd|ƒdj|ƒS(suformat_alignment(align1, align2, score, begin, end) -> string Format the alignment prettily into a string. s%s s%s%s t t|s Score=%g R(RbR$(talign1talign2R_R€RR((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pytformat_alignments #Nt__((((($R%ttypestBioRRzRRGRPRORURQRR‘R}RR|R—Ržt _PRECISIONRSR;R<R>RkR¯R´t cpairwise2t ImportErrortsystmodulesR#t this_modulet__dict__tkeysR'R(((s€/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/pairwise2.pytLsD —  9 Q Š K