o RŀgR@sbdZddlZedZddZddZdd Zd d Zd d ZddZ ddZ ddZ ddZ dS)z)Methods for parsing codeml results files.Nz -*\d+\.\d+cCsbd}d}td}td}td}td}td}|D]} t| } dd| D} || } | d ur>| d |d <q|| } | d urN| d |d <|| }|d ursg|d <t|d }t|D] }|d  iqfd}q|| }|d ur|d |d<q|| }|d ur|d }|dkr||d<d}nd}d| vr| r| d|d<q|||fS)zOParse the basic information that should be present in most codeml output files.Fz'.+ \(in paml version (\d+\.\d+[a-z]*).*z Model:\s+(.+)z!\(([0-9]+) genes: separate data\)z"Codon frequenc[a-z\s]{3,7}:\s+(.+)zSite-class models:\s*([^\s]*)cSg|]}t|qSfloat.0valrrP/var/www/html/myenv/lib/python3.10/site-packages/Bio/Phylo/PAML/_parse_codeml.py !z parse_basics..NversionmodelgenesTz codon modelsite-class modelzln LmaxrzlnL max) recompileline_floats_refindallmatchgroupsearchintrangeappend)linesresults multi_models multi_genes version_remodel_re num_genes_re codon_freq_re siteclass_relineline_floats_res line_floats version_res model_res num_genes_res num_genesncodon_freq_res siteclass_ressiteclass_modelrrr parse_basicssP                r0cCsi}td}td}|d}|s|durd}dddd d d d d |}|r|d} d} d} d} t|D]1\} }||}|rf| durY| dusJJt|| | | | | | d<| } t|d} d|i} q5t| | ddkrt|| d| } | | | d<nWd|i} t|| } | ||<nId}d}t|D],\} }||}|r|durt||| | | ||<| }t|d}d|di} q||durt||d| } | ||<t|dkr|d}|rt|dkr||d<|St|dkr||d<|S)z:Determine which NSsites models are present and parse them.zModel (\d+):\s+(.+)zGene\s+([0-9]+)\s+.+rN one-ratiorr )r1 NearlyNeutralPositiveSelectiondiscretebetazbeta&w>1M2a_relr descriptionNSsites) rrget enumerater parse_modelrrlen)rrrrns_sitesr!gene_rer/ current_modelr current_gene gene_start model_resultsline_numr%gene_res model_startr)m0rrr parse_nssitesLs~              rLc Csi}d}d}d}d}d}td}td} td} |D]B} t| } dd| D} | | }| | }d| vrT| rT| d |d <td | }|durSt|d }qt| |krc|sc| |d <qd| vrjd}q|r{t| |kr{| |d<d}qd| vr| r| d |d<q|| durd| vsd| vr|r| |d<d}q|r| |d<d}q|r| |d<d}q| |d<qd| vrd}qd| vrd}qd| vrd}qd| vr| r| d d| |d<qd| vr| r| d |d <qd!| vr| r| d |d"<qd#| vr | r | |d"<qd$| vr6ttd%| d }| d&dur(i|d&<| d | d d'|d&|<qd(| vrE| rE| d |d)<qd*| vrT| rT| d |d+<q| d d,d-ksf| d d.d/krot | }||d0<q| d d,d1kr| d0}t | |}||d0<qd2| vrtd3| }|r| d0}t|d }t || |}||d0<q| d d4d5kr| d0}td| |}||d0<q| d d4d6kr| d0}td| |}||d0<q|durA| rA|d }| d7duri|d7<| d d}t|d t|d t|d,t|d8t|d9t|d:t|d;t|d<d=|d7|<q|r`g}|D]}||d t|d fqH|t|q|rh||d><|S)?z,Parse an individual NSsites model's results.FNz^\([\w #:',.()]*\);\s*$z\s+(\d+\.\.\d+)[\s+\d+\.\d+]+z"(?.z lnL(ntime:rlnLz!lnL\(ntime:\s+\d+\s+np:\s+(\d+)\)r zparameter listzSEs for parameters:TSEsz tree length =z tree length:#zdS treezdN treez omega treetreezdS tree:zdN tree:z w ratios as labels for TreeView:z rates forg?ratesz kappa (ts/tv)kappaz omega (dN/dS)omegaz w (dN/dS)zgene # z gene # (\d+)r)rSrTztree length for dNdNztree length for dSdSr2zp: proportionz site classeszw:z branch type zbranch type (\d) z foreground wz background wbranchesr3r4)tNSrTrUrVzN*dNzS*dS parameters)rrrrrrrrAstripinsertr>parse_siteclass_proportionsparse_siteclass_omegasparse_clademodelcparse_branch_site_asplitrrupdatedict)rrraSEs_flag dS_tree_flag dN_tree_flag w_tree_flag num_paramstree_re branch_remodel_params_rer%r&r' branch_res model_paramsnp_resgene_num site_classes branch_typebranch_type_nobranchparamsfloat_model_paramsparamrrr r@s                       $              r@cCs.i}|rtt|D] }d||i||<q |S)zFind proportion of alignment assigned to each class. For models which have multiple site classes, find the proportion of the alignment assigned to each class. rX)rrA)r'rwr,rrr rdRs rdcCsFtd|}|rt|dkrdStt|D] }||||d<q|S)zFind omega estimate for each class. For models which have multiple site classes, find the omega estimated for each class. z\d{1,3}\.\d{5}rNrT)rrrAr)r%rwr'r,rrr re_s recCs\|rt|dkr dStt|D]}||ddur!i||d<||||d|<q|S)z,Parse results specific to the clade model C.rN branch typesrArr>)ryr'rwr,rrr rfrs rfcCsv|rt|dkr dStt|D](}||ddur!i||d<|r.||||dd<q||||dd<q|S)z2Parse results specific to the branch site A model.rNr~ foreground backgroundr)rr'rwr,rrr rg}s rgc Cs8td}i}d}d}|D]}t|}dd|D}||} | r<| d}| d}||vr4i||<||vr.r r2rMrr]r3r[r\)r^r`r_rTrUrVpairwise)rrrrrrrAri) rrpair_rerseq1seq2r%r&r'pair_resrrr parse_pairwisesB       rc Csri}g}d}d}td}|D]}t|}dd|D} d|vr&d}d}nd|vr.d}d}||} | r|s9|r| d} | |vrI|| |r~|d d urVi|d <i|d | <t t | D]} | | |d | || <| | |d || | <qbq|d d uri|d <i|d | <t t | D]} | | |d | || <| | |d || | <qq|r||d <|S) z+Parse amino acid sequence distance results.Fz (.+)\s{5,15}cSrrrrrrr r r z#parse_distances..z AA distancesTzML distances of aa seqs.r rawNml distances) rrrrrrrbrr>rrA) rrr sequencesraw_aa_distances_flagml_aa_distances_flag matrix_row_rer%r&r'matrix_row_resseq_nameirrr parse_distancessJ       r) __doc__rrrr0rLr@rdrerfrgrrrrrr s =P7   -