XfQ pdZddlZddlZddlmZddlmZGddeZGdd eZ d Z dS) zYClasses for the support of baseml. Maximum likelihood analysis of nucleotide sequences. N) _parse_baseml)PamlceZdZdZdS) BasemlErrorzDBASEML failed. Run with verbose=True to view BASEML's error message.N)__name__ __module__ __qualname____doc__5lib/python3.11/site-packages/Bio/Phylo/PAML/baseml.pyrrsNNNNr rc4eZdZdZd dZdZdZdZd d ZdS) Basemlz1An interface to BASEML, part of the PAML package.Nc :tj|||||.tj|st d||_d|_iddddddddddd dd dd dd dd dddddddddddddddddddddddd|_dS)zInitialize the Baseml 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. N'The specified tree file does not exist.z baseml.ctlnoisyverboserunmodemodel model_optionsMgenendataclock fix_kappakappa fix_alphaalphaMalphancatGfix_rhorhonparK)nhomogetSE RateAncestor Small_Diff cleandataicode fix_blengthmethod) r__init__ospathexistsFileNotFoundErrortreectl_file_options)self alignmentr1 working_dirout_files rr,zBaseml.__init__sR dI{H===  7>>$'' S'(QRRR $  T t  t  T  T  T   T  T    T    T  d  T  t 4! " T# $ 3    r c |t|jd5}|d|jd|d|jd|d|jd|jD]}|d |dd kr|dd krD|dd vr:|jd -|d |dd |jd h||dd|dd ddddS#1swxYwYdS)zDynamically build a BASEML control file from the options. The control file is written to the location specified by the ctl_file property of the baseml class. wz seqfile =  z outfile = z treefile = rNrrr) zmodel = z z = ) _set_rel_pathsopenr2write_rel_alignment _rel_out_file _rel_treer3items)r4 ctl_handleoptions rwrite_ctl_filezBaseml.write_ctl_fileDs  $- % % A   A$*=AAA B B B   @$*<@@@ A A A   =4>=== > > >---// A A!9$!9//!9''F1I,@,@}_5A"((TvayTTDM/4RTT!  F1I!?!?&)!?!?!?@@@@) A  A A A A A A A A A A A A A A A A A AsDD<<EEci}tj|std|t |5}|D]}|}|ddd}|dkrd|vrtd||d\}}|}|}|dkr||_|d kr||_ |d kr||_ ||j vrtd ||d krt|d kr-|rt||d <d|d<|dd}|dd } t||d <| |d<|d|vsd|vr# t#|} n5#t$$r|} Yn'wxYw t|} n#t$$r|} YnwxYw| ||< dddn #1swxYwY|j D]!}||vr|||j |<d|j |<"dS)zCParse a control file and load the options into the Baseml instance.zFile not found: *rr=z Malformed line in control file: seqfiletreefileoutfilezInvalid option: rNr .ze-)r-r.isfiler0r>stripsplitAttributeErrorr5r1r7r3KeyErrorlenisdigitint partitionfloat ValueError) r4r2 temp_optionsrDline uncommentedrEvalue model_num model_optconverted_values r read_ctl_filezBaseml.read_ctl_filefs w~~h''+ C#$Cx$C$CDD Dh( C:&'C'CD::<=H$> H  H$ H  H$$H(+H(ctj||j1tj|j|j|_dSdS)zMake file/directory paths relative to the PWD (PRIVATE). BASEML requires that all paths specified in the control file be relative to the directory from which it is called rather than absolute paths. N)rr=r1r-r.relpathr6rB)r4s rr=zBaseml._set_rel_pathssE D!!! 9 W__TY8HIIDNNN ! r FbasemlTc|jtdtj|jst dt j|||||rt|j SdS)akRun baseml using the current configuration. Check that the tree attribute is specified and exists, and then run baseml. If parse is True then read and return the result, otherwise return none. The arguments may be passed as either absolute or relative paths, despite the fact that BASEML requires relative paths. NzTree file not specified.r) r1r[r-r.r/r0rrunreadr7)r4r2rcommandparses rrhz Baseml.runsv 9 788 8w~~di(( O#$MNN N x'222  ' && &tr )NNNN)NFrfT) rr r r r,rFrcr=rhr r rrrsx;;' ' ' ' R A A AD3-3-3-j J J Jr rci}tj|stdt |5}|}dddn #1swxYwY|st dtj||\}}tj |||}| dt d|S)zParse a BASEML results file.zResults file does not exist.Nz[Empty results file. Did BASEML exit successfully? Run 'Baseml.run()' with 'verbose=True'.versionzInvalid results file) r-r.r/r0r> readlinesr[r parse_basicsparse_parametersget) results_fileresultshandlelines num_paramss rririsG 7>>, ' '@ >??? l  #v  ""###############   6   *6ugFFWj,UGZHHG{{9%/000 NsA!!A%(A%) r r-os.pathrIr_pamlrEnvironmentErrorrrrir r rrzs  OOOOO"OOO_____T___Dr