Xf"hdZddlZddlmZddlmZGddeZGdd eZ d Z dS) zaClasses for the support of CODEML. Maximum likelihood analysis using codon substitution models. N) _parse_codeml)PamlceZdZdZdS) CodemlErrorzDCODEML failed. Run with verbose=True to view CODEML's error message.N)__name__ __module__ __qualname____doc__5lib/python3.11/site-packages/Bio/Phylo/PAML/codeml.pyrrsNNNNr rc:eZdZdZd dZdZdZdZdZd d Z dS)Codemlz1An interface to CODEML, part of the PAML package.NcBtj|||||.tj|st d||_d|_iddddddddddd dd dd dd dd dddddddddddddddddddddddddddd |_dS)atInitialize the codeml instance. The user may optionally pass in strings specifying the locations of the input alignment and tree files, the working directory and the final output file. Other options found in the CODEML control have typical settings by default to run site class models 0, 1 and 2 on a nucleotide alignment. N'The specified tree file does not exist.z codeml.ctlnoisyverboserunmodeseqtype CodonFreqndataclockaaDist aaRatefilemodelNSsitesicodeMgene fix_kappakappa fix_omegaomega) fix_alphaalphaMalphancatGgetSE RateAncestor Small_Diff cleandata fix_blengthmethodrhofix_rho) r__init__ospathexistsFileNotFoundErrortreectl_file_options)self alignmentr5 working_dirout_files rr0zCodeml.__init__s^ dI{H===  7>>$'' S'(QRRR $  T t  t  t    T   T  d  $  T  t  T  T    T ! " T# $ ;    r c~|t|jd5}|d|jd|d|jd|d|jd|jD]}|d |dd krGd d |dD}||dd |d^||dd |dd ddddS#1swxYwYdS) zDynamically build a CODEML control file from the options. The control file is written to the location specified by the ctl_file property of the codeml class. wz seqfile =  z outfile = z treefile = rNrr c34K|]}t|VdSNstr.0sites r z(Codeml.write_ctl_file.._s(&G>s4yy&G&G&G&G&G&Gr  = ) _set_rel_pathsopenr6write_rel_alignment _rel_out_file _rel_treer7itemsjoin)r8 ctl_handleoptionrs rwrite_ctl_filezCodeml.write_ctl_fileIs  $- % % E   A$*=AAA B B B   @$*<@@@ A A A   =4>=== > > >---// E E!9$!9 ))"hh&G&GVAY&G&G&GGGG$$q %A%Ag%A%A%ABBBB$$q %C%CfQi%C%C%CDDDD E  E E E E E E E E E E E E E E E E E EsC:D22D69D6c bi}tj|std|t |5}|D]}|}|ddd}|dkrld|vrtd||dd\}}|}|}|dkr||_|d kr||_ |d kr||_ |d kr{|d }tt|D]B} t|| || <#t$rtd || dwxYw||d <<||jvrt#d|d|vr# t%|} n5#t$r|} Yn'wxYw t|} n#t$r|} YnwxYw| ||< dddn #1swxYwY|jD]!}||vr|||j|<d|j|<"dS)zCParse a control file and load the options into the Codeml instance.zFile not found: *rr=z Malformed line in control file: seqfiletreefileoutfilerr?zInvalid site class: NzInvalid option: .)r1r2isfiler4rJstripsplitAttributeErrorr9r5r;rangelenint ValueError TypeErrorr7KeyErrorfloat) r8r6 temp_optionsrQline uncommentedrRvalue site_classesnconverted_values r read_ctl_filezCodeml.read_ctl_fileds w~~h'', C#$Cx$C$CDD Dh) C:&(C(CD::<G;GG;GG; G$!G;#G$$ G;;G?G?c&|jD]v}|ddkrH|d@dd|dD}t|dd|Vt|dd|dwdS)z8Print out all of the options and their current settings.rrrNr?c34K|]}t|VdSrArBrDs rrGz'Codeml.print_options..s("C"C3t99"C"C"C"C"C"Cr rH)r7rOrPprint)r8rRrs r print_optionszCodeml.print_optionssm))++ 4 4FayI%%&)*?(("C"C"C"C"CCC00w00111122vay223333 4 4r ctj||j1tj|j|j|_dSdS)zMake all file/directory paths relative to the PWD (PRIVATE). CODEML requires that all paths specified in the control file be relative to the directory from which it is called rather than absolute paths. N)rrIr5r1r2relpathr:rN)r8s rrIzCodeml._set_rel_pathssE D!!! 9 W__TY8HIIDNNN ! r FcodemlTc|jtdtj|jst dt j|||||rt|j SdS)aRun codeml using the current configuration. If parse is True then read and return the results, otherwise return None. The arguments may be passed as either absolute or relative paths, despite the fact that CODEML requires relative paths. NzTree file not specified.r) r5rcr1r2r3r4rrunreadr;)r8r6rcommandparses rrwz Codeml.runsv 9 788 8w~~di(( O#$MNN N x'222  ' && &tr )NNNN)NFruT) rr r r r0rSrnrrrIrwr r rrrs;;- - - - ^EEE64-4-4-l 4 4 4 J J Jr rci}tj|stdt |5}|}dddn #1swxYwY|st dtj||\}}}tj ||||}tj ||}tj ||}|st d|S)zParse a CODEML results file.zResults file does not exist.Nz[Empty results file. Did CODEML exit successfully? Run 'Codeml.run()' with 'verbose=True'.zInvalid results file) r1r2r3r4rJ readlinesrcr parse_basics parse_nssitesparse_pairwiseparse_distances) results_fileresultshandlelines multi_models multi_geness rrxrxs.G 7>>, ' '@ >??? l  #v  ""###############   6   ,9+EeW+U+U(WlK)%, TTG*5'::G+E7;;G 1/000 NsA!!A%(A%) r os.pathr1rVr_pamlrEnvironmentErrorrrrxr r rrs OOOOO"OOOjjjjjTjjjZr