# Copyright 2009 by Cymon J. Cox. All rights reserved. # # This file is part of the Biopython distribution and governed by your # choice of the "Biopython License Agreement" or the "BSD 3-Clause License". # Please see the LICENSE file that should have been included as part of this # package. """Command line wrapper for the multiple alignment program MUSCLE.""" from Bio.Application import _Option, _Switch, AbstractCommandline class MuscleCommandline(AbstractCommandline): r"""Command 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. """ def __init__(self, cmd="muscle", **kwargs): """Initialize the class.""" CLUSTERING_ALGORITHMS = ["upgma", "upgmb", "neighborjoining"] DISTANCE_MEASURES_ITER1 = [ "kmer6_6", "kmer20_3", "kmer20_4", "kbit20_3", "kmer4_6", ] DISTANCE_MEASURES_ITER2 = DISTANCE_MEASURES_ITER1 + [ "pctid_kimura", "pctid_log", ] OBJECTIVE_SCORES = ["sp", "ps", "dp", "xp", "spf", "spm"] TREE_ROOT_METHODS = ["pseudo", "midlongestspan", "minavgleafdist"] # The mucleotide arguments for the sequence type parameter in MUSCLE (-seqtype) # were updated at somepoint in MUSCLE version 3.8. Prior to the update # 'nucleo' was used for nucleotide. This has been updated to 'rna' and 'dna'. 'nucleo' kept for # backwards compatibility with older MUSCLE versions. SEQUENCE_TYPES = ["protein", "rna", "dna", "nucleo", "auto"] WEIGHTING_SCHEMES = [ "none", "clustalw", "henikoff", "henikoffpb", "gsc", "threeway", ] self.parameters = [ # Can't use "in" as the final alias as this # is a reserved word in python: _Option( ["-in", "in", "input"], "Input filename", filename=True, equate=False ), _Option(["-out", "out"], "Output filename", filename=True, equate=False), _Switch( ["-diags", "diags"], "Find diagonals (faster for similar sequences)" ), _Switch(["-profile", "profile"], "Perform a profile alignment"), _Option( ["-in1", "in1"], "First input filename for profile alignment", filename=True, equate=False, ), _Option( ["-in2", "in2"], "Second input filename for a profile alignment", filename=True, equate=False, ), # anchorspacing Integer 32 Minimum spacing # between anchor cols _Option( ["-anchorspacing", "anchorspacing"], "Minimum spacing between anchor columns", checker_function=lambda x: isinstance(x, int), equate=False, ), # center Floating point [1] Center parameter. # Should be negative. _Option( ["-center", "center"], "Center parameter - should be negative", checker_function=lambda x: isinstance(x, float), equate=False, ), # cluster1 upgma upgmb Clustering method. _Option( ["-cluster1", "cluster1"], "Clustering method used in iteration 1", checker_function=lambda x: x in CLUSTERING_ALGORITHMS, equate=False, ), # cluster2 upgmb cluster1 is used # neighborjoining in iteration 1 and # 2, cluster2 in # later iterations. _Option( ["-cluster2", "cluster2"], "Clustering method used in iteration 2", checker_function=lambda x: x in CLUSTERING_ALGORITHMS, equate=False, ), # diaglength Integer 24 Minimum length of # diagonal. _Option( ["-diaglength", "diaglength"], "Minimum length of diagonal", checker_function=lambda x: isinstance(x, int), equate=True, ), # diagmargin Integer 5 Discard this many # positions at ends # of diagonal. _Option( ["-diagmargin", "diagmargin"], "Discard this many positions at ends of diagonal", checker_function=lambda x: isinstance(x, int), equate=False, ), # distance1 kmer6_6 Kmer6_6(amino) or Distance measure # kmer20_3 Kmer4_6(nucleo) for iteration 1 # kmer20_4 # kbit20_3 # kmer4_6 _Option( ["-distance1", "distance1"], "Distance measure for iteration 1", checker_function=lambda x: x in DISTANCE_MEASURES_ITER1, equate=False, ), # distance2 kmer6_6 pctid_kimura Distance measure # kmer20_3 for iterations # kmer20_4 2, 3 ... # kbit20_3 # pctid_kimura # pctid_log _Option( ["-distance2", "distance2"], "Distance measure for iteration 2", checker_function=lambda x: x in DISTANCE_MEASURES_ITER2, equate=False, ), # gapextend Floating point [1] The gap extend score _Option( ["-gapextend", "gapextend"], "Gap extension penalty", checker_function=lambda x: isinstance(x, float), equate=False, ), # gapopen Floating point [1] The gap open score # Must be negative. _Option( ["-gapopen", "gapopen"], "Gap open score - negative number", checker_function=lambda x: isinstance(x, float), equate=False, ), # hydro Integer 5 Window size for # determining whether # a region is # hydrophobic. _Option( ["-hydro", "hydro"], "Window size for hydrophobic region", checker_function=lambda x: isinstance(x, int), equate=False, ), # hydrofactor Floating point 1.2 Multiplier for gap # open/close # penalties in # hydrophobic regions _Option( ["-hydrofactor", "hydrofactor"], "Multiplier for gap penalties in hydrophobic regions", checker_function=lambda x: isinstance(x, float), equate=False, ), # log File name None. Log file name # (delete existing # file). _Option(["-log", "log"], "Log file name", filename=True, equate=False), # loga File name None. Log file name # (append to existing # file). _Option( ["-loga", "loga"], "Log file name (append to existing file)", filename=True, equate=False, ), # matrix File name None. File name for # substitution matrix # in NCBI or WU-BLAST # format. If you # specify your own # matrix, you should # also specify: # -gapopen # -gapextend # -center 0.0 _Option( ["-matrix", "matrix"], "path to NCBI or WU-BLAST format protein substitution " "matrix - also set -gapopen, -gapextend and -center", filename=True, equate=False, ), # diagbreak Integer 1 Maximum distance # between two # diagonals that # allows them to # merge into one # diagonal. _Option( ["-diagbreak", "diagbreak"], "Maximum distance between two diagonals that allows " "them to merge into one diagonal", checker_function=lambda x: isinstance(x, int), equate=False, ), _Option( ["-maxdiagbreak", "maxdiagbreak"], # deprecated 3.8 "Deprecated in v3.8, use -diagbreak instead.", checker_function=lambda x: isinstance(x, int), equate=False, ), # maxhours Floating point None. Maximum time to # run in hours. The # actual time may # exceed requested # limit by a few # minutes. Decimals # are allowed, so 1.5 # means one hour and # 30 minutes. _Option( ["-maxhours", "maxhours"], "Maximum time to run in hours", checker_function=lambda x: isinstance(x, float), equate=False, ), # maxiters Integer 1, 2 ... 16 Maximum number of # iterations. _Option( ["-maxiters", "maxiters"], "Maximum number of iterations", checker_function=lambda x: isinstance(x, int), equate=False, ), # maxtrees Integer 1 Maximum number of # new trees to build # in iteration 2. _Option( ["-maxtrees", "maxtrees"], "Maximum number of trees to build in iteration 2", checker_function=lambda x: isinstance(x, int), equate=False, ), # minbestcolscore Floating point [1] Minimum score a # column must have to # be an anchor. _Option( ["-minbestcolscore", "minbestcolscore"], "Minimum score a column must have to be an anchor", checker_function=lambda x: isinstance(x, float), equate=False, ), # minsmoothscore Floating point [1] Minimum smoothed # score a column must # have to be an # anchor. _Option( ["-minsmoothscore", "minsmoothscore"], "Minimum smoothed score a column must have to be an anchor", checker_function=lambda x: isinstance(x, float), equate=False, ), # objscore sp spm Objective score # ps used by tree # dp dependent # xp refinement. # spf sp=sum-of-pairs # spm score. (dimer # approximation) # spm=sp for < 100 # seqs, otherwise spf # dp=dynamic # programming score. # ps=average profile- # sequence score. # xp=cross profile # score. _Option( ["-objscore", "objscore"], "Objective score used by tree dependent refinement", checker_function=lambda x: x in OBJECTIVE_SCORES, equate=False, ), # refinewindow Integer 200 Length of window # for -refinew. _Option( ["-refinewindow", "refinewindow"], "Length of window for -refinew", checker_function=lambda x: isinstance(x, int), equate=False, ), # root1 pseudo pseudo Method used to root _Option( ["-root1", "root1"], "Method used to root tree in iteration 1", checker_function=lambda x: x in TREE_ROOT_METHODS, equate=False, ), # root2 midlongestspan tree; root1 is # minavgleafdist used in iteration 1 # and 2, root2 in # later iterations. _Option( ["-root2", "root2"], "Method used to root tree in iteration 2", checker_function=lambda x: x in TREE_ROOT_METHODS, equate=False, ), # scorefile File name None File name where to # write a score file. # This contains one # line for each column # in the alignment. # The line contains # the letters in the # column followed by # the average BLOSUM62 # score over pairs of # letters in the # column. _Option( ["-scorefile", "scorefile"], "Score file name, contains one line for each column" " in the alignment with average BLOSUM62 score", filename=True, equate=False, ), # seqtype protein auto Sequence type. # dna (MUSCLE version > 3.8) # rna (MUSCLE version > 3.8) # auto # nucleo (only valid for MUSCLE versions < 3.8) _Option( ["-seqtype", "seqtype"], "Sequence type", checker_function=lambda x: x in SEQUENCE_TYPES, equate=False, ), # smoothscoreceil Floating point [1] Maximum value of # column score for # smoothing purposes. _Option( ["-smoothscoreceil", "smoothscoreceil"], "Maximum value of column score for smoothing", checker_function=lambda x: isinstance(x, float), equate=False, ), # smoothwindow Integer 7 Window used for # anchor column # smoothing. _Option( ["-smoothwindow", "smoothwindow"], "Window used for anchor column smoothing", checker_function=lambda x: isinstance(x, int), equate=False, ), # spscore File name Compute SP # objective score of # multiple alignment. _Option( ["-spscore", "spscore"], "Compute SP objective score of multiple alignment", filename=True, equate=False, ), # SUEFF Floating point value 0.1 Constant used in # between 0 and 1. UPGMB clustering. # Determines the # relative fraction # of average linkage # (SUEFF) vs. nearest # neighbor linkage # (1 SUEFF). _Option( ["-sueff", "sueff"], "Constant used in UPGMB clustering", checker_function=lambda x: isinstance(x, float), equate=False, ), # tree1 File name None Save tree _Option( ["-tree1", "tree1"], "Save Newick tree from iteration 1", equate=False ), # tree2 first or second # iteration to given # file in Newick # (Phylip-compatible) # format. _Option( ["-tree2", "tree2"], "Save Newick tree from iteration 2", equate=False ), # usetree File name None Use given tree as # guide tree. Must by # in Newick # (Phyip-compatible) # format. _Option( ["-usetree", "usetree"], "Use given Newick tree as guide tree", filename=True, equate=False, ), # weight1 none clustalw Sequence weighting _Option( ["-weight1", "weight1"], "Weighting scheme used in iteration 1", checker_function=lambda x: x in WEIGHTING_SCHEMES, equate=False, ), # weight2 henikoff scheme. # henikoffpb weight1 is used in # gsc iterations 1 and 2. # clustalw weight2 is used for # threeway tree-dependent # refinement. # none=all sequences # have equal weight. # henikoff=Henikoff & # Henikoff weighting # scheme. # henikoffpb=Modified # Henikoff scheme as # used in PSI-BLAST. # clustalw=CLUSTALW # method. # threeway=Gotoh # three-way method. _Option( ["-weight2", "weight2"], "Weighting scheme used in iteration 2", checker_function=lambda x: x in WEIGHTING_SCHEMES, equate=False, ), # ################### FORMATS #################################### # Multiple formats can be specified on the command line # If -msf appears it will be used regardless of other formats # specified. If -clw appears (and not -msf), clustalw format will # be used regardless of other formats specified. If both -clw and # -clwstrict are specified -clwstrict will be used regardless of # other formats specified. If -fasta is specified and not -msf, # -clw, or clwstrict, fasta will be used. If -fasta and -html are # specified -fasta will be used. Only if -html is specified alone # will html be used. I kid ye not. # clw no Write output in CLUSTALW format # (default is FASTA). _Switch( ["-clw", "clw"], "Write output in CLUSTALW format (with a MUSCLE header)", ), # clwstrict no Write output in CLUSTALW format with # the "CLUSTAL W (1.81)" header rather # than the MUSCLE version. This is # useful when a post-processing step is # picky about the file header. _Switch( ["-clwstrict", "clwstrict"], "Write output in CLUSTALW format with version 1.81 header", ), # fasta yes Write output in FASTA format. # Alternatives include clw, # clwstrict, msf and html. _Switch(["-fasta", "fasta"], "Write output in FASTA format"), # html no Write output in HTML format (default # is FASTA). _Switch(["-html", "html"], "Write output in HTML format"), # msf no Write output in MSF format (default # is FASTA). _Switch(["-msf", "msf"], "Write output in MSF format"), # Phylip interleaved - undocumented as of 3.7 _Switch(["-phyi", "phyi"], "Write output in PHYLIP interleaved format"), # Phylip sequential - undocumented as of 3.7 _Switch(["-phys", "phys"], "Write output in PHYLIP sequential format"), # ################# Additional specified output files ######### _Option( ["-phyiout", "phyiout"], "Write PHYLIP interleaved output to specified filename", filename=True, equate=False, ), _Option( ["-physout", "physout"], "Write PHYLIP sequential format to specified filename", filename=True, equate=False, ), _Option( ["-htmlout", "htmlout"], "Write HTML output to specified filename", filename=True, equate=False, ), _Option( ["-clwout", "clwout"], "Write CLUSTALW output (with MUSCLE header) to specified filename", filename=True, equate=False, ), _Option( ["-clwstrictout", "clwstrictout"], "Write CLUSTALW output (with version 1.81 header) to " "specified filename", filename=True, equate=False, ), _Option( ["-msfout", "msfout"], "Write MSF format output to specified filename", filename=True, equate=False, ), _Option( ["-fastaout", "fastaout"], "Write FASTA format output to specified filename", filename=True, equate=False, ), # ############# END FORMATS ################################### # anchors yes Use anchor optimization in tree # dependent refinement iterations. _Switch( ["-anchors", "anchors"], "Use anchor optimisation in tree dependent refinement iterations", ), # noanchors no Disable anchor optimization. Default # is anchors. _Switch( ["-noanchors", "noanchors"], "Do not use anchor optimisation in tree dependent " "refinement iterations", ), # brenner no Use Steven Brenner's method for # computing the root alignment. _Switch( ["-brenner", "brenner"], "Use Steve Brenner's root alignment method" ), # cluster no Perform fast clustering of input # sequences. Use the tree1 option to # save the tree. _Switch( ["-cluster", "cluster"], "Perform fast clustering of input sequences, " "use -tree1 to save tree", ), # dimer no Use dimer approximation for the # SP score (faster, less accurate). _Switch( ["-dimer", "dimer"], "Use faster (slightly less accurate) dimer approximation" "for the SP score", ), # group yes Group similar sequences together # in the output. This is the default. # See also stable. _Switch(["-group", "group"], "Group similar sequences in output"), # ############# log-expectation profile score #################### # One of either -le, -sp, or -sv # # According to the doc, spn is default and the only option for # nucleotides: this doesn't appear to be true. -le, -sp, and -sv # can be used and produce numerically different logs # (what is going on?) # # spn fails on proteins # le maybe Use log-expectation profile score # (VTML240). Alternatives are to use sp # or sv. This is the default for amino # acid sequences. _Switch(["-le", "le"], "Use log-expectation profile score (VTML240)"), # sv no Use sum-of-pairs profile score # (VTML240). Default is le. _Switch(["-sv", "sv"], "Use sum-of-pairs profile score (VTML240)"), # sp no Use sum-of-pairs protein profile # score (PAM200). Default is le. _Switch(["-sp", "sp"], "Use sum-of-pairs protein profile score (PAM200)"), # spn maybe Use sum-of-pairs nucleotide profile # score (BLASTZ parameters). This is # the only option for nucleotides, # and is therefore the default. _Switch( ["-spn", "spn"], "Use sum-of-pairs protein nucleotide profile score" ), # ########## END log-expectation profile score ################### # quiet no Do not display progress messages. _Switch(["-quiet", "quiet"], "Do not display progress messages"), # refine no Input file is already aligned, skip # first two iterations and begin tree # dependent refinement. _Switch(["-refine", "refine"], "Only do tree dependent refinement"), # refinew no Refine an alignment by dividing it # into non-overlapping windows and # re-aligning each window. Typically # used for whole-genome nucleotide # alignments. _Switch( ["-refinew", "refinew"], "Only do tree dependent refinement using sliding window approach", ), # core yes in muscle, Do not catch exceptions. # no in muscled. _Switch(["-core", "core"], "Do not catch exceptions"), # nocore no in muscle, Catch exceptions and give an # yes in muscled. error message if possible. _Switch(["-nocore", "nocore"], "Catch exceptions"), # stable no Preserve input order of sequences # in output file. Default is to group # sequences by similarity (group). _Switch( ["-stable", "stable"], "Do not group similar sequences in output (not supported in v3.8)", ), # termgaps4 yes Use 4-way test for treatment of # terminal gaps. # (Cannot be disabled in this version). # # termgapsfull no Terminal gaps penalized with # full penalty. [1] Not fully # supported in this version # # termgapshalf yes Terminal gaps penalized with # half penalty. [1] Not fully # supported in this version # # termgapshalflonger no Terminal gaps penalized with # half penalty if gap relative # to longer sequence, otherwise with # full penalty. [1] Not fully # supported in this version # # verbose no Write parameter settings and # progress messages to log file. _Switch(["-verbose", "verbose"], "Write parameter settings and progress"), # version no Write version string to # stdout and exit _Switch(["-version", "version"], "Write version string to stdout and exit"), ] AbstractCommandline.__init__(self, cmd, **kwargs) if __name__ == "__main__": from Bio._utils import run_doctest run_doctest()