o Rŀg@sZdZddlmZddlmZddlmZGdddeZedkr+ddlmZed Sd S) z?Command line wrapper for the multiple alignment program MUSCLE.)_Option)_Switch)AbstractCommandlinec@seZdZdZdddZdS)MuscleCommandlineaCommand line wrapper for the multiple alignment program MUSCLE. http://www.drive5.com/muscle/ Notes ----- Last checked against version: 3.7, briefly against 3.8 References ---------- Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97. Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5(1): 113. Examples -------- >>> from Bio.Align.Applications import MuscleCommandline >>> muscle_exe = r"C:\Program Files\Alignments\muscle3.8.31_i86win32.exe" >>> in_file = r"C:\My Documents\unaligned.fasta" >>> out_file = r"C:\My Documents\aligned.fasta" >>> muscle_cline = MuscleCommandline(muscle_exe, input=in_file, out=out_file) >>> print(muscle_cline) "C:\Program Files\Alignments\muscle3.8.31_i86win32.exe" -in "C:\My Documents\unaligned.fasta" -out "C:\My Documents\aligned.fasta" You would typically run the command line with muscle_cline() or via the Python subprocess module, as described in the Biopython tutorial. musclec sFgdgdddggdgdgdgdgtgd d d d d tddgdd d d tddgdtddgdtddgdd d d tddgdd d d tddgdd d!d d"td#d$gd%d&d!d d"td'd(gd)fd*d!d d"td+d,gd-fd.d!d d"td/d0gd1d2d!d d"td3d4gd5d6d!d d"td7d8gd9fd:d!d d"td;dd!d d"td?d@gdAdBd!d d"tdCdDgdEdFd!d d"tdGdHgdIdJd!d d"tdKdLgdMdNd!d d"tdOdPgdQd d d tdRdSgdTd d d tdUdVgdWd d d tdXdYgdZd[d!d d"td\d]gd^d_d!d d"td`dagdbdcd!d d"tdddegdfdgd!d d"tdhdigdjdkd!d d"tdldmgdndod!d d"tdpdqgdrdsd!d d"tdtdugdvfdwd!d d"tdxdygdzd{d!d d"td|d}gd~fdd!d d"tddgdfdd!d d"tddgdd d d tddgdfdd!d d"tddgddd!d d"tddgddd!d d"tddgdd d d tddgddd!d d"tddgdd dtddgdd dtddgdd d d tddgdfdd!d d"tddgdfdd!d d"tddgdtddgdtddgdtddgdtddgdtddgdtddgdtddgdd d d tddgdd d d tddgdd d d tddgdd d d tddgdd d d tddgdd d d tddgdd d d tddgd؃tddgdۃtddgdރtddgdtddgdtddgdtddgdtddgdtddgdtddgdtddgdtddgdtddgdtddgdtddgdtddgdtddgdtd d gd |_tj||fi|d S( zInitialize the class.)upgmaupgmbneighborjoining)kmer6_6kmer20_3kmer20_4kbit20_3kmer4_6 pctid_kimura pctid_log)sppsdpxpspfspm)pseudomidlongestspanminavgleafdist)proteinrnadnanucleoauto)noneclustalwhenikoff henikoffpbgscthreeway)z-inininputzInput filenameTF)filenameequatez-outoutzOutput filenamez-diagsdiagsz-Find diagonals (faster for similar sequences)z-profileprofilezPerform a profile alignmentz-in1in1z*First input filename for profile alignmentz-in2in2z-Second input filename for a profile alignmentz-anchorspacing anchorspacingz&Minimum spacing between anchor columnscS t|tSN isinstanceintxr6R/var/www/html/myenv/lib/python3.10/site-packages/Bio/Align/Applications/_Muscle.pyh z,MuscleCommandline.__init__..)checker_functionr(z-centercenterz%Center parameter - should be negativecSr/r0r2floatr4r6r6r7r8pr9z -cluster1cluster1z%Clustering method used in iteration 1c|vSr0r6r4CLUSTERING_ALGORITHMSr6r7r8wz -cluster2cluster2z%Clustering method used in iteration 2cr?r0r6r4r@r6r7r8rBz -diaglength diaglengthzMinimum length of diagonalcSr/r0r1r4r6r6r7r8r9z -diagmargin diagmarginz/Discard this many positions at ends of diagonalcSr/r0r1r4r6r6r7r8r9z -distance1 distance1z Distance measure for iteration 1cr?r0r6r4)DISTANCE_MEASURES_ITER1r6r7r8rBz -distance2 distance2z Distance measure for iteration 2cr?r0r6r4)DISTANCE_MEASURES_ITER2r6r7r8rBz -gapextend gapextendzGap extension penaltycSr/r0r<r4r6r6r7r8r9z-gapopengapopenz Gap open score - negative numbercSr/r0r<r4r6r6r7r8r9z-hydrohydroz"Window size for hydrophobic regioncSr/r0r1r4r6r6r7r8r9z -hydrofactor hydrofactorz3Multiplier for gap penalties in hydrophobic regionscSr/r0r<r4r6r6r7r8r9z-loglogz Log file namez-logalogaz'Log file name (append to existing file)z-matrixmatrixzgpath to NCBI or WU-BLAST format protein substitution matrix - also set -gapopen, -gapextend and -centerz -diagbreak diagbreakzRMaximum distance between two diagonals that allows them to merge into one diagonalcSr/r0r1r4r6r6r7r8r9z -maxdiagbreak maxdiagbreakz+Deprecated in v3.8, use -diagbreak instead.cSr/r0r1r4r6r6r7r8r9z -maxhoursmaxhourszMaximum time to run in hourscSr/r0r<r4r6r6r7r8 r9z -maxitersmaxiterszMaximum number of iterationscSr/r0r1r4r6r6r7r8r9z -maxtreesmaxtreesz/Maximum number of trees to build in iteration 2cSr/r0r1r4r6r6r7r8r9z-minbestcolscoreminbestcolscorez0Minimum score a column must have to be an anchorcSr/r0r<r4r6r6r7r8&r9z-minsmoothscoreminsmoothscorez9Minimum smoothed score a column must have to be an anchorcSr/r0r<r4r6r6r7r80r9z -objscoreobjscorez1Objective score used by tree dependent refinementcr?r0r6r4)OBJECTIVE_SCORESr6r7r8ErBz -refinewindow refinewindowzLength of window for -refinewcSr/r0r1r4r6r6r7r8Mr9z-root1root1z'Method used to root tree in iteration 1cr?r0r6r4TREE_ROOT_METHODSr6r7r8TrBz-root2root2z'Method used to root tree in iteration 2cr?r0r6r4r\r6r7r8^rBz -scorefile scorefilez_Score file name, contains one line for each column in the alignment with average BLOSUM62 scorez-seqtypeseqtypez Sequence typecr?r0r6r4)SEQUENCE_TYPESr6r7r8|rBz-smoothscoreceilsmoothscoreceilz+Maximum value of column score for smoothingcSr/r0r<r4r6r6r7r8r9z -smoothwindow smoothwindowz'Window used for anchor column smoothingcSr/r0r1r4r6r6r7r8r9z-spscorespscorez0Compute SP objective score of multiple alignmentz-sueffsueffz!Constant used in UPGMB clusteringcSr/r0r<r4r6r6r7r8r9z-tree1tree1z!Save Newick tree from iteration 1)r(z-tree2tree2z!Save Newick tree from iteration 2z-usetreeusetreez#Use given Newick tree as guide treez-weight1weight1z$Weighting scheme used in iteration 1cr?r0r6r4WEIGHTING_SCHEMESr6r7r8rBz-weight2weight2z$Weighting scheme used in iteration 2cr?r0r6r4rjr6r7r8rBz-clwclwz6Write output in CLUSTALW format (with a MUSCLE header)z -clwstrict clwstrictz8Write output in CLUSTALW format with version 1.81 headerz-fastafastazWrite output in FASTA formatz-htmlhtmlzWrite output in HTML formatz-msfmsfzWrite output in MSF formatz-phyiphyiz)Write output in PHYLIP interleaved formatz-physphysz(Write output in PHYLIP sequential formatz-phyioutphyioutz5Write PHYLIP interleaved output to specified filenamez-physoutphysoutz4Write PHYLIP sequential format to specified filenamez-htmlouthtmloutz'Write HTML output to specified filenamez-clwoutclwoutz@Write CLUSTALW output (with MUSCLE header) to specified filenamez -clwstrictout clwstrictoutzFWrite CLUSTALW output (with version 1.81 header) to specified filenamez-msfoutmsfoutz-Write MSF format output to specified filenamez -fastaoutfastaoutz/Write FASTA format output to specified filenamez-anchorsanchorsz?Use anchor optimisation in tree dependent refinement iterationsz -noanchors noanchorszFDo not use anchor optimisation in tree dependent refinement iterationsz-brennerbrennerz)Use Steve Brenner's root alignment methodz-clusterclusterzCPerform fast clustering of input sequences, use -tree1 to save treez-dimerdimerzGUse faster (slightly less accurate) dimer approximationfor the SP scorez-groupgroupz!Group similar sequences in outputz-lelez+Use log-expectation profile score (VTML240)z-svsvz(Use sum-of-pairs profile score (VTML240)z-sprz/Use sum-of-pairs protein profile score (PAM200)z-spnspnz1Use sum-of-pairs protein nucleotide profile scorez-quietquietz Do not display progress messagesz-refinerefinez!Only do tree dependent refinementz-refinewrefinewz?Only do tree dependent refinement using sliding window approachz-corecorezDo not catch exceptionsz-nocorenocorezCatch exceptionsz-stablestablez@Do not group similar sequences in output (not supported in v3.8)z-verboseverbosez%Write parameter settings and progressz-versionversionz'Write version string to stdout and exitN)rr parametersr__init__)selfcmdkwargsr6)rArGrIrYrar]rkr7r.s   !( 2 :CN Z ais} (/>FOXbw   #/ 8AJX_ g ov  !* 1 4 7 9 ;=CIOU\bkqx~    "' , 06 <?C [^`zMuscleCommandline.__init__N)r)__name__ __module__ __qualname____doc__rr6r6r6r7rsr__main__) run_doctestN) rBio.Applicationrrrrr Bio._utilsrr6r6r6r7s   "