o Rŀg @sfdZddlmZddlmZddlmZddlmZGdddeZedkr1dd lm Z e d Sd S) zJCommand line wrapper for the multiple sequence alignment program MSAProbs.) _Argument)_Option)_Switch)AbstractCommandlinec@seZdZdZdddZdS)MSAProbsCommandlineaVCommand line wrapper for MSAProbs. http://msaprobs.sourceforge.net Notes ----- Last checked against version: 0.9.7 References ---------- Yongchao Liu, Bertil Schmidt, Douglas L. Maskell: "MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities". Bioinformatics, 2010, 26(16): 1958 -1964 Examples -------- >>> from Bio.Align.Applications import MSAProbsCommandline >>> in_file = "unaligned.fasta" >>> out_file = "aligned.cla" >>> cline = MSAProbsCommandline(infile=in_file, outfile=out_file, clustalw=True) >>> print(cline) msaprobs -o aligned.cla -clustalw unaligned.fasta You would typically run the command line with cline() or via the Python subprocess module, as described in the Biopython tutorial. msaprobscKstgdddddtddgdd d d td d gdtddgddd d tgdddd d tddgdtddgdddtgddtdd gd!td"gd#ddg |_tj||fi|d$S)%zInitialize the class.)z-oz --outfileoutfilez0specify the output file name (STDOUT by default)TF)filenameequatez -num_threads numthreadszFspecify the number of threads used, and otherwise detect automaticallycSs t|tS)N isinstanceintxrT/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/Applications/_MSAProbs.py9s z.MSAProbsCommandline.__init__..)checker_functionz -clustalwclustalwz2use CLUSTALW output format instead of FASTA formatz-c consistencyzDuse 0 <= REPS <= 5 (default: 2) passes of consistency transformationcS"t|tod|kodkSS)Nrr rrrrrB")z-irz--iterative-refinementiterative_refinementzBuse 0 <= REPS <= 1000 (default: 10) passes of iterative-refinementcSr)Nrir rrrrrGrz-vverbosez-report progress while aligning (default: off)z-annotannotz3write annotation for multiple alignment to FILENAME)r )z-az--alignment-orderalignment_orderzIprint sequences in alignment order rather than input order (default: off)z-versionversionzprint out version of MSAPROBSinfilezMultiple sequence input fileN)rrr parametersr__init__)selfcmdkwargsrrrr!,sN  'zMSAProbsCommandline.__init__N)r)__name__ __module__ __qualname____doc__r!rrrrrsr__main__) run_doctestN) r(Bio.Applicationrrrrrr% Bio._utilsr*rrrrs    J