Package Bio :: Package Emboss :: Module Applications
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Source Code for Module Bio.Emboss.Applications

   1  # Copyright 2001-2009 Brad Chapman. 
   2  # Revisions copyright 2009-2010 by Peter Cock. 
   3  # Revisions copyright 2009 by David Winter. 
   4  # Revisions copyright 2009-2010 by Leighton Pritchard. 
   5  # All rights reserved. 
   6  # This code is part of the Biopython distribution and governed by its 
   7  # license.  Please see the LICENSE file that should have been included 
   8  # as part of this package. 
   9  """Code to interact with and run various EMBOSS programs. 
  10   
  11  These classes follow the AbstractCommandline interfaces for running 
  12  programs. 
  13  """ 
  14   
  15  from __future__ import print_function 
  16   
  17  from Bio.Application import _Option, _Switch, AbstractCommandline 
  18   
  19   
20 -class _EmbossMinimalCommandLine(AbstractCommandline):
21 """Base Commandline object for EMBOSS wrappers (PRIVATE). 22 23 This is provided for subclassing, it deals with shared options 24 common to all the EMBOSS tools: 25 26 - auto Turn off prompts 27 - stdout Write standard output 28 - filter Read standard input, write standard output 29 - options Prompt for standard and additional values 30 - debug Write debug output to program.dbg 31 - verbose Report some/full command line options 32 - help Report command line options. More 33 information on associated and general 34 qualifiers can be found with -help -verbose 35 - warning Report warnings 36 - error Report errors 37 - fatal Report fatal errors 38 - die Report dying program messages 39 """
40 - def __init__(self, cmd=None, **kwargs):
41 assert cmd is not None 42 extra_parameters = [ 43 _Switch(["-auto", "auto"], 44 """Turn off prompts. 45 46 Automatic mode disables prompting, so we recommend you set 47 this argument all the time when calling an EMBOSS tool from 48 Biopython. 49 """), 50 _Switch(["-stdout", "stdout"], 51 "Write standard output."), 52 _Switch(["-filter", "filter"], 53 "Read standard input, write standard output."), 54 _Switch(["-options", "options"], 55 """Prompt for standard and additional values. 56 57 If you are calling an EMBOSS tool from within Biopython, 58 we DO NOT recommend using this option. 59 """), 60 _Switch(["-debug", "debug"], 61 "Write debug output to program.dbg."), 62 _Switch(["-verbose", "verbose"], 63 "Report some/full command line options"), 64 _Switch(["-help", "help"], 65 """Report command line options. 66 67 More information on associated and general qualifiers can 68 be found with -help -verbose 69 """), 70 _Switch(["-warning", "warning"], 71 "Report warnings."), 72 _Switch(["-error", "error"], 73 "Report errors."), 74 _Switch(["-die", "die"], 75 "Report dying program messages."), 76 ] 77 try: 78 #Insert extra parameters - at the start just in case there 79 #are any arguments which must come last: 80 self.parameters = extra_parameters + self.parameters 81 except AttributeError: 82 #Should we raise an error? The subclass should have set this up! 83 self.parameters = extra_parameters 84 AbstractCommandline.__init__(self, cmd, **kwargs)
85 86
87 -class _EmbossCommandLine(_EmbossMinimalCommandLine):
88 """Base Commandline object for EMBOSS wrappers (PRIVATE). 89 90 This is provided for subclassing, it deals with shared options 91 common to all the EMBOSS tools plus: 92 93 - outfile Output filename 94 95 """
96 - def __init__(self, cmd=None, **kwargs):
97 assert cmd is not None 98 extra_parameters = [ 99 _Option(["-outfile", "outfile"], 100 "Output filename", 101 filename=True), 102 ] 103 try: 104 #Insert extra parameters - at the start just in case there 105 #are any arguments which must come last: 106 self.parameters = extra_parameters + self.parameters 107 except AttributeError: 108 #Should we raise an error? The subclass should have set this up! 109 self.parameters = extra_parameters 110 _EmbossMinimalCommandLine.__init__(self, cmd, **kwargs)
111
112 - def _validate(self):
113 #Check the outfile, filter, or stdout option has been set. 114 #We can't simply do this via the required flag for the outfile 115 #output - this seems the simplest solution. 116 if not (self.outfile or self.filter or self.stdout): 117 raise ValueError("You must either set outfile (output filename), " 118 "or enable filter or stdout (output to stdout).") 119 return _EmbossMinimalCommandLine._validate(self)
120 121
122 -class Primer3Commandline(_EmbossCommandLine):
123 """Commandline object for the Primer3 interface from EMBOSS. 124 125 The precise set of supported arguments depends on your version of EMBOSS. 126 This version accepts arguments current at EMBOSS 6.1.0, but in order to 127 remain backwards compatible also support the old argument names as well. 128 129 e.g. Using EMBOSS 6.1.0 or later, 130 131 >>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True) 132 >>> cline.explainflag = True 133 >>> cline.osizeopt=20 134 >>> cline.psizeopt=200 135 >>> cline.outfile = "myresults.out" 136 >>> cline.bogusparameter = 1967 # Invalid parameter 137 Traceback (most recent call last): 138 ... 139 ValueError: Option name bogusparameter was not found. 140 >>> print(cline) 141 eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -psizeopt=200 -osizeopt=20 -explainflag=True 142 143 The equivalent for anyone still using an older version of EMBOSS would be: 144 145 >>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True) 146 >>> cline.explainflag = True 147 >>> cline.oligosize=20 # Old EMBOSS, instead of osizeopt 148 >>> cline.productosize=200 # Old EMBOSS, instead of psizeopt 149 >>> cline.outfile = "myresults.out" 150 >>> print(cline) 151 eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -productosize=200 -oligosize=20 -explainflag=True 152 153 """
154 - def __init__(self, cmd="eprimer3", **kwargs):
155 self.parameters = [ 156 _Option(["-sequence", "sequence"], 157 "Sequence to choose primers from.", 158 is_required=True), 159 _Option(["-task", "task"], 160 "Tell eprimer3 what task to perform."), 161 _Option(["-hybridprobe", "hybridprobe"], 162 "Find an internal oligo to use as a hyb probe."), 163 _Option(["-numreturn", "numreturn"], 164 "Maximum number of primer pairs to return."), 165 _Option(["-includedregion", "includedregion"], 166 "Subregion of the sequence in which to pick primers."), 167 _Option(["-target", "target"], 168 "Sequence to target for flanking primers."), 169 _Option(["-excludedregion", "excludedregion"], 170 "Regions to exclude from primer picking."), 171 _Option(["-forwardinput", "forwardinput"], 172 "Sequence of a forward primer to check."), 173 _Option(["-reverseinput", "reverseinput"], 174 "Sequence of a reverse primer to check."), 175 _Option(["-gcclamp", "gcclamp"], 176 "The required number of Gs and Cs at the 3' of each primer."), 177 _Option(["-osize", "osize"], 178 "Optimum length of a primer oligo."), 179 _Option(["-minsize", "minsize"], 180 "Minimum length of a primer oligo."), 181 _Option(["-maxsize", "maxsize"], 182 "Maximum length of a primer oligo."), 183 _Option(["-otm", "otm"], 184 "Optimum melting temperature for a primer oligo."), 185 _Option(["-mintm", "mintm"], 186 "Minimum melting temperature for a primer oligo."), 187 _Option(["-maxtm", "maxtm"], 188 "Maximum melting temperature for a primer oligo."), 189 _Option(["-maxdifftm", "maxdifftm"], 190 "Maximum difference in melting temperatures between " 191 "forward and reverse primers."), 192 _Option(["-ogcpercent", "ogcpercent"], 193 "Optimum GC% for a primer."), 194 _Option(["-mingc", "mingc"], 195 "Minimum GC% for a primer."), 196 _Option(["-maxgc", "maxgc"], 197 "Maximum GC% for a primer."), 198 _Option(["-saltconc", "saltconc"], 199 "Millimolar salt concentration in the PCR."), 200 _Option(["-dnaconc", "dnaconc"], 201 "Nanomolar concentration of annealing oligos in the PCR."), 202 _Option(["-maxpolyx", "maxpolyx"], 203 "Maximum allowable mononucleotide repeat length in a primer."), 204 #Primer length: 205 _Option(["-productosize", "productosize"], 206 """Optimum size for the PCR product (OBSOLETE). 207 208 Option replaced in EMBOSS 6.1.0 by -psizeopt 209 """), 210 _Option(["-psizeopt", "psizeopt"], 211 """Optimum size for the PCR product. 212 213 Option added in EMBOSS 6.1.0, replacing -productosize 214 """), 215 _Option(["-productsizerange", "productsizerange"], 216 """Acceptable range of length for the PCR product (OBSOLETE). 217 218 Option replaced in EMBOSS 6.1.0 by -prange 219 """), 220 _Option(["-prange", "prange"], 221 """Acceptable range of length for the PCR product. 222 223 Option added in EMBOSS 6.1.0, replacing -productsizerange 224 """), 225 #Primer temperature: 226 _Option(["-productotm", "productotm"], 227 """Optimum melting temperature for the PCR product (OBSOLETE). 228 229 Option replaced in EMBOSS 6.1.0 by -ptmopt 230 """), 231 _Option(["-ptmopt", "ptmopt"], 232 """Optimum melting temperature for the PCR product. 233 234 Option added in EMBOSS 6.1.0, replacing -productotm 235 """), 236 _Option(["-productmintm", "productmintm"], 237 """Minimum allowed melting temperature for the amplicon (OBSOLETE) 238 239 Option replaced in EMBOSS 6.1.0 by -ptmmin 240 """), 241 _Option(["-ptmmin", "ptmmin"], 242 """Minimum allowed melting temperature for the amplicon."), 243 244 Option added in EMBOSS 6.1.0, replacing -productmintm 245 """), 246 _Option(["-productmaxtm", "productmaxtm"], 247 """Maximum allowed melting temperature for the amplicon (OBSOLETE). 248 249 Option replaced in EMBOSS 6.1.0 by -ptmmax 250 """), 251 _Option(["-ptmmax", "ptmmax"], 252 """Maximum allowed melting temperature for the amplicon."), 253 254 Option added in EMBOSS 6.1.0, replacing -productmaxtm 255 """), 256 #Note to self, should be -oexcludedregion not -oexcluderegion 257 _Option(["-oexcludedregion", "oexcludedregion"], 258 """Do not pick internal oligos in this region."), 259 260 Option added in EMBOSS 6.1.0, replacing -oligoexcludedregion. 261 """), 262 _Option(["-oligoexcludedregion", "oligoexcludedregion"], 263 """Do not pick internal oligos in this region (OBSOLETE)."), 264 265 Option replaced in EMBOSS 6.1.0 by -oexcluderegion. 266 """), 267 _Option(["-oligoinput", "oligoinput"], 268 "Sequence of the internal oligo."), 269 #Oligo length: 270 _Option(["-oligosize", "oligosize"], 271 """Optimum length of internal oligo (OBSOLETE). 272 273 Option replaced in EMBOSS 6.1.0 by -osizeopt. 274 """), 275 _Option(["-osizeopt", "osizeopt"], 276 """Optimum length of internal oligo. 277 278 Option added in EMBOSS 6.1.0, replaces -oligosize 279 """), 280 _Option(["-oligominsize", "oligominsize"], 281 """Minimum length of internal oligo (OBSOLETE)."), 282 283 Option replaced in EMBOSS 6.1.0 by -ominsize. 284 """), 285 _Option(["-ominsize", "ominsize"], 286 """Minimum length of internal oligo." 287 288 Option added in EMBOSS 6.1.0, replaces -oligominsize 289 """), 290 _Option(["-oligomaxsize", "oligomaxsize"], 291 """Maximum length of internal oligo (OBSOLETE). 292 293 Option replaced in EMBOSS 6.1.0 by -omaxsize. 294 """), 295 _Option(["-omaxsize", "omaxsize"], 296 """Maximum length of internal oligo. 297 298 Option added in EMBOSS 6.1.0, replaces -oligomaxsize 299 """), 300 #Oligo GC temperature: 301 _Option(["-oligotm", "oligotm"], 302 """Optimum melting temperature of internal oligo (OBSOLETE). 303 304 Option replaced in EMBOSS 6.1.0 by -otmopt. 305 """), 306 _Option(["-otmopt", "otmopt"], 307 """Optimum melting temperature of internal oligo. 308 309 Option added in EMBOSS 6.1.0. 310 """), 311 _Option(["-oligomintm", "oligomintm"], 312 """Minimum melting temperature of internal oligo (OBSOLETE). 313 314 Option replaced in EMBOSS 6.1.0 by -otmmin. 315 """), 316 _Option(["-otmmin", "otmmin"], 317 """Minimum melting temperature of internal oligo. 318 319 Option added in EMBOSS 6.1.0, replacing -oligomintm 320 """), 321 _Option(["-oligomaxtm", "oligomaxtm"], 322 """Maximum melting temperature of internal oligo (OBSOLETE). 323 324 Option replaced in EMBOSS 6.1.0 by -otmmax. 325 """), 326 _Option(["-otmmax", "otmmax"], 327 """Maximum melting temperature of internal oligo. 328 329 Option added in EMBOSS 6.1.0, replacing -oligomaxtm 330 """), 331 #Oligo GC percent: 332 _Option(["-oligoogcpercent", "oligoogcpercent"], 333 """Optimum GC% for internal oligo (OBSOLETE). 334 335 Option replaced in EMBOSS 6.1.0 by -ogcopt. 336 """), 337 _Option(["-ogcopt", "ogcopt"], 338 """Optimum GC% for internal oligo." 339 340 Option added in EMBOSS 6.1.0, replacing -oligoogcpercent 341 """), 342 _Option(["-oligomingc", "oligomingc"], 343 """Minimum GC% for internal oligo (OBSOLETE). 344 345 Option replaced in EMBOSS 6.1.0 by -ogcmin. 346 """), 347 _Option(["-ogcmin", "ogcmin"], 348 """Minimum GC% for internal oligo. 349 350 Option added in EMBOSS 6.1.0, replacing -oligomingc 351 """), 352 _Option(["-oligomaxgc", "oligomaxgc"], 353 """Maximum GC% for internal oligo. 354 355 Option replaced in EMBOSS 6.1.0 by -ogcmax 356 """), 357 _Option(["-ogcmax", "ogcmax"], 358 """Maximum GC% for internal oligo."), 359 360 Option added in EMBOSS 6.1.0, replacing -oligomaxgc 361 """), 362 #Oligo salt concentration: 363 _Option(["-oligosaltconc", "oligosaltconc"], 364 """Millimolar concentration of salt in the hybridisation."), 365 366 Option replaced in EMBOSS 6.1.0 by -osaltconc 367 """), 368 _Option(["-osaltconc", "osaltconc"], 369 """Millimolar concentration of salt in the hybridisation."), 370 371 Option added in EMBOSS 6.1.0, replacing -oligosaltconc 372 """), 373 _Option(["-oligodnaconc", "oligodnaconc"], 374 """Nanomolar concentration of internal oligo in the hybridisation. 375 376 Option replaced in EMBOSS 6.1.0 by -odnaconc 377 """), 378 _Option(["-odnaconc", "odnaconc"], 379 """Nanomolar concentration of internal oligo in the hybridisation. 380 381 Option added in EMBOSS 6.1.0, replacing -oligodnaconc 382 """), 383 #Oligo self complementarity 384 _Option(["-oligoselfany", "oligoselfany"], 385 """Maximum allowable alignment score for self-complementarity (OBSOLETE). 386 387 Option replaced in EMBOSS 6.1.0 by -oanyself 388 """), 389 _Option(["-oanyself", "oanyself"], 390 """Maximum allowable alignment score for self-complementarity."), 391 392 Option added in EMBOSS 6.1.0, replacing -oligoselfany 393 """), 394 _Option(["-oligoselfend", "oligoselfend"], 395 """Maximum allowable 3`-anchored global alignment score " 396 for self-complementarity (OBSOLETE). 397 398 Option replaced in EMBOSS 6.1.0 by -oendself 399 """), 400 _Option(["-oendself", "oendself"], 401 """Max 3`-anchored self-complementarity global alignment score. 402 403 Option added in EMBOSS 6.1.0, replacing -oligoselfend 404 """), 405 _Option(["-oligomaxpolyx", "oligomaxpolyx"], 406 """Maximum length of mononucleotide repeat in internal oligo (OBSOLETE). 407 408 Option replaced in EMBOSS 6.1.0 by -opolyxmax 409 """), 410 _Option(["-opolyxmax", "opolyxmax"], 411 """Maximum length of mononucleotide repeat in internal oligo."), 412 413 Option added in EMBOSS 6.1.0, replacing -oligomaxpolyx 414 """), 415 _Option(["-mispriminglibraryfile", "mispriminglibraryfile"], 416 "File containing library of sequences to avoid amplifying"), 417 _Option(["-maxmispriming", "maxmispriming"], 418 "Maximum allowed similarity of primers to sequences in " 419 "library specified by -mispriminglibrary"), 420 _Option(["-oligomaxmishyb", "oligomaxmishyb"], 421 """Maximum alignment score for hybridisation of internal oligo to 422 library specified by -oligomishyblibraryfile (OBSOLETE). 423 424 Option replaced in EMBOSS 6.1.0 by -omishybmax 425 """), 426 _Option(["-omishybmax", "omishybmax"], 427 """Maximum alignment score for hybridisation of internal oligo to 428 library specified by -mishyblibraryfile. 429 430 Option added in EMBOSS 6.1.0, replacing -oligomaxmishyb 431 """), 432 _Option(["-oligomishyblibraryfile", "oligomishyblibraryfile"], 433 434 """Library file of seqs to avoid internal oligo hybridisation (OBSOLETE). 435 436 Option replaced in EMBOSS 6.1.0 by -mishyblibraryfile 437 """), 438 _Option(["-mishyblibraryfile", "mishyblibraryfile"], 439 """Library file of seqs to avoid internal oligo hybridisation. 440 441 Option added in EMBOSS 6.1.0, replacing -oligomishyblibraryfile 442 """), 443 _Option(["-explainflag", "explainflag"], 444 "Produce output tags with eprimer3 statistics"), 445 ] 446 _EmbossCommandLine.__init__(self, cmd, **kwargs)
447 448
449 -class PrimerSearchCommandline(_EmbossCommandLine):
450 """Commandline object for the primersearch program from EMBOSS. 451 """
452 - def __init__(self, cmd="primersearch", **kwargs):
453 self.parameters = [ 454 _Option(["-seqall", "-sequences", "sequences", "seqall"], 455 "Sequence to look for the primer pairs in.", 456 is_required=True), 457 #When this wrapper was written primersearch used -sequences 458 #as the argument name. Since at least EMBOSS 5.0 (and 459 #perhaps earlier) this has been -seqall instead. 460 _Option(["-infile", "-primers", "primers", "infile"], 461 "File containing the primer pairs to search for.", 462 filename=True, 463 is_required=True), 464 #When this wrapper was written primersearch used -primers 465 #as the argument name. Since at least EMBOSS 5.0 (and 466 #perhaps earlier) this has been -infile instead. 467 _Option(["-mismatchpercent", "mismatchpercent"], 468 "Allowed percentage mismatch (any integer value, default 0).", 469 is_required=True), 470 _Option(["-snucleotide", "snucleotide"], 471 "Sequences are nucleotide (boolean)"), 472 _Option(["-sprotein", "sprotein"], 473 "Sequences are protein (boolean)"), 474 ] 475 _EmbossCommandLine.__init__(self, cmd, **kwargs)
476 477
478 -class FDNADistCommandline(_EmbossCommandLine):
479 """Commandline object for the fdnadist program from EMBOSS. 480 481 fdnadist is an EMBOSS wrapper for the PHYLIP program dnadist for 482 calulating distance matrices from DNA sequence files. 483 """
484 - def __init__(self, cmd = "fdnadist", **kwargs):
485 self.parameters = [ 486 _Option(["-sequence", "sequence"], 487 "seq file to use (phylip)", 488 filename=True, 489 is_required=True), 490 _Option(["-method", "method"], 491 "sub. model [f,k,j,l,s]", 492 is_required=True), 493 _Option(["-gamma", "gamma"], 494 "gamma [g, i,n]"), 495 _Option(["-ncategories", "ncategories"], 496 "number of rate catergories (1-9)"), 497 _Option(["-rate", "rate"], 498 "rate for each category"), 499 _Option(["-categories", "categories"], 500 "File of substitution rate categories"), 501 _Option(["-weights", "weights"], 502 "weights file"), 503 _Option(["-gammacoefficient", "gammacoefficient"], 504 "value for gamma (> 0.001)"), 505 _Option(["-invarfrac", "invarfrac"], 506 "proportoin of invariant sites"), 507 _Option(["-ttratio", "ttratio"], 508 "ts/tv ratio"), 509 _Option(["-freqsfrom", "freqsfrom"], 510 "use emprical base freqs"), 511 _Option(["-basefreq", "basefreq"], 512 "specify basefreqs"), 513 _Option(["-lower", "lower"], 514 "lower triangle matrix (y/N)")] 515 _EmbossCommandLine.__init__(self, cmd, **kwargs)
516 517
518 -class FTreeDistCommandline(_EmbossCommandLine):
519 """Commandline object for the ftreedist program from EMBOSS. 520 521 ftreedist is an EMBOSS wrapper for the PHYLIP program treedist used for 522 calulating distance measures between phylogentic trees. 523 """
524 - def __init__(self, cmd = "ftreedist", **kwargs):
525 self.parameters = [ 526 _Option(["-intreefile", "intreefile"], 527 "tree file to score (phylip)", 528 filename=True, 529 is_required=True), 530 _Option(["-dtype", "dtype"], 531 "distance type ([S]ymetric, [b]ranch score)"), 532 _Option(["-pairing", "pairing"], 533 "tree pairing method ([A]djacent pairs, all [p]ossible pairs)"), 534 _Option(["-style", "style"], 535 "output style - [V]erbose, [f]ill, [s]parse"), 536 _Option(["-noroot", "noroot"], 537 "treat trees as rooted [N/y]"), 538 _Option(["-outgrno", "outgrno"], 539 "which taxon to root the trees with (starts from 0)")] 540 _EmbossCommandLine.__init__(self, cmd, **kwargs)
541 542
543 -class FNeighborCommandline(_EmbossCommandLine):
544 """Commandline object for the fneighbor program from EMBOSS. 545 546 fneighbor is an EMBOSS wrapper for the PHYLIP program neighbor used for 547 calulating neighbor-joining or UPGMA trees from distance matrices. 548 """
549 - def __init__(self, cmd = "fneighbor", **kwargs):
550 self.parameters = [ 551 _Option(["-datafile", "datafile"], 552 "dist file to use (phylip)", 553 filename=True, 554 is_required=True), 555 _Option(["-matrixtype", "matrixtype"], 556 "is martrix [S]quare pr [u]pper or [l]ower"), 557 _Option(["-treetype", "treetype"], 558 "nj or UPGMA tree (n/u)"), 559 _Option(["-outgrno", "outgrno" ], 560 "taxon to use as OG"), 561 _Option(["-jumble", "jumble"], 562 "randommise input order (Y/n)"), 563 _Option(["-seed", "seed"], 564 "provide a random seed"), 565 _Option(["-trout", "trout"], 566 "write tree (Y/n)"), 567 _Option(["-outtreefile", "outtreefile"], 568 "filename for output tree"), 569 _Option(["-progress", "progress"], 570 "print progress (Y/n)"), 571 _Option(["-treeprint", "treeprint"], 572 "print tree (Y/n)")] 573 _EmbossCommandLine.__init__(self, cmd, **kwargs)
574 575
576 -class FSeqBootCommandline(_EmbossCommandLine):
577 """Commandline object for the fseqboot program from EMBOSS. 578 579 fseqboot is an EMBOSS wrapper for the PHYLIP program seqboot used to 580 pseudo-sample alignment files. 581 """
582 - def __init__(self, cmd = "fseqboot", **kwargs):
583 self.parameters = [ 584 _Option(["-sequence", "sequence"], 585 "seq file to sample (phylip)", 586 filename=True, 587 is_required=True), 588 _Option(["-categories", "catergories"], 589 "file of input categories"), 590 _Option(["-weights", "weights"], 591 " weights file"), 592 _Option(["-test", "test"], 593 "specify operation, default is bootstrap"), 594 _Option(["-regular", "regular"], 595 "absolute number to resample"), 596 _Option(["-fracsample", "fracsample"], 597 "fraction to resample"), 598 _Option(["-rewriteformat", "rewriteformat"], 599 "output format ([P]hyilp, [n]exus, [x]ml"), 600 _Option(["-seqtype", "seqtype"], 601 "output format ([D]na, [p]rotein, [r]na"), 602 _Option(["-blocksize", "blocksize"], 603 "print progress (Y/n)"), 604 _Option(["-reps", "reps"], 605 "how many replicates, defaults to 100)"), 606 _Option(["-justweights", "jusweights"], 607 "what to write out [D]atasets of just [w]eights"), 608 _Option(["-seed", "seed"], 609 "specify random seed"), 610 _Option(["-dotdiff", "dotdiff"], 611 "Use dot-differencing? [Y/n]"),] 612 _EmbossCommandLine.__init__(self, cmd, **kwargs)
613 614
615 -class FDNAParsCommandline(_EmbossCommandLine):
616 """Commandline object for the fdnapars program from EMBOSS. 617 618 fdnapars is an EMBOSS version of the PHYLIP program dnapars, for 619 estimating trees from DNA sequences using parsiomny. Calling this command 620 without providing a value for the option "-intreefile" will invoke 621 "interactive mode" (and as a result fail if called with subprocess) if 622 "-auto" is not set to true. 623 """
624 - def __init__(self, cmd = "fdnapars", **kwargs):
625 self.parameters = [ 626 _Option(["-sequence", "sequence"], 627 "seq file to use (phylip)", 628 filename=True, 629 is_required=True), 630 _Option(["-intreefile", "intreefile"], 631 "Phylip tree file"), 632 _Option(["-weights", "weights"], 633 "weights file"), 634 _Option(["-maxtrees", "maxtrees"], 635 "max trees to save during run"), 636 _Option(["-thorough", "thorough"], 637 "more thorough search (Y/n)"), 638 _Option(["-rearrange", "rearrange"], 639 "Rearrange on jsut 1 best tree (Y/n)"), 640 _Option(["-transversion", "transversion"], 641 "Use tranversion parsimony (y/N)"), 642 _Option(["-njumble", "njumble"], 643 "number of times to randomise input order (default is 0)"), 644 _Option(["-seed", "seed"], 645 "provide random seed"), 646 _Option(["-outgrno", "outgrno"], 647 "Specify outgroup"), 648 _Option(["-thresh", "thresh"], 649 "Use threshold parsimony (y/N)"), 650 _Option(["-threshold", "threshold"], 651 "Threshold value"), 652 _Option(["-trout", "trout"], 653 "Write trees to file (Y/n)"), 654 _Option(["-outtreefile", "outtreefile"], 655 "filename for output tree"), 656 _Option(["-dotdiff", "dotdiff"], 657 "Use dot-differencing? [Y/n]")] 658 _EmbossCommandLine.__init__(self, cmd, **kwargs)
659 660
661 -class FProtParsCommandline(_EmbossCommandLine):
662 """Commandline object for the fdnapars program from EMBOSS. 663 664 fprotpars is an EMBOSS version of the PHYLIP program protpars, for 665 estimating trees from protein sequences using parsiomny. Calling this 666 command without providing a value for the option "-intreefile" will invoke 667 "interactive mode" (and as a result fail if called with subprocess) if 668 "-auto" is not set to true. 669 """
670 - def __init__(self, cmd = "fprotpars", **kwargs):
671 self.parameters = [ 672 _Option(["-sequence", "sequence"], 673 "seq file to use (phylip)", 674 filename=True, 675 is_required=True), 676 _Option(["-intreefile", "intreefile"], 677 "Phylip tree file to score"), 678 _Option(["-outtreefile", "outtreefile"], 679 "phylip tree output file", 680 filename=True, 681 is_required=True), 682 _Option(["-weights", "weights"], 683 "weights file"), 684 _Option(["-whichcode", "whichcode"], 685 "which genetic code, [U,M,V,F,Y]]"), 686 _Option(["-njumble", "njumble"], 687 "number of times to randomise input order (default is 0)"), 688 _Option(["-seed", "seed"], 689 "provide random seed"), 690 _Option(["-outgrno", "outgrno"], 691 "Specify outgroup"), 692 _Option(["-thresh", "thresh"], 693 "Use threshold parsimony (y/N)"), 694 _Option(["-threshold", "threshold"], 695 "Threshold value"), 696 _Option(["-trout", "trout"], 697 "Write trees to file (Y/n)"), 698 _Option(["-dotdiff", "dotdiff"], 699 "Use dot-differencing? [Y/n]")] 700 _EmbossCommandLine.__init__(self, cmd, **kwargs)
701 702
703 -class FProtDistCommandline(_EmbossCommandLine):
704 """Commandline object for the fprotdist program from EMBOSS. 705 706 fprotdist is an EMBOSS wrapper for the PHYLIP program protdist used to 707 estimate trees from protein sequences using parsimony 708 """
709 - def __init__(self, cmd = "fprotdist", **kwargs):
710 self.parameters = [ 711 _Option(["-sequence", "sequence"], 712 "seq file to use (phylip)", 713 filename=True, 714 is_required=True), 715 _Option(["-ncategories", "ncategories"], 716 "number of rate catergories (1-9)"), 717 _Option(["-rate", "rate"], 718 "rate for each category"), 719 _Option(["-catergories", "catergories"], 720 "file of rates"), 721 _Option(["-weights", "weights"], 722 "weights file"), 723 _Option(["-method", "method"], 724 "sub. model [j,h,d,k,s,c]"), 725 _Option(["-gamma", "gamma"], 726 "gamma [g, i,c]"), 727 _Option(["-gammacoefficient", "gammacoefficient"], 728 "value for gamma (> 0.001)"), 729 _Option(["-invarcoefficient", "invarcoefficient"], 730 "float for variation of substitution rate among sites"), 731 _Option(["-aacateg", "aacateg"], 732 "Choose the category to use [G,C,H]"), 733 _Option(["-whichcode", "whichcode"], 734 "genetic code [c,m,v,f,y]"), 735 _Option(["-ease", "ease"], 736 "Pob change catergory (float between -0 and 1)"), 737 _Option(["-ttratio", "ttratio"], 738 "Transition/transversion ratio (0-1)"), 739 _Option(["-basefreq", "basefreq"], 740 "DNA base frequencies (space separated list)")] 741 _EmbossCommandLine.__init__(self, cmd, **kwargs)
742 743
744 -class FConsenseCommandline(_EmbossCommandLine):
745 """Commandline object for the fconsense program from EMBOSS. 746 747 fconsense is an EMBOSS wrapper for the PHYLIP program consense used to 748 calculate consensus trees. 749 """
750 - def __init__(self, cmd = "fconsense", **kwargs):
751 self.parameters = [ 752 _Option(["-intreefile", "intreefile"], 753 "file with phylip trees to make consensus from", 754 filename=True, 755 is_required=True), 756 _Option(["-method", "method"], 757 "consensus method [s, mr, MRE, ml]"), 758 _Option(["-mlfrac", "mlfrac"], 759 "cut-off freq for a branch to appear in consensus (0.5-1.0)"), 760 _Option(["-root", "root"], 761 "treat trees as rooted (YES, no)"), 762 _Option(["-outgrno", "outgrno"], 763 "OTU to use as outgroup (starts from 0)"), 764 _Option(["-trout", "trout"], 765 "treat trees as rooted (YES, no)"), 766 _Option(["-outtreefile", "outtreefile"], 767 "Phylip tree output file (optional)")] 768 _EmbossCommandLine.__init__(self, cmd, **kwargs)
769 770
771 -class WaterCommandline(_EmbossCommandLine):
772 """Commandline object for the water program from EMBOSS. 773 """
774 - def __init__(self, cmd="water", **kwargs):
775 self.parameters = [ 776 _Option(["-asequence", "asequence"], 777 "First sequence to align", 778 filename=True, 779 is_required=True), 780 _Option(["-bsequence", "bsequence"], 781 "Second sequence to align", 782 filename=True, 783 is_required=True), 784 _Option(["-gapopen", "gapopen"], 785 "Gap open penalty", 786 is_required=True), 787 _Option(["-gapextend", "gapextend"], 788 "Gap extension penalty", 789 is_required=True), 790 _Option(["-datafile", "datafile"], 791 "Matrix file", 792 filename=True), 793 _Switch(["-nobrief", "nobrief"], 794 "Display extended identity and similarity"), 795 _Switch(["-brief", "brief"], 796 "Display brief identity and similarity"), 797 _Option(["-similarity", "similarity"], 798 "Display percent identity and similarity"), 799 _Option(["-snucleotide", "snucleotide"], 800 "Sequences are nucleotide (boolean)"), 801 _Option(["-sprotein", "sprotein"], 802 "Sequences are protein (boolean)"), 803 _Option(["-aformat", "aformat"], 804 "Display output in a different specified output format")] 805 _EmbossCommandLine.__init__(self, cmd, **kwargs)
806 807
808 -class NeedleCommandline(_EmbossCommandLine):
809 """Commandline object for the needle program from EMBOSS. 810 """
811 - def __init__(self, cmd="needle", **kwargs):
812 self.parameters = [ 813 _Option(["-asequence", "asequence"], 814 "First sequence to align", 815 filename=True, 816 is_required=True), 817 _Option(["-bsequence", "bsequence"], 818 "Second sequence to align", 819 filename=True, 820 is_required=True), 821 _Option(["-gapopen", "gapopen"], 822 "Gap open penalty", 823 is_required=True), 824 _Option(["-gapextend", "gapextend"], 825 "Gap extension penalty", 826 is_required=True), 827 _Option(["-datafile", "datafile"], 828 "Matrix file", 829 filename=True), 830 _Option(["-endweight", "endweight"], 831 "Apply And gap penalties"), 832 _Option(["-endopen", "endopen"], 833 "The score taken away when an end gap is created."), 834 _Option(["-endextend", "endextend"], 835 "The score added to the end gap penality for each base or " 836 "residue in the end gap."), 837 _Switch(["-nobrief", "nobrief"], 838 "Display extended identity and similarity"), 839 _Switch(["-brief", "brief"], 840 "Display brief identity and similarity"), 841 _Option(["-similarity", "similarity"], 842 "Display percent identity and similarity"), 843 _Option(["-snucleotide", "snucleotide"], 844 "Sequences are nucleotide (boolean)"), 845 _Option(["-sprotein", "sprotein"], 846 "Sequences are protein (boolean)"), 847 _Option(["-aformat", "aformat"], 848 "Display output in a different specified output format")] 849 _EmbossCommandLine.__init__(self, cmd, **kwargs)
850 851
852 -class NeedleallCommandline(_EmbossCommandLine):
853 """Commandline object for the needleall program from EMBOSS. 854 """
855 - def __init__(self, cmd="needleall", **kwargs):
856 self.parameters = [ 857 _Option(["-asequence", "asequence"], 858 "First sequence to align", 859 filename=True, 860 is_required=True), 861 _Option(["-bsequence", "bsequence"], 862 "Second sequence to align", 863 filename=True, 864 is_required=True), 865 _Option(["-gapopen", "gapopen"], 866 "Gap open penalty", 867 is_required=True), 868 _Option(["-gapextend", "gapextend"], 869 "Gap extension penalty", 870 is_required=True), 871 _Option(["-datafile", "datafile"], 872 "Matrix file", 873 filename=True), 874 _Option(["-minscore", "minscore"], 875 "Exclude alignments with scores below this threshold score."), 876 _Option(["-errorfile", "errorfile"], 877 "Error file to be written to."), 878 _Option(["-endweight", "endweight"], 879 "Apply And gap penalties"), 880 _Option(["-endopen", "endopen"], 881 "The score taken away when an end gap is created."), 882 _Option(["-endextend", "endextend"], 883 "The score added to the end gap penality for each base or " 884 "residue in the end gap."), 885 _Switch(["-nobrief", "nobrief"], 886 "Display extended identity and similarity"), 887 _Switch(["-brief", "brief"], 888 "Display brief identity and similarity"), 889 _Option(["-similarity", "similarity"], 890 "Display percent identity and similarity"), 891 _Option(["-snucleotide", "snucleotide"], 892 "Sequences are nucleotide (boolean)"), 893 _Option(["-sprotein", "sprotein"], 894 "Sequences are protein (boolean)"), 895 _Option(["-aformat", "aformat"], 896 "Display output in a different specified output format")] 897 _EmbossCommandLine.__init__(self, cmd, **kwargs)
898 899
900 -class StretcherCommandline(_EmbossCommandLine):
901 """Commandline object for the stretcher program from EMBOSS. 902 """
903 - def __init__(self, cmd="stretcher", **kwargs):
904 self.parameters = [ 905 _Option(["-asequence", "asequence"], 906 "First sequence to align", 907 filename=True, 908 is_required=True), 909 _Option(["-bsequence", "bsequence"], 910 "Second sequence to align", 911 filename=True, 912 is_required=True), 913 _Option(["-gapopen", "gapopen"], 914 "Gap open penalty", 915 is_required=True, 916 checker_function=lambda value: isinstance(value, int)), 917 _Option(["-gapextend", "gapextend"], 918 "Gap extension penalty", 919 is_required=True, 920 checker_function=lambda value: isinstance(value, int)), 921 _Option(["-datafile", "datafile"], 922 "Matrix file", 923 filename=True), 924 _Option(["-snucleotide", "snucleotide"], 925 "Sequences are nucleotide (boolean)"), 926 _Option(["-sprotein", "sprotein"], 927 "Sequences are protein (boolean)"), 928 _Option(["-aformat", "aformat"], 929 "Display output in a different specified output format")] 930 _EmbossCommandLine.__init__(self, cmd, **kwargs)
931 932
933 -class FuzznucCommandline(_EmbossCommandLine):
934 """Commandline object for the fuzznuc program from EMBOSS. 935 """
936 - def __init__(self, cmd="fuzznuc", **kwargs):
937 self.parameters = [ 938 _Option(["-sequence", "sequence"], 939 "Sequence database USA", 940 is_required=True), 941 _Option(["-pattern", "pattern"], 942 "Search pattern, using standard IUPAC one-letter codes", 943 is_required=True), 944 _Option(["-mismatch", "mismatch"], 945 "Number of mismatches", 946 is_required=True), 947 _Option(["-complement", "complement"], 948 "Search complementary strand"), 949 _Option(["-rformat", "rformat"], 950 "Specify the report format to output in.")] 951 _EmbossCommandLine.__init__(self, cmd, **kwargs)
952 953
954 -class Est2GenomeCommandline(_EmbossCommandLine):
955 """Commandline object for the est2genome program from EMBOSS. 956 """
957 - def __init__(self, cmd="est2genome", **kwargs):
958 self.parameters = [ 959 _Option(["-est", "est"], 960 "EST sequence(s)", 961 is_required=True), 962 _Option(["-genome", "genome"], 963 "Genomic sequence", 964 is_required=True), 965 _Option(["-match", "match"], 966 "Score for matching two bases"), 967 _Option(["-mismatch", "mismatch"], 968 "Cost for mismatching two bases"), 969 _Option(["-gappenalty", "gappenalty"], 970 "Cost for deleting a single base in either sequence, " 971 "excluding introns"), 972 _Option(["-intronpenalty", "intronpenalty"], 973 "Cost for an intron, independent of length."), 974 _Option(["-splicepenalty", "splicepenalty"], 975 "Cost for an intron, independent of length " 976 "and starting/ending on donor-acceptor sites"), 977 _Option(["-minscore", "minscore"], 978 "Exclude alignments with scores below this threshold score."), 979 _Option(["-reverse", "reverse"], 980 "Reverse the orientation of the EST sequence"), 981 _Option(["-splice", "splice"], 982 "Use donor and acceptor splice sites."), 983 _Option(["-mode", "mode"], 984 "This determines the comparion mode. 'both', 'forward' " 985 "'reverse'"), 986 _Option(["-best", "best"], 987 "You can print out all comparisons instead of just the best"), 988 _Option(["-space", "space"], 989 "for linear-space recursion."), 990 _Option(["-shuffle", "shuffle"], 991 "Shuffle"), 992 _Option(["-seed", "seed"], 993 "Random number seed"), 994 _Option(["-align", "align"], 995 "Show the alignment."), 996 _Option(["-width", "width"], 997 "Alignment width") 998 ] 999 _EmbossCommandLine.__init__(self, cmd, **kwargs)
1000 1001
1002 -class ETandemCommandline(_EmbossCommandLine):
1003 """Commandline object for the etandem program from EMBOSS. 1004 """
1005 - def __init__(self, cmd="etandem", **kwargs):
1006 self.parameters = [ 1007 _Option(["-sequence", "sequence"], 1008 "Sequence", 1009 filename=True, 1010 is_required=True), 1011 _Option(["-minrepeat", "minrepeat"], 1012 "Minimum repeat size", 1013 is_required=True), 1014 _Option(["-maxrepeat", "maxrepeat"], 1015 "Maximum repeat size", 1016 is_required=True), 1017 _Option(["-threshold", "threshold"], 1018 "Threshold score"), 1019 _Option(["-mismatch", "mismatch"], 1020 "Allow N as a mismatch"), 1021 _Option(["-uniform", "uniform"], 1022 "Allow uniform consensus"), 1023 _Option(["-rformat", "rformat"], 1024 "Output report format")] 1025 _EmbossCommandLine.__init__(self, cmd, **kwargs)
1026 1027
1028 -class EInvertedCommandline(_EmbossCommandLine):
1029 """Commandline object for the einverted program from EMBOSS. 1030 """
1031 - def __init__(self, cmd="einverted", **kwargs):
1032 self.parameters = [ 1033 _Option(["-sequence", "sequence"], 1034 "Sequence", 1035 filename=True, 1036 is_required=True), 1037 _Option(["-gap", "gap"], 1038 "Gap penalty", 1039 filename=True, 1040 is_required=True), 1041 _Option(["-threshold", "threshold"], 1042 "Minimum score threshold", 1043 is_required=True), 1044 _Option(["-match", "match"], 1045 "Match score", 1046 is_required=True), 1047 _Option(["-mismatch", "mismatch"], 1048 "Mismatch score", 1049 is_required=True), 1050 _Option(["-maxrepeat", "maxrepeat"], 1051 "Maximum separation between the start and end of repeat"), 1052 ] 1053 _EmbossCommandLine.__init__(self, cmd, **kwargs)
1054 1055
1056 -class PalindromeCommandline(_EmbossCommandLine):
1057 """Commandline object for the palindrome program from EMBOSS. 1058 """
1059 - def __init__(self, cmd="palindrome", **kwargs):
1060 self.parameters = [ 1061 _Option(["-sequence", "sequence"], 1062 "Sequence", 1063 filename=True, 1064 is_required=True), 1065 _Option(["-minpallen", "minpallen"], 1066 "Minimum palindrome length", 1067 is_required=True), 1068 _Option(["-maxpallen", "maxpallen"], 1069 "Maximum palindrome length", 1070 is_required=True), 1071 _Option(["-gaplimit", "gaplimit"], 1072 "Maximum gap between repeats", 1073 is_required=True), 1074 _Option(["-nummismatches", "nummismatches"], 1075 "Number of mismatches allowed", 1076 is_required=True), 1077 _Option(["-overlap", "overlap"], 1078 "Report overlapping matches", 1079 is_required=True), 1080 ] 1081 _EmbossCommandLine.__init__(self, cmd, **kwargs)
1082 1083
1084 -class TranalignCommandline(_EmbossCommandLine):
1085 """Commandline object for the tranalign program from EMBOSS. 1086 """
1087 - def __init__(self, cmd="tranalign", **kwargs):
1088 self.parameters = [ 1089 _Option(["-asequence", "asequence"], 1090 "Nucleotide sequences to be aligned.", 1091 filename=True, 1092 is_required=True), 1093 _Option(["-bsequence", "bsequence"], 1094 "Protein sequence alignment", 1095 filename=True, 1096 is_required=True), 1097 _Option(["-outseq", "outseq"], 1098 "Output sequence file.", 1099 filename=True, 1100 is_required=True), 1101 _Option(["-table", "table"], 1102 "Code to use")] 1103 _EmbossCommandLine.__init__(self, cmd, **kwargs)
1104 1105
1106 -class DiffseqCommandline(_EmbossCommandLine):
1107 """Commandline object for the diffseq program from EMBOSS. 1108 """
1109 - def __init__(self, cmd="diffseq", **kwargs):
1110 self.parameters = [ 1111 _Option(["-asequence", "asequence"], 1112 "First sequence to compare", 1113 filename=True, 1114 is_required=True), 1115 _Option(["-bsequence", "bsequence"], 1116 "Second sequence to compare", 1117 filename=True, 1118 is_required=True), 1119 _Option(["-wordsize", "wordsize"], 1120 "Word size to use for comparisons (10 default)", 1121 is_required=True), 1122 _Option(["-aoutfeat", "aoutfeat"], 1123 "File for output of first sequence's features", 1124 filename=True, 1125 is_required=True), 1126 _Option(["-boutfeat", "boutfeat"], 1127 "File for output of second sequence's features", 1128 filename=True, 1129 is_required=True), 1130 _Option(["-rformat", "rformat"], 1131 "Output report file format") 1132 ] 1133 _EmbossCommandLine.__init__(self, cmd, **kwargs)
1134 1135
1136 -class IepCommandline(_EmbossCommandLine):
1137 """Commandline for EMBOSS iep: calculated isoelectric point and charge. 1138 1139 Example: 1140 1141 >>> from Bio.Emboss.Applications import IepCommandline 1142 >>> iep_cline = IepCommandline(sequence="proteins.faa", 1143 ... outfile="proteins.txt") 1144 >>> print(iep_cline) 1145 iep -outfile=proteins.txt -sequence=proteins.faa 1146 1147 You would typically run the command line with iep_cline() or via the 1148 Python subprocess module, as described in the Biopython tutorial. 1149 """
1150 - def __init__(self, cmd="iep", **kwargs):
1151 self.parameters = [ 1152 _Option(["-sequence", "sequence"], 1153 "Protein sequence(s) filename", 1154 filename=True, 1155 is_required=True), 1156 _Option(["-amino", "amino"], 1157 """Number of N-termini 1158 1159 Integer 0 (default) or more. 1160 """), 1161 _Option(["-carboxyl", "carboxyl"], 1162 """Number of C-termini 1163 1164 Integer 0 (default) or more. 1165 """), 1166 _Option(["-lysinemodified", "lysinemodified"], 1167 """Number of modified lysines 1168 1169 Integer 0 (default) or more. 1170 """), 1171 _Option(["-disulphides", "disulphides"], 1172 """Number of disulphide bridges 1173 1174 Integer 0 (default) or more. 1175 """), 1176 #Should we implement the -termini switch as well? 1177 _Option(["-notermini", "notermini"], 1178 "Exclude (True) or include (False) charge at N and C terminus."), 1179 ] 1180 _EmbossCommandLine.__init__(self, cmd, **kwargs)
1181 1182 1183 #seqret uses -outseq, not -outfile, so use the base class:
1184 -class SeqretCommandline(_EmbossMinimalCommandLine):
1185 """Commandline object for the seqret program from EMBOSS. 1186 1187 This tool allows you to interconvert between different sequence file 1188 formats (e.g. GenBank to FASTA). Combining Biopython's Bio.SeqIO module 1189 with seqret using a suitable intermediate file format can allow you to 1190 read/write to an even wider range of file formats. 1191 1192 This wrapper currently only supports the core functionality, things like 1193 feature tables (in EMBOSS 6.1.0 onwards) are not yet included. 1194 """
1195 - def __init__(self, cmd="seqret", **kwargs):
1196 self.parameters = [ 1197 _Option(["-sequence", "sequence"], 1198 "Input sequence(s) filename", 1199 filename=True), 1200 _Option(["-outseq", "outseq"], 1201 "Output sequence file.", 1202 filename=True), 1203 _Option(["-sformat", "sformat"], 1204 "Input sequence(s) format (e.g. fasta, genbank)"), 1205 _Option(["-osformat", "osformat"], 1206 "Output sequence(s) format (e.g. fasta, genbank)"), 1207 ] 1208 _EmbossMinimalCommandLine.__init__(self, cmd, **kwargs)
1209
1210 - def _validate(self):
1211 #Check the outfile, filter, or stdout option has been set. 1212 #We can't simply do this via the required flag for the outfile 1213 #output - this seems the simplest solution. 1214 if not (self.outseq or self.filter or self.stdout): 1215 raise ValueError("You must either set outfile (output filename), " 1216 "or enable filter or stdout (output to stdout).") 1217 if not (self.sequence or self.filter or self.stdint): 1218 raise ValueError("You must either set sequence (input filename), " 1219 "or enable filter or stdin (input from stdin).") 1220 return _EmbossMinimalCommandLine._validate(self)
1221 1222
1223 -class SeqmatchallCommandline(_EmbossCommandLine):
1224 """ Commandline object for the seqmatchall program from EMBOSS 1225 1226 e.g. 1227 >>> cline = SeqmatchallCommandline(sequence="opuntia.fasta", outfile="opuntia.txt") 1228 >>> cline.auto = True 1229 >>> cline.wordsize = 18 1230 >>> cline.aformat = "pair" 1231 >>> print(cline) 1232 seqmatchall -auto -outfile=opuntia.txt -sequence=opuntia.fasta -wordsize=18 -aformat=pair 1233 1234 """
1235 - def __init__(self, cmd="seqmatchall", **kwargs):
1236 self.parameters = [ 1237 _Option(["-sequence", "sequence"], 1238 "Readable set of sequences", 1239 filename=True, 1240 is_required=True), 1241 _Option(["-wordsize", "wordsize"], 1242 "Word size (Integer 2 or more, default 4)"), 1243 _Option(["-aformat", "aformat"], 1244 "Display output in a different specified output format"), 1245 ] 1246 _EmbossCommandLine.__init__(self, cmd, **kwargs)
1247 1248
1249 -def _test():
1250 """Run the Bio.Emboss.Applications module doctests.""" 1251 import doctest 1252 doctest.testmod()
1253 1254 if __name__ == "__main__": 1255 #Run the doctests 1256 _test() 1257