o Rŀg@s6dZddlZddlZGdddeZGdddZdS)zPBase class for the support of PAML, Phylogenetic Analysis by Maximum Likelihood.Nc@seZdZdZdS) PamlErrorzKpaml has failed. Run with verbose=True to view the error message. N)__name__ __module__ __qualname____doc__rrH/var/www/html/myenv/lib/python3.10/site-packages/Bio/Phylo/PAML/_paml.pyrsrc@sZeZdZdZdddZddZddZd d Zd d Zd dZ ddZ ddZ ddZ dS)Pamlz&Base class for wrapping PAML commands.NcCsL|dur t|_n||_|durtj|std||_||_i|_dS)zInitialize the class.N,The specified alignment file does not exist.) osgetcwd working_dirpathexistsFileNotFoundError alignmentout_file_options)selfrr rrrr__init__s   z Paml.__init__cCdS)zWrite control file.Nrrrrrwrite_ctl_file%zPaml.write_ctl_filecCr)zRead control file.Nrrrrr read_ctl_file(rzPaml.read_ctl_filecCs.|jD]}t|dd|dqdS)z8Print out all of the options and their current settings.rz = N)ritemsprintroptionrrr print_options+szPaml.print_optionscKs6|D]\}}||jvrtd|||j|<qdS)zSet the value of an option. This function abstracts the options dict to prevent the user from adding options that do not exist or misspelling options. Invalid option: N)rrKeyError)rkwargsrvaluerrr set_options0s    zPaml.set_optionscCs"||jvr td||j|S)zReturn the value of an option.r!)rr"getrrrr get_option<s   zPaml.get_optioncCst|jS)z%Return the values of all the options.)listrrrrrrget_all_optionsCszPaml.get_all_optionscCs^|jdur tj|j|_|jdurtj|j|j|_|jdur-tj|j|j|_dSdS)aConvert all file/directory locations to paths relative to the current working directory (PRIVATE). paml requires that all paths specified in the control file be relative to the directory from which it is called rather than absolute paths. N) r r rrelpath_rel_working_dirr_rel_alignmentr _rel_out_filerrrr_set_rel_pathsGs   zPaml._set_rel_pathscCs6|jdur tdtj|jstd|jdurtd|jdur&tdt}tj|js7t |jt |j|durI| |j }n tj|sStd|r]t ||g}nttj}t j||g||d}Wdn1swwYt ||dkrtd ||f|dkrtd ||fdS) a~Run a paml program using the current configuration. Check that the class attributes exist and raise an error if not. Then run the command and check if it succeeds with a return code of 0, otherwise raise an error. The arguments may be passed as either absolute or relative paths, despite the fact that paml requires relative paths. NzAlignment file not specified.r zOutput file not specified.z Working directory not specified.z*The specified control file does not exist.)stdoutstderrrzM%s has failed (return code %i). Run with verbose = True to view error messagez+The %s process was killed (return code %i).)r ValueErrorr rrrrr r mkdirchdirrctl_file subprocesscallopendevnullrOSError)rr4verbosecommandcwd result_codednrrrrunUsD         zPaml.run)NNN) rrrrrrrr r%r'r)r.r?rrrrr s    r )rr r5EnvironmentErrorrr rrrrs