ó ÊïLc@sûddlmZddlmZmZddlmZmZddlZddl m Z d„Z d„Z d„Z d „Zd „Zd „Zd „Zd „Zd„Zd„Zd„Zedd„Zdd„Zd„Zd„Zddd„ZdS(iÿÿÿÿ(tsqrt(targvtexit(tseptmkdirN(tbuiltin_tpl_dircCsŠ|}tjd|tjƒ}xe|r…tt|jƒdƒƒ}|jd|jƒdd|dƒ}tjd|tjƒ}q!W|S(Ns !!!(.*?)!!!is!!!i(tretsearcht MULTILINEtstrtevaltgroupstreplace(ttemplatetexecuted_templatetmatcht exec_result((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pyt exec_templates  cCs1|gkrÀ|}|}xJ|D]B}|\}}|dt|ƒ7}|jd|t|ƒƒ}qWt|ddƒ} t|ƒ} | jddƒjddƒ} | j| ƒ| jƒ|gS|d\}} g} xP| D]H}||fg}|j|ƒt|||d |ƒ}| j|ƒqÝW| SdS( Nt_t?s.partws s s ii(R R topenRtwritetclosetextendt process_para(t in_stringtout_file_prefixt para_listt curr_valuesR tf_namettuptnametvaltfRtclean_templatetrngtfnamest new_valuest more_names((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pyRs*         cCs6d}x)td|dƒD]}||d7}qW|S(Ntis (trange(tmotifttimestret_strti((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytdupe9scCs&|d|}|d|}||fS(Ni((tx_maxty_maxtpostytx((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytget_xy_from_matrix?sc Csft|||ƒ\}}t|||ƒ\}}||d||ddkr^t|ƒdSdSdS(Niit s0 (R4R ( R/R0R3R2tmigtmy_xtmy_ytother_xtother_y((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pyt get_step_2dDs  c Cstd}xgtd||dƒD]N}x;td||dƒD]"}|t|||||ƒ7}q<W|d7}qW|S(NR(is (R)R;(R/R0R6tmig_matR3R2((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytgenerate_ssm2d_matMs  cCsd}xttd|dƒD]_}xLtd|dƒD]7}||krS|d7}q4|dt|ƒd7}q4W|d7}qW|S(NR(is0 s!!!s!!! s (R)R (t total_sizeR6R<R3R2((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytgenerate_island_matUs  cCsZd}xMtd|dƒD]8}x%td|dƒD]}|d7}q4W|d7}qW|S(NR(is0 s (R)(R>tnull_matR3R2((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytgenerate_null_mat`s cCsŠd}x=td|dƒD](}|t|ƒdt|ƒd7}qW|t|ƒdt|dƒdtd|||ƒd7}|S(NR(iR5s 0 1 1 0 1 s 0 1 gð?s 0 1 (R)R (ttR>t join_sizet orig_sizeteventsR-((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytgenerate_join_eventshs &@cCs|S(N((R((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pyt no_processoroscCs||ƒ}t|||gƒS(N(R(RRRRtspecific_processorttext((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pyt process_textrs t.cCs7|jƒ}tj||gƒ}t|||g|ƒS(N(treadRtjoinRJ(t par_streamt out_prefixtparamsRHtout_dirRIR((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytgenerate_modelƒs cCs™|dkr1ttjt|dgƒdƒ}n"ttj||dgƒdƒ}|jƒ}x)|dkrŠ|j|ƒ|jƒ}qbW|jƒdS(s Gets a demograpy template. Most probably this model needs to be sent to GenCases. stream - Writable stream. param - Template file. tp_dir - Directory where to find the template, if None use an internal template s.partrR(N(tNoneRRRMRtreadlineRR(tstreamtmodelttp_dirR"tl((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytget_demography_template‹s %"  c Cs‡|jdƒ|jtt|ƒƒdƒ|jdƒxI|D]A}|jdj|dgtd„t|dƒƒƒdƒq>WdS(Ns4//Number of contiguous linkage blocks in chromosome s sj//Per Block: Data type, No. of loci, Recombination rate to the right-side locus, plus optional parameters R5icSs t|ƒS(N(R (R3((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pyt¨si(RR tlenRMtmaptlist(RVtlocitlocus((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pyt _gen_loci¢s   cCsàtd„|dƒ}|jdƒt|ƒdks@|dkrZ|jt|ƒdƒn|jt|ƒdƒxh|D]`}|d}|d}t|ƒdkr´t||ƒqxx!t|ƒD]}t||ƒqÁWqxWdS(s³ Writes a Simcoal2 loci template part. stream - Writable stream. chr - Chromosome list. Current loci list: [(chr_repeats,[(marker, (params))])] chr_repeats --> Number of chromosome repeats marker --> 'SNP', 'DNA', 'RFLP', 'MICROSAT' params --> Simcoal2 parameters for markers (list of floats or ints - if to be processed by generate_model) cSs ||dS(Ni((R3R2((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pyR[¹sisº//Number of independent (unlinked) chromosomes, and "chromosome structure" flag: 0 for identical structure across chromosomes, and 1 for different structures on different chromosomes. is 1 s 0 N(treduceRR\R RaR)(RVtchrstnum_chrstchrtrepeatsR_R-((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytget_chr_template«s    cCsyt|tddƒ}t|||ƒt||ƒ|jƒt|tddƒ}t|||d|ƒ|jƒdS(sT Writes a complete SimCoal2 template file. This joins together get_demography_template and get_chr_template, which are feed into generate_model Please check the three functions for parameters (model from get_demography_template, chrs from get_chr_template and params from generate_model). stmp.parRRSRQN(RRRZRgRRR(RWRcRPRQRXRVRN((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pytgenerate_simcoal_from_templateÈs   (tmathRtsysRRtosRRRtBio.PopGen.SimCoalRRRR.R4R;R=R?RARFRGRJRRRTRZRaRgRh(((s<C:\Python27\Lib\site-packages\Bio\PopGen\SimCoal\Template.pyts(