o Rŀgd@sPdZddlZddlmZddlmZGdddeZGdd d eZ d d Z dS) zClasses for the support of yn00. Yang and Nielsen 2000, estimating synonymous and nonsynonymous substitution rates in pairwise comparison of protein-coding DNA sequences. N) _parse_yn00)Pamlc@seZdZdZdS) Yn00Errorz@yn00 failed. Run with verbose=True to view yn00's error message.N)__name__ __module__ __qualname____doc__r r G/var/www/html/myenv/lib/python3.10/site-packages/Bio/Phylo/PAML/yn00.pyrsrc@s4eZdZdZdddZddZddZdd d ZdS)Yn00z/An interface to yn00, part of the PAML package.NcCs,t||||d|_dddddd|_dS)zInitialize the Yn00 instance. The user may optionally pass in strings specifying the locations of the input alignment, the working directory and the final output file. zyn00.ctlN)verboseicode weighting commonf3x4ndata)r__init__ctl_file_options)self alignment working_dirout_filer r r rs z Yn00.__init__cCs|t|jd;}|d|jd|d|jd|jD]}|ddur-q$||dd|ddq$WddS1sHwYdS) zDynamically build a yn00 control file from the options. The control file is written to the location specified by the ctl_file property of the yn00 class. wz seqfile =  z outfile = rNrz = )_set_rel_pathsopenrwrite_rel_alignment _rel_out_fileritems)r ctl_handleoptionr r r write_ctl_file,s  "zYn00.write_ctl_filec Csni}tj|std|t|}|D]x}|}|ddd}|dkrd|vr3td||d\}}|}|}|dkrJ||_q|d krR||_ q||j vr^t d |d |vsfd |vrxzt |}Wnt yw|}Ynwzt|}Wn t y|}Ynw|||<qWd n1swY|j D]}||vr|||j |<qd |j |<qd S)zAParse a control file and load the options into the yn00 instance.zFile not found: *rr=z Malformed line in control file: seqfileoutfilezInvalid option: .ze-N)ospathisfileFileNotFoundErrorrstripsplitAttributeErrorrrrKeyErrorfloat ValueErrorint) rr temp_optionsr!line uncommentedr"valueconverted_valuer r r read_ctl_file?sR         zYn00.read_ctl_fileFyn00TcCs"t|||||rt|jSdS)zRun yn00 using the current configuration. If parse is True then read and return the result, otherwise return None. N)rrunreadr)rrr commandparser r r r<is zYn00.run)NNN)NFr;T)rrrr rr#r:r<r r r r r s  *r c Csi}tj|s tdt| }|}Wdn1swY|s*tdt|D]>\}}d|vr;|d}q.d|vrPt ||||\}}|d}q.d|vrlt |||||}t ||dd||}q.|sstd|S) zParse a yn00 results file.zResults file does not exist.NzWEmpty results file. Did YN00 exit successfully? Run 'Yn00.run()' with 'verbose=True'.z(A) Nei-Gojobori (1986) methodrz (B) Yang & Nielsen (2000) methodz(C) LWL85, LPB93 & LWLm methodszInvalid results file.) r*r+existsr-r readlinesr3 enumerater parse_ng86 parse_yn00 parse_others) results_fileresultshandlelinesline_numr6 ng86_start sequences yn00_startr r r r=us:      r=) r os.pathr*r%r_pamlrEnvironmentErrorrr r=r r r r s   ]