Package Bio :: Package Phylo :: Package Applications :: Module _Raxml
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Source Code for Module Bio.Phylo.Applications._Raxml

  1  # Copyright 2012 by Eric Talevich.  All rights reserved. 
  2  # This code is part of the Biopython distribution and governed by its license. 
  3  # Please see the LICENSE file that should have been included as part of this 
  4  # package. 
  5  """Command-line wrapper for the tree inference program RAxML. 
  6   
  7  Derived from the help page for RAxML version 7.3 by Alexandros Stamatakis, but 
  8  should work for any version 7.X (and probably earlier for most options). 
  9  """ 
 10  from __future__ import print_function 
 11  from Bio._py3k import basestring 
 12   
 13  __docformat__ = "restructuredtext en" 
 14   
 15  from Bio.Application import _Option, _Switch, AbstractCommandline 
 16   
 17   
18 -class RaxmlCommandline(AbstractCommandline):
19 """Command-line wrapper for the tree inference program RAxML. 20 21 The required parameters are 'sequences' (-s), 'model' (-m) and 'name' (-n). 22 The parameter 'parsimony_seed' (-p) must also be set for RAxML, but if you 23 do not specify it, this wrapper will set the seed to 10000 for you. 24 25 Example: 26 27 >>> from Bio.Phylo.Applications import RaxmlCommandline 28 >>> raxml_cline = RaxmlCommandline(sequences="Tests/Phylip/interlaced2.phy", 29 ... model="PROTCATWAG", name="interlaced2") 30 >>> print(raxml_cline) 31 raxmlHPC -m PROTCATWAG -n interlaced2 -p 10000 -s Tests/Phylip/interlaced2.phy 32 33 You would typically run the command line with raxml_cline() or via 34 the Python subprocess module, as described in the Biopython tutorial. 35 36 Citation: 37 38 Stamatakis A. 39 RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with 40 Thousands of Taxa and Mixed Models. 41 Bioinformatics 2006, 22(21):2688-2690. 42 43 Homepage: http://sco.h-its.org/exelixis/software.html 44 """ 45
46 - def __init__(self, cmd='raxmlHPC', **kwargs):
47 self.parameters = [ 48 _Option(['-a', 'weight_filename'], 49 "Name of a column weight file to assign individual weights " 50 "to each column of the alignment. Those weights must be " 51 "integers separated by any type and number of whitespaces " 52 "within a separate file.", 53 filename=True, 54 equate=False, 55 ), 56 57 _Option(['-b', 'bootstrap_seed'], 58 "Random seed for bootstrapping.", 59 equate=False, 60 ), 61 62 _Option(['-c', 'num_categories'], 63 "Number of distinct rate categories for RAxML when " 64 "evolution model is set to GTRCAT or GTRMIX." 65 "Individual per-site rates are categorized into this " 66 "many rate categories to accelerate computations. " 67 "Default: 25.", 68 equate=False, 69 ), 70 71 _Switch(['-d', 'random_starting_tree'], 72 "Start ML optimization from random starting tree." 73 ), 74 75 _Option(['-e', 'epsilon'], 76 "Set model optimization precision in log likelihood units " 77 "for final optimization of tree topology under MIX/MIXI " 78 "or GAMMA/GAMMAI." 79 "Default: 0.1 for models not using proportion of " 80 "invariant sites estimate; 0.001 for models using " 81 "proportion of invariant sites estimate.", 82 equate=False, 83 ), 84 85 _Option(['-E', 'exclude_filename'], 86 "An exclude file name, containing a specification of " 87 "alignment positions you wish to exclude. Format is " 88 "similar to Nexus, the file shall contain entries like " 89 "'100-200 300-400'; to exclude a single column write, " 90 "e.g., '100-100'. If you use a mixed model, an " 91 "appropriately adapted model file will be written.", 92 filename=True, 93 equate=False, 94 ), 95 96 _Option(['-f', 'algorithm'], 97 """Select algorithm: 98 a: Rapid Bootstrap analysis and search for best-scoring ML 99 tree in one program run. 100 b: Draw bipartition information on a tree provided with '-t' 101 based on multiple trees (e.g. form a bootstrap) in a file 102 specifed by '-z'. 103 c: Check if the alignment can be properly read by RAxML. 104 d: New rapid hill-climbing (DEFAULT). 105 e: Optimize model+branch lengths for given input tree under 106 GAMMA/GAMMAI only. 107 g: Compute per site log Likelihoods for one ore more trees 108 passed via '-z' and write them to a file that can be read 109 by CONSEL. 110 h: Compute log likelihood test (SH-test) between best tree 111 passed via '-t' and a bunch of other trees passed via '-z'. 112 i: Perform a really thorough bootstrap, refinement of final 113 bootstrap tree under GAMMA and a more exhaustive algorithm. 114 j: Generate a bunch of bootstrapped alignment files from an 115 original alignemnt file. 116 m: Compare bipartitions between two bunches of trees passed 117 via '-t' and '-z' respectively. This will return the 118 Pearson correlation between all bipartitions found in the 119 two tree files. A file called 120 RAxML_bipartitionFrequencies.outputFileName will be 121 printed that contains the pair-wise bipartition 122 frequencies of the two sets. 123 n: Compute the log likelihood score of all trees contained 124 in a tree file provided by '-z' under GAMMA or 125 GAMMA+P-Invar. 126 o: Old and slower rapid hill-climbing. 127 p: Perform pure stepwise MP addition of new sequences to an 128 incomplete starting tree. 129 s: Split up a multi-gene partitioned alignment into the 130 respective subalignments. 131 t: Do randomized tree searches on one fixed starting tree. 132 w: Compute ELW test on a bunch of trees passed via '-z'. 133 x: Compute pair-wise ML distances, ML model parameters will 134 be estimated on an MP starting tree or a user-defined 135 tree passed via '-t', only allowed for GAMMA-based models 136 of rate heterogeneity.""", 137 checker_function=(lambda x: 138 isinstance(x, basestring) and len(x) == 1), 139 equate=False, 140 ), 141 142 _Option(['-g', 'grouping_constraint'], 143 "File name of a multifurcating constraint tree. " 144 "this tree does not need to be comprehensive, i.e. " 145 "contain all taxa.", 146 filename=True, 147 equate=False, 148 ), 149 150 _Option(['-i', 'rearrangements'], 151 "Initial rearrangement setting for the subsequent " 152 "application of topological changes phase.", 153 equate=False, 154 ), 155 156 _Switch(['-j', 'checkpoints'], 157 "Write checkpoints (intermediate tree topologies)." 158 ), 159 160 _Switch(['-k', 'bootstrap_branch_lengths'], 161 "Print bootstrapped trees with branch lengths. " 162 "The bootstraps will run a bit longer, because model " 163 "parameters will be optimized at the end of each run. " 164 "Use with CATMIX/PROTMIX or GAMMA/GAMMAI." 165 ), 166 167 _Option(['-l', 'cluster_threshold'], 168 "Threshold for sequence similarity clustering. " 169 "RAxML will then print out an alignment to a file " 170 "called sequenceFileName.reducedBy.threshold that " 171 "only contains sequences <= the specified threshold " 172 "that must be between 0.0 and 1.0. RAxML uses the " 173 "QT-clustering algorithm to perform this task. " 174 "In addition, a file called " 175 "RAxML_reducedList.outputFileName will be written " 176 "that contains clustering information.", 177 equate=False, 178 ), 179 180 _Option(['-L', 'cluster_threshold_fast'], 181 "Same functionality as '-l', but uses a less " 182 "exhaustive and thus faster clustering algorithm. " 183 "This is intended for very large datasets with more " 184 "than 20,000-30,000 sequences.", 185 equate=False, 186 ), 187 188 _Option(['-m', 'model'], 189 """Model of Nucleotide or Amino Acid Substitution: 190 191 NUCLEOTIDES: 192 193 GTRCAT : GTR + Optimization of substitution rates + Optimization of site-specific 194 evolutionary rates which are categorized into numberOfCategories distinct 195 rate categories for greater computational efficiency 196 if you do a multiple analysis with '-#' or '-N' but without bootstrapping the program 197 will use GTRMIX instead 198 GTRGAMMA : GTR + Optimization of substitution rates + GAMMA model of rate 199 heterogeneity (alpha parameter will be estimated) 200 GTRMIX : Inference of the tree under GTRCAT 201 and thereafter evaluation of the final tree topology under GTRGAMMA 202 GTRCAT_GAMMA : Inference of the tree with site-specific evolutionary rates. 203 However, here rates are categorized using the 4 discrete GAMMA rates. 204 Evaluation of the final tree topology under GTRGAMMA 205 GTRGAMMAI : Same as GTRGAMMA, but with estimate of proportion of invariable sites 206 GTRMIXI : Same as GTRMIX, but with estimate of proportion of invariable sites 207 GTRCAT_GAMMAI : Same as GTRCAT_GAMMA, but with estimate of proportion of invariable sites 208 209 AMINO ACIDS: 210 211 PROTCATmatrixName[F] : specified AA matrix + Optimization of substitution rates + Optimization of site-specific 212 evolutionary rates which are categorized into numberOfCategories distinct 213 rate categories for greater computational efficiency 214 if you do a multiple analysis with '-#' or '-N' but without bootstrapping the program 215 will use PROTMIX... instead 216 PROTGAMMAmatrixName[F] : specified AA matrix + Optimization of substitution rates + GAMMA model of rate 217 heterogeneity (alpha parameter will be estimated) 218 PROTMIXmatrixName[F] : Inference of the tree under specified AA matrix + CAT 219 and thereafter evaluation of the final tree topology under specified AA matrix + GAMMA 220 PROTCAT_GAMMAmatrixName[F] : Inference of the tree under specified AA matrix and site-specific evolutionary rates. 221 However, here rates are categorized using the 4 discrete GAMMA rates. 222 Evaluation of the final tree topology under specified AA matrix + GAMMA 223 PROTGAMMAImatrixName[F] : Same as PROTGAMMAmatrixName[F], but with estimate of proportion of invariable sites 224 PROTMIXImatrixName[F] : Same as PROTMIXmatrixName[F], but with estimate of proportion of invariable sites 225 PROTCAT_GAMMAImatrixName[F] : Same as PROTCAT_GAMMAmatrixName[F], but with estimate of proportion of invariable sites 226 227 Available AA substitution models: DAYHOFF, DCMUT, JTT, MTREV, WAG, RTREV, CPREV, VT, BLOSUM62, MTMAM, GTR 228 With the optional 'F' appendix you can specify if you want to use empirical base frequencies 229 Please not that for mixed models you can in addition specify the per-gene AA model in 230 the mixed model file (see manual for details) 231 """, 232 equate=False, 233 ), 234 235 _Switch(['-M', 'partition_branch_lengths'], 236 "Switch on estimation of individual per-partition " 237 "branch lengths. Only has effect when used in " 238 "combination with 'partition_filename' ('-q'). " 239 "Branch lengths for individual partitions will be " 240 "printed to separate files. A weighted average of the " 241 "branch lengths is computed by using the respective " 242 "partition lengths. " 243 ), 244 245 _Option(['-n', 'name'], 246 "Name used in the output files.", 247 filename=True, 248 equate=False, 249 ), 250 251 _Option(['-o', 'outgroup'], 252 "Name of a single outgroup or a comma-separated list " 253 "of outgroups, eg '-o Rat' or '-o Rat,Mouse'. In case " 254 "that multiple outgroups are not monophyletic the " 255 "first name in the list will be selected as outgroup. " 256 "Don't leave spaces between taxon names!", 257 checker_function=lambda x: len(x.split()) == 1, 258 equate=False, 259 ), 260 261 _Option(['-q', 'partition_filename'], 262 "File name containing the assignment of models to " 263 "alignment partitions for multiple models of " 264 "substitution. For the syntax of this file please " 265 "consult the RAxML manual.", 266 filename=True, 267 equate=False, 268 ), 269 270 _Option(['-p', 'parsimony_seed'], 271 "Random number seed for the parsimony inferences. " 272 "This allows you to reproduce your results and will " 273 "help developers debug the program. This option HAS " 274 "NO EFFECT in the parallel MPI version.", 275 equate=False, 276 ), 277 278 _Option(['-P', 'protein_model'], 279 "File name of a user-defined AA (Protein) substitution " 280 "model. This file must contain 420 entries, the first " 281 "400 being the AA substitution rates (this must be a " 282 "symmetric matrix) and the last 20 are the empirical " 283 "base frequencies.", 284 filename=True, 285 equate=False, 286 ), 287 288 _Option(['-r', 'binary_constraint'], 289 "File name of a binary constraint tree. " 290 "This tree does not need to be comprehensive, i.e. " 291 "contain all taxa.", 292 filename=True, 293 equate=False, 294 ), 295 296 _Option(['-s', 'sequences'], 297 "Name of the alignment data file, in PHYLIP format.", 298 filename=True, 299 equate=False, 300 ), 301 302 _Option(['-t', 'starting_tree'], 303 "File name of a user starting tree, in Newick format.", 304 filename=True, 305 equate=False, 306 ), 307 308 _Option(['-T', 'threads'], 309 "Number of threads to run. " 310 "PTHREADS VERSION ONLY! " 311 "Make sure to set this at most the number of CPUs " 312 "you have on your machine, otherwise, there will be " 313 "a huge performance decrease!", 314 equate=False, 315 ), 316 317 _Option(['-u', 'num_bootstrap_searches'], 318 "Number of multiple bootstrap searches per replicate. " 319 "Use this to obtain better ML trees for each " 320 "replicate. Default: 1 ML search per bootstrap " 321 "replicate.", 322 equate=False, 323 ), 324 325 _Switch(['-v', 'version'], 326 "Display version information." 327 ), 328 329 _Option(['-w', 'working_dir'], 330 "Name of the working directory where RAxML will " 331 "write its output files. Default: current directory.", 332 filename=True, 333 equate=False, 334 ), 335 336 _Option(['-x', 'rapid_bootstrap_seed'], 337 "Random seed for rapid bootstrapping.", 338 equate=False, 339 ), 340 341 _Switch(['-y', 'parsimony'], 342 "Only compute a parsimony starting tree, then exit." 343 ), 344 345 _Option(['-z', 'bipartition_filename'], 346 "Name of a file containing multiple trees, e.g. from " 347 "a bootstrap run, that shall be used to draw " 348 "bipartition values onto a tree provided with '-t'. " 349 "It can also be used to compute per-site log " 350 "likelihoods in combination with '-f g', and to read " 351 "a bunch of trees for a couple of other options " 352 "('-f h', '-f m', '-f n').", 353 filename=True, 354 equate=False, 355 ), 356 357 _Option(['-N', '-#', 'num_replicates'], 358 "Number of alternative runs on distinct starting trees. " 359 "In combination with the '-b' option, this will invoke a " 360 "multiple bootstrap analysis. " 361 "DEFAULT: 1 single analysis." 362 "Note that '-N' has been added as an alternative since " 363 "'-#' sometimes caused problems with certain MPI job " 364 "submission systems, since '-#' is often used to start " 365 "comments. ", 366 equate=False, 367 ), 368 ] 369 AbstractCommandline.__init__(self, cmd, **kwargs) 370 # ENH: enforce -s, -n and -m 371 if not self.parsimony_seed: 372 self.parsimony_seed = 10000
373