ó ¤ï Ic@sRddlZddlZddlmZddlmZdefd„ƒYZdS(iÿÿÿÿN(t RanaConfig(t complementt PrintFormatcBsòeZdZejZejZejZeeZeeZej Z eeZ d„Z dd„Z ddd„Z gdgdd„Zd„Zd„Zd „Zd „Zgdd „Zgdd „Zgdd „Zgdd„Zd„ZRS(sBPrintFormat allow the printing of results of restriction analysis.cCsdS(s)PrintFormat() -> new PrintFormat InstanceN((tself((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyt__init__EstlistcCsF|dkr|j|_n'|dkr6|j|_n |j|_dS(skPF.print_as([what='list']) -> print the results as specified. Valid format are : 'list' -> alphabetical order 'number' -> number of sites in the sequence 'map' -> a map representation of the sequence with the sites. If you want more flexibility over-ride the virtual method make_format. tmaptnumberN(t _make_mapt make_formatt _make_numbert _make_list(Rtwhat((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pytprint_asIs   tcCs€|s|j}ngg}}xC|jƒD]5\}}|rT|j||fƒq,|j|ƒq,W|j||||ƒGHdS(sÒPF.print_that(dct, [title[, s1]]) -> Print dct nicely formatted. dct is a dictionary as returned by a RestrictionBatch.search() title is the title of the map. It must be a formated string, i.e. you must include the line break. s1 is the title separating the list of enzymes that have sites from those without sites. s1 must be a formatted string as well. The format of print_that is a list.N(tresultst iteritemstappendR (Rtdctttitlets1tlstnctktv((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyt print_that]s   cCs|j||||ƒS(sÇPF.make_format(cut, nc, title, s) -> string Virtual method. Here to be pointed to one of the _make_* methods. You can as well create a new method and point make_format to it.(R (RtcutRRR((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyR uscCs |j||ƒ|j||ƒS(s|PF._make_number(ls,title, nc,s1) -> string. return a string of form : title. enzyme1 : position1, position2. enzyme2 : position1, position2, position3. ls is a list of cutting enzymes. title is the title. nc is a list of non cutting enzymes. s1 is the sentence before the non cutting enzymes.(t_make_list_onlyt_make_nocut_only(RRRRR((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyR scCs |j||ƒ|j||ƒS(s¡PF._make_number(ls,title, nc,s1) -> string. return a string of form : title. enzyme1, position | AAAAAAAAAAAAAAAAAAAAA... ||||||||||||||||||||| TTTTTTTTTTTTTTTTTTTTT... ls is a list of cutting enzymes. title is the title. nc is a list of non cutting enzymes. s1 is the sentence before the non cutting enzymes.(t_make_map_onlyR(RRRRR((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyRscCs |j||ƒ|j||ƒS(s§PF._make_number(ls,title, nc,s1) -> string. title. enzyme which cut 1 time : enzyme1 : position1. enzyme which cut 2 times : enzyme2 : position1, position2. ... ls is a list of cutting enzymes. title is the title. nc is a list of non cutting enzymes. s1 is the sentence before the non cutting enzymes.(t_make_number_onlyR(RRRRR((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyR ¢scCs||j||ƒS(sePF._make_nocut(ls,title, nc,s1) -> string. return a formatted string of the non cutting enzymes. ls is a list of cutting enzymes -> will not be used. Here for compatibility with make_format. title is the title. nc is a list of non cutting enzymes. s1 is the sentence before the non cutting enzymes.(R(RRRRR((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyt _make_nocut¶s c Cs³|s |S|jƒd}|p#d}dj}xh|D]`}||tjt|ƒ|jƒfƒ}t|ƒ|jkr6|||dfƒ}d}q6q6W|||dfƒ}|S(sßPF._make_nocut_only(nc, s1) -> string. return a formatted string of the non cutting enzymes. nc is a list of non cutting enzymes. s1 is the sentence before the non cutting enzymes. Rs, Enzymes which do not cut the sequence. s (tsorttjointstrtljustt NameWidthtlentlinesize( RRRRRtstt stringsitetJointkey((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyRÃs    ' cCs|s |S|j||ƒS(sJPF._make_list_only(ls, title) -> string. return a string of form : title. enzyme1 : position1, position2. enzyme2 : position1, position2, position3. ... ls is a list of results. title is a string. Non cutting enzymes are not included.(t_PrintFormat__next_section(RRRRR((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyRÙsc CsÎ|s |S|jd„ƒt|ƒ}d}g}x{|D]s\}} t| ƒ} | |kr™|d|7}|j||ƒ}|| fg| }}q9n|j|| fƒq9W|d|7}|j||ƒS(s§PF._make_number_only(ls, title) -> string. return a string of form : title. enzyme which cut 1 time : enzyme1 : position1. enzyme which cut 2 times : enzyme2 : position1, position2. ... ls is a list of results. title is a string. Non cutting enzymes are not included.cSs!tt|dƒt|dƒƒS(Ni(tcmpR%(txty((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pytsis enzymes which cut %i times : (R titerR%R+R( RRRRRtiteratortcur_lentnew_secttnametsitestl((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyRës    c! Cs9|s |Sg|D]\}}t|ƒ^q}|jƒ|pBd}i} x^|D]V\} } xG| D]?} | | kr‘| | jt| ƒƒqet| ƒg| | string. return a string of form : title. enzyme1, position | AAAAAAAAAAAAAAAAAAAAA... ||||||||||||||||||||| TTTTTTTTTTTTTTTTTTTTT... ls is a list of results. title is a string. Non cutting enzymes are not included. Rii<t|t i;s iiis (ii( R"R RtkeysR%tsequencetxrangetindexttostringRR!R#trjust(!RRRRRR-R.t resultKeysRt enzymemaptenzymeRtctmappingtcutloctcountertlengthR6R*R:t revsequencetatbaset emptylineR)tlinetstntlineotline2tlinetotRtmapunit((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyRs°%                   )$' #'   )$'%!cCs,|jƒd|j|jd}|j|j}tjd|ƒ}ddj}}xÐ|D]È\}} d} |djg| D]} t| ƒ^q~ƒdfƒ} t | ƒ|krñgtj || ƒD]} | j ƒ^qÇ} |j| ƒ} n| } ||t|ƒj |jƒd| dfƒ}q\W|S(smFP.__next_section(ls, into) -> string. ls is a list of tuple (string, [int, int]). into is a string to which the formatted ls will be added. Format ls as a string of lines : The form is : enzyme1 : position1. enzyme2 : position2, position3. then add the formatted ls to tot return tot.s R8s([\w,\s()]){1,%i}[,\.]Rs, t.s : ( R R$tIndentR&tMaxSizetretcompileR!R"R%tfinditertgroupR#(RRtintot indentationR&tpattseveralR)R4R5R(tsiteR6R-((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyt__next_section}s 4++(t__name__t __module__t__doc__tRanaConft ConsoleWidthR$RTtCmodulot PrefWidthRSR&RR RR R RR RRRRRR+(((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyR:s*             %m( RUt itertoolstBio.RestrictionRRbtBio.Restriction.DNAUtilsRtobjectR(((sŽ/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/Restriction/PrintFormat.pyt s  ,