o Rŀg@sfdZddlmZddlmZddlmZddlmZGdddeZedkr1dd lm Z e d Sd S) zACommand line wrapper for the multiple alignment program PROBCONS.) _Argument)_Option)_Switch)AbstractCommandlinec@seZdZdZdddZdS)ProbconsCommandlineaCommand line wrapper for the multiple alignment program PROBCONS. http://probcons.stanford.edu/ Notes ----- Last checked against version: 1.12 References ---------- Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. Examples -------- To align a FASTA file (unaligned.fasta) with the output in ClustalW format, and otherwise default settings, use: >>> from Bio.Align.Applications import ProbconsCommandline >>> probcons_cline = ProbconsCommandline(input="unaligned.fasta", ... clustalw=True) >>> print(probcons_cline) probcons -clustalw unaligned.fasta You would typically run the command line with probcons_cline() or via the Python subprocess module, as described in the Biopython tutorial. Note that PROBCONS will write the alignment to stdout, which you may want to save to a file and then parse, e.g.:: stdout, stderr = probcons_cline() with open("aligned.aln", "w") as handle: handle.write(stdout) from Bio import AlignIO align = AlignIO.read("aligned.fasta", "clustalw") Alternatively, to parse the output with AlignIO directly you can use StringIO to turn the string into a handle:: stdout, stderr = probcons_cline() from io import StringIO from Bio import AlignIO align = AlignIO.read(StringIO(stdout), "clustalw") probconscKstddgdtgdddddd tgd d d ddd tgd ddddd tddgdtddgdtddgdtddgdddtgddddtgdd tgd!d"ddtgd#d$td%gd&d'd'd(g |_tj||fi|d)S)*zInitialize the class.z -clustalwclustalwz)Use CLUSTALW output format instead of MFA)z-ccz --consistency consistencyzDUse 0 <= REPS <= 5 (default: 2) passes of consistency transformationcS |tdvS)NrangexrT/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/Applications/_Probcons.pyM z.ProbconsCommandline.__init__..F)checker_functionequate)z-irz--iterative-refinementziterative-refinementirzCUse 0 <= REPS <= 1000 (default: 100) passes of iterative-refinementcSr )Nir rrrrrSr)z-prez--pre-trainingz pre-trainingprez6Use 0 <= REPS <= 20 (default: 0) rounds of pretrainingcSr )Nr rrrrrYrz-pairspairsz&Generate all-pairs pairwise alignmentsz-viterbiviterbizJUse Viterbi algorithm to generate all pairs (automatically enables -pairs)z-verboseverbosez-Report progress while aligning (default: off)z-annotannotz3Write annotation for multiple alignment to FILENAME)r)z-ttz--traintrainzMCompute EM transition probabilities, store in FILENAME (default: no training))z-eez --emissions emissionsz5Also reestimate emission probabilities (default: off))z-ppz --paramfile paramfilezRead parameters from FILENAME)z-az--alignment-orderzalignment-orderazIPrint sequences in alignment order rather than input order (default: off)inputz>Input file name. Must be multiple FASTA alignment (MFA) formatT)filename is_requiredN)rrr parametersr__init__)selfcmdkwargsrrrr)?sx EzProbconsCommandline.__init__N)r)__name__ __module__ __qualname____doc__r)rrrrrs/r__main__) run_doctestN) r0Bio.Applicationrrrrrr- Bio._utilsr2rrrrs    z