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 Bio.Application import _Option, _Switch, AbstractCommandline 16 17

18 -class _EmbossMinimalCommandLine(AbstractCommandline):

19 """Base Commandline object for EMBOSS wrappers (PRIVATE). 20 21 This is provided for subclassing, it deals with shared options 22 common to all the EMBOSS tools: 23 24 - auto Turn off prompts 25 - stdout Write standard output 26 - filter Read standard input, write standard output 27 - options Prompt for standard and additional values 28 - debug Write debug output to program.dbg 29 - verbose Report some/full command line options 30 - help Report command line options. More 31 information on associated and general 32 qualifiers can be found with -help -verbose 33 - warning Report warnings 34 - error Report errors 35 - fatal Report fatal errors 36 - die Report dying program messages 37 """

38 - def __init__(self, cmd=None, **kwargs):

39 assert cmd is not None 40 extra_parameters = [ 41 _Switch(["-auto","auto"], 42 """Turn off prompts. 43 44 Automatic mode disables prompting, so we recommend you set 45 this argument all the time when calling an EMBOSS tool from 46 Biopython. 47 """), 48 _Switch(["-stdout","stdout"], 49 "Write standard output."), 50 _Switch(["-filter","filter"], 51 "Read standard input, write standard output."), 52 _Switch(["-options","options"], 53 """Prompt for standard and additional values. 54 55 If you are calling an EMBOSS tool from within Biopython, 56 we DO NOT recommend using this option. 57 """), 58 _Switch(["-debug","debug"], 59 "Write debug output to program.dbg."), 60 _Switch(["-verbose","verbose"], 61 "Report some/full command line options"), 62 _Switch(["-help","help"], 63 """Report command line options. 64 65 More information on associated and general qualifiers can 66 be found with -help -verbose 67 """), 68 _Switch(["-warning","warning"], 69 "Report warnings."), 70 _Switch(["-error","error"], 71 "Report errors."), 72 _Switch(["-die","die"], 73 "Report dying program messages."), 74 ] 75 try: 76 #Insert extra parameters - at the start just in case there 77 #are any arguments which must come last: 78 self.parameters = extra_parameters + self.parameters 79 except AttributeError: 80 #Should we raise an error? The subclass should have set this up! 81 self.parameters = extra_parameters 82 AbstractCommandline.__init__(self, cmd, **kwargs)

83 84

85 -class _EmbossCommandLine(_EmbossMinimalCommandLine):

86 """Base Commandline object for EMBOSS wrappers (PRIVATE). 87 88 This is provided for subclassing, it deals with shared options 89 common to all the EMBOSS tools plus: 90 91 - outfile Output filename 92 93 """

94 - def __init__(self, cmd=None, **kwargs):

95 assert cmd is not None 96 extra_parameters = [ 97 _Option(["-outfile","outfile"], 98 "Output filename", 99 filename=True), 100 ] 101 try: 102 #Insert extra parameters - at the start just in case there 103 #are any arguments which must come last: 104 self.parameters = extra_parameters + self.parameters 105 except AttributeError: 106 #Should we raise an error? The subclass should have set this up! 107 self.parameters = extra_parameters 108 _EmbossMinimalCommandLine.__init__(self, cmd, **kwargs)

109

110 - def _validate(self):

111 #Check the outfile, filter, or stdout option has been set. 112 #We can't simply do this via the required flag for the outfile 113 #output - this seems the simplest solution. 114 if not (self.outfile or self.filter or self.stdout): 115 raise ValueError("You must either set outfile (output filename), " 116 "or enable filter or stdout (output to stdout).") 117 return _EmbossMinimalCommandLine._validate(self)

118 119

120 -class Primer3Commandline(_EmbossCommandLine):

121 """Commandline object for the Primer3 interface from EMBOSS. 122 123 The precise set of supported arguments depends on your version of EMBOSS. 124 This version accepts arguments current at EMBOSS 6.1.0, but in order to 125 remain backwards compatible also support the old argument names as well. 126 127 e.g. Using EMBOSS 6.1.0 or later, 128 129 >>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True) 130 >>> cline.explainflag = True 131 >>> cline.osizeopt=20 132 >>> cline.psizeopt=200 133 >>> cline.outfile = "myresults.out" 134 >>> cline.bogusparameter = 1967 # Invalid parameter 135 Traceback (most recent call last): 136 ... 137 ValueError: Option name bogusparameter was not found. 138 >>> print cline 139 eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -psizeopt=200 -osizeopt=20 -explainflag=True 140 141 The equivalent for anyone still using an older version of EMBOSS would be: 142 143 >>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True) 144 >>> cline.explainflag = True 145 >>> cline.oligosize=20 # Old EMBOSS, instead of osizeopt 146 >>> cline.productosize=200 # Old EMBOSS, instead of psizeopt 147 >>> cline.outfile = "myresults.out" 148 >>> print cline 149 eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -productosize=200 -oligosize=20 -explainflag=True 150 151 """

152 - def __init__(self, cmd="eprimer3", **kwargs):

153 self.parameters = [ 154 _Option(["-sequence","sequence"], 155 "Sequence to choose primers from.", 156 is_required=True), 157 _Option(["-task","task"], 158 "Tell eprimer3 what task to perform."), 159 _Option(["-hybridprobe","hybridprobe"], 160 "Find an internal oligo to use as a hyb probe."), 161 _Option(["-numreturn","numreturn"], 162 "Maximum number of primer pairs to return."), 163 _Option(["-includedregion","includedregion"], 164 "Subregion of the sequence in which to pick primers."), 165 _Option(["-target","target"], 166 "Sequence to target for flanking primers."), 167 _Option(["-excludedregion","excludedregion"], 168 "Regions to exclude from primer picking."), 169 _Option(["-forwardinput","forwardinput"], 170 "Sequence of a forward primer to check."), 171 _Option(["-reverseinput","reverseinput"], 172 "Sequence of a reverse primer to check."), 173 _Option(["-gcclamp","gcclamp"], 174 "The required number of Gs and Cs at the 3' of each primer."), 175 _Option(["-osize","osize"], 176 "Optimum length of a primer oligo."), 177 _Option(["-minsize","minsize"], 178 "Minimum length of a primer oligo."), 179 _Option(["-maxsize","maxsize"], 180 "Maximum length of a primer oligo."), 181 _Option(["-otm","otm"], 182 "Optimum melting temperature for a primer oligo."), 183 _Option(["-mintm","mintm"], 184 "Minimum melting temperature for a primer oligo."), 185 _Option(["-maxtm","maxtm"], 186 "Maximum melting temperature for a primer oligo."), 187 _Option(["-maxdifftm","maxdifftm"], 188 "Maximum difference in melting temperatures between " 189 "forward and reverse primers."), 190 _Option(["-ogcpercent","ogcpercent"], 191 "Optimum GC% for a primer."), 192 _Option(["-mingc","mingc"], 193 "Minimum GC% for a primer."), 194 _Option(["-maxgc","maxgc"], 195 "Maximum GC% for a primer."), 196 _Option(["-saltconc","saltconc"], 197 "Millimolar salt concentration in the PCR."), 198 _Option(["-dnaconc","dnaconc"], 199 "Nanomolar concentration of annealing oligos in the PCR."), 200 _Option(["-maxpolyx","maxpolyx"], 201 "Maximum allowable mononucleotide repeat length in a primer."), 202 #Primer length: 203 _Option(["-productosize","productosize"], 204 """Optimum size for the PCR product (OBSOLETE). 205 206 Option replaced in EMBOSS 6.1.0 by -psizeopt 207 """), 208 _Option(["-psizeopt", "psizeopt"], 209 """Optimum size for the PCR product. 210 211 Option added in EMBOSS 6.1.0, replacing -productosize 212 """), 213 _Option(["-productsizerange","productsizerange"], 214 """Acceptable range of length for the PCR product (OBSOLETE). 215 216 Option replaced in EMBOSS 6.1.0 by -prange 217 """), 218 _Option(["-prange", "prange"], 219 """Acceptable range of length for the PCR product. 220 221 Option added in EMBOSS 6.1.0, replacing -productsizerange 222 """), 223 #Primer temperature: 224 _Option(["-productotm","productotm"], 225 """Optimum melting temperature for the PCR product (OBSOLETE). 226 227 Option replaced in EMBOSS 6.1.0 by -ptmopt 228 """), 229 _Option(["-ptmopt", "ptmopt"], 230 """Optimum melting temperature for the PCR product. 231 232 Option added in EMBOSS 6.1.0, replacing -productotm 233 """), 234 _Option(["-productmintm","productmintm"], 235 """Minimum allowed melting temperature for the amplicon (OBSOLETE) 236 237 Option replaced in EMBOSS 6.1.0 by -ptmmin 238 """), 239 _Option(["-ptmmin", "ptmmin"], 240 """Minimum allowed melting temperature for the amplicon."), 241 242 Option added in EMBOSS 6.1.0, replacing -productmintm 243 """), 244 _Option(["-productmaxtm","productmaxtm"], 245 """Maximum allowed melting temperature for the amplicon (OBSOLETE). 246 247 Option replaced in EMBOSS 6.1.0 by -ptmmax 248 """), 249 _Option(["-ptmmax", "ptmmax"], 250 """Maximum allowed melting temperature for the amplicon."), 251 252 Option added in EMBOSS 6.1.0, replacing -productmaxtm 253 """), 254 #Note to self, should be -oexcludedregion not -oexcluderegion 255 _Option(["-oexcludedregion", "oexcludedregion"], 256 """Do not pick internal oligos in this region."), 257 258 Option added in EMBOSS 6.1.0, replacing -oligoexcludedregion. 259 """), 260 _Option(["-oligoexcludedregion", "oligoexcludedregion"], 261 """Do not pick internal oligos in this region (OBSOLETE)."), 262 263 Option replaced in EMBOSS 6.1.0 by -oexcluderegion. 264 """), 265 _Option(["-oligoinput","oligoinput"], 266 "Sequence of the internal oligo."), 267 #Oligo length: 268 _Option(["-oligosize","oligosize"], 269 """Optimum length of internal oligo (OBSOLETE). 270 271 Option replaced in EMBOSS 6.1.0 by -osizeopt. 272 """), 273 _Option(["-osizeopt", "osizeopt"], 274 """Optimum length of internal oligo. 275 276 Option added in EMBOSS 6.1.0, replaces -oligosize 277 """), 278 _Option(["-oligominsize","oligominsize"], 279 """Minimum length of internal oligo (OBSOLETE)."), 280 281 Option replaced in EMBOSS 6.1.0 by -ominsize. 282 """), 283 _Option(["-ominsize", "ominsize"], 284 """Minimum length of internal oligo." 285 286 Option added in EMBOSS 6.1.0, replaces -oligominsize 287 """), 288 _Option(["-oligomaxsize","oligomaxsize"], 289 """Maximum length of internal oligo (OBSOLETE). 290 291 Option replaced in EMBOSS 6.1.0 by -omaxsize. 292 """), 293 _Option(["-omaxsize", "omaxsize"], 294 """Maximum length of internal oligo. 295 296 Option added in EMBOSS 6.1.0, replaces -oligomaxsize 297 """), 298 #Oligo GC temperature: 299 _Option(["-oligotm","oligotm"], 300 """Optimum melting temperature of internal oligo (OBSOLETE). 301 302 Option replaced in EMBOSS 6.1.0 by -otmopt. 303 """), 304 _Option(["-otmopt", "otmopt"], 305 """Optimum melting temperature of internal oligo. 306 307 Option added in EMBOSS 6.1.0. 308 """), 309 _Option(["-oligomintm","oligomintm"], 310 """Minimum melting temperature of internal oligo (OBSOLETE). 311 312 Option replaced in EMBOSS 6.1.0 by -otmmin. 313 """), 314 _Option(["-otmmin", "otmmin"], 315 """Minimum melting temperature of internal oligo. 316 317 Option added in EMBOSS 6.1.0, replacing -oligomintm 318 """), 319 _Option(["-oligomaxtm","oligomaxtm"], 320 """Maximum melting temperature of internal oligo (OBSOLETE). 321 322 Option replaced in EMBOSS 6.1.0 by -otmmax. 323 """), 324 _Option(["-otmmax", "otmmax"], 325 """Maximum melting temperature of internal oligo. 326 327 Option added in EMBOSS 6.1.0, replacing -oligomaxtm 328 """), 329 #Oligo GC percent: 330 _Option(["-oligoogcpercent","oligoogcpercent"], 331 """Optimum GC% for internal oligo (OBSOLETE). 332 333 Option replaced in EMBOSS 6.1.0 by -ogcopt. 334 """), 335 _Option(["-ogcopt", "ogcopt"], 336 """Optimum GC% for internal oligo." 337 338 Option added in EMBOSS 6.1.0, replacing -oligoogcpercent 339 """), 340 _Option(["-oligomingc","oligomingc"], 341 """Minimum GC% for internal oligo (OBSOLETE). 342 343 Option replaced in EMBOSS 6.1.0 by -ogcmin. 344 """), 345 _Option(["-ogcmin", "ogcmin"], 346 """Minimum GC% for internal oligo. 347 348 Option added in EMBOSS 6.1.0, replacing -oligomingc 349 """), 350 _Option(["-oligomaxgc","oligomaxgc"], 351 """Maximum GC% for internal oligo. 352 353 Option replaced in EMBOSS 6.1.0 by -ogcmax 354 """), 355 _Option(["-ogcmax", "ogcmax"], 356 """Maximum GC% for internal oligo."), 357 358 Option added in EMBOSS 6.1.0, replacing -oligomaxgc 359 """), 360 #Oligo salt concentration: 361 _Option(["-oligosaltconc","oligosaltconc"], 362 """Millimolar concentration of salt in the hybridisation."), 363 364 Option replaced in EMBOSS 6.1.0 by -osaltconc 365 """), 366 _Option(["-osaltconc", "osaltconc"], 367 """Millimolar concentration of salt in the hybridisation."), 368 369 Option added in EMBOSS 6.1.0, replacing -oligosaltconc 370 """), 371 _Option(["-oligodnaconc","oligodnaconc"], 372 """Nanomolar concentration of internal oligo in the hybridisation. 373 374 Option replaced in EMBOSS 6.1.0 by -odnaconc 375 """), 376 _Option(["-odnaconc", "odnaconc"], 377 """Nanomolar concentration of internal oligo in the hybridisation. 378 379 Option added in EMBOSS 6.1.0, replacing -oligodnaconc 380 """), 381 #Oligo self complementarity 382 _Option(["-oligoselfany","oligoselfany"], 383 """Maximum allowable alignment score for self-complementarity (OBSOLETE). 384 385 Option replaced in EMBOSS 6.1.0 by -oanyself 386 """), 387 _Option(["-oanyself", "oanyself"], 388 """Maximum allowable alignment score for self-complementarity."), 389 390 Option added in EMBOSS 6.1.0, replacing -oligoselfany 391 """), 392 _Option(["-oligoselfend","oligoselfend"], 393 """Maximum allowable 3`-anchored global alignment score " 394 for self-complementarity (OBSOLETE). 395 396 Option replaced in EMBOSS 6.1.0 by -oendself 397 """), 398 _Option(["-oendself", "oendself"], 399 """Max 3`-anchored self-complementarity global alignment score. 400 401 Option added in EMBOSS 6.1.0, replacing -oligoselfend 402 """), 403 _Option(["-oligomaxpolyx","oligomaxpolyx"], 404 """Maximum length of mononucleotide repeat in internal oligo (OBSOLETE). 405 406 Option replaced in EMBOSS 6.1.0 by -opolyxmax 407 """), 408 _Option(["-opolyxmax", "opolyxmax"], 409 """Maximum length of mononucleotide repeat in internal oligo."), 410 411 Option added in EMBOSS 6.1.0, replacing -oligomaxpolyx 412 """), 413 _Option(["-mispriminglibraryfile","mispriminglibraryfile"], 414 "File containing library of sequences to avoid amplifying"), 415 _Option(["-maxmispriming","maxmispriming"], 416 "Maximum allowed similarity of primers to sequences in " 417 "library specified by -mispriminglibrary"), 418 _Option(["-oligomaxmishyb","oligomaxmishyb"], 419 """Maximum alignment score for hybridisation of internal oligo to 420 library specified by -oligomishyblibraryfile (OBSOLETE). 421 422 Option replaced in EMBOSS 6.1.0 by -omishybmax 423 """), 424 _Option(["-omishybmax", "omishybmax"], 425 """Maximum alignment score for hybridisation of internal oligo to 426 library specified by -mishyblibraryfile. 427 428 Option added in EMBOSS 6.1.0, replacing -oligomaxmishyb 429 """), 430 _Option(["-oligomishyblibraryfile", "oligomishyblibraryfile"], 431 432 """Library file of seqs to avoid internal oligo hybridisation (OBSOLETE). 433 434 Option replaced in EMBOSS 6.1.0 by -mishyblibraryfile 435 """), 436 _Option(["-mishyblibraryfile", "mishyblibraryfile"], 437 """Library file of seqs to avoid internal oligo hybridisation. 438 439 Option added in EMBOSS 6.1.0, replacing -oligomishyblibraryfile 440 """), 441 _Option(["-explainflag","explainflag"], 442 "Produce output tags with eprimer3 statistics"), 443 ] 444 _EmbossCommandLine.__init__(self, cmd, **kwargs)

445 446

447 -class PrimerSearchCommandline(_EmbossCommandLine):

448 """Commandline object for the primersearch program from EMBOSS. 449 """

450 - def __init__(self, cmd="primersearch", **kwargs):

451 self.parameters = [ 452 _Option(["-seqall","-sequences","sequences","seqall"], 453 "Sequence to look for the primer pairs in.", 454 is_required=True), 455 #When this wrapper was written primersearch used -sequences 456 #as the argument name. Since at least EMBOSS 5.0 (and 457 #perhaps earlier) this has been -seqall instead. 458 _Option(["-infile","-primers","primers","infile"], 459 "File containing the primer pairs to search for.", 460 filename=True, 461 is_required=True), 462 #When this wrapper was written primersearch used -primers 463 #as the argument name. Since at least EMBOSS 5.0 (and 464 #perhaps earlier) this has been -infile instead. 465 _Option(["-mismatchpercent","mismatchpercent"], 466 "Allowed percentage mismatch (any integer value, default 0).", 467 is_required=True), 468 _Option(["-snucleotide","snucleotide"], 469 "Sequences are nucleotide (boolean)"), 470 _Option(["-sprotein","sprotein"], 471 "Sequences are protein (boolean)"), 472 ] 473 _EmbossCommandLine.__init__(self, cmd, **kwargs)

474 475

476 -class FDNADistCommandline(_EmbossCommandLine):

477 """Commandline object for the fdnadist program from EMBOSS. 478 479 fdnadist is an EMBOSS wrapper for the PHYLIP program dnadist for 480 calulating distance matrices from DNA sequence files. 481 """

482 - def __init__(self, cmd = "fdnadist", **kwargs):

483 self.parameters = [ 484 _Option(["-sequence", "sequence"], 485 "seq file to use (phylip)", 486 filename=True, 487 is_required=True), 488 _Option(["-method", "method"], 489 "sub. model [f,k,j,l,s]", 490 is_required=True), 491 _Option(["-gamma", "gamma"], 492 "gamma [g, i,n]"), 493 _Option(["-ncategories", "ncategories"], 494 "number of rate catergories (1-9)"), 495 _Option(["-rate", "rate"], 496 "rate for each category"), 497 _Option(["-categories","categories"], 498 "File of substitution rate categories"), 499 _Option(["-weights", "weights"], 500 "weights file"), 501 _Option(["-gammacoefficient", "gammacoefficient"], 502 "value for gamma (> 0.001)"), 503 _Option(["-invarfrac", "invarfrac"], 504 "proportoin of invariant sites"), 505 _Option(["-ttratio", "ttratio"], 506 "ts/tv ratio"), 507 _Option(["-freqsfrom", "freqsfrom"], 508 "use emprical base freqs"), 509 _Option(["-basefreq", "basefreq"], 510 "specify basefreqs"), 511 _Option(["-lower", "lower"], 512 "lower triangle matrix (y/N)")] 513 _EmbossCommandLine.__init__(self, cmd, **kwargs)

514 515

516 -class FTreeDistCommandline(_EmbossCommandLine):

517 """Commandline object for the ftreedist program from EMBOSS. 518 519 ftreedist is an EMBOSS wrapper for the PHYLIP program treedist used for 520 calulating distance measures between phylogentic trees. 521 """

522 - def __init__(self, cmd = "ftreedist", **kwargs):

523 self.parameters = [ 524 _Option(["-intreefile", "intreefile"], 525 "tree file to score (phylip)", 526 filename=True, 527 is_required=True), 528 _Option(["-dtype", "dtype"], 529 "distance type ([S]ymetric, [b]ranch score)"), 530 _Option(["-pairing", "pairing"], 531 "tree pairing method ([A]djacent pairs, all [p]ossible pairs)"), 532 _Option(["-style", "style"], 533 "output style - [V]erbose, [f]ill, [s]parse"), 534 _Option(["-noroot", "noroot"], 535 "treat trees as rooted [N/y]"), 536 _Option(["-outgrno", "outgrno"], 537 "which taxon to root the trees with (starts from 0)")] 538 _EmbossCommandLine.__init__(self, cmd, **kwargs)

539 540

541 -class FNeighborCommandline(_EmbossCommandLine):

542 """Commandline object for the fneighbor program from EMBOSS. 543 544 fneighbor is an EMBOSS wrapper for the PHYLIP program neighbor used for 545 calulating neighbor-joining or UPGMA trees from distance matrices. 546 """

547 - def __init__(self, cmd = "fneighbor", **kwargs):

548 self.parameters = [ 549 _Option(["-datafile", "datafile"], 550 "dist file to use (phylip)", 551 filename=True, 552 is_required=True), 553 _Option(["-matrixtype", "matrixtype"], 554 "is martrix [S]quare pr [u]pper or [l]ower"), 555 _Option(["-treetype", "treetype"], 556 "nj or UPGMA tree (n/u)"), 557 _Option(["-outgrno","outgrno" ], 558 "taxon to use as OG"), 559 _Option(["-jumble", "jumble"], 560 "randommise input order (Y/n)"), 561 _Option(["-seed", "seed"], 562 "provide a random seed"), 563 _Option(["-trout", "trout"], 564 "write tree (Y/n)"), 565 _Option(["-outtreefile", "outtreefile"], 566 "filename for output tree"), 567 _Option(["-progress", "progress"], 568 "print progress (Y/n)"), 569 _Option(["-treeprint", "treeprint"], 570 "print tree (Y/n)")] 571 _EmbossCommandLine.__init__(self, cmd, **kwargs)

572 573

574 -class FSeqBootCommandline(_EmbossCommandLine):

575 """Commandline object for the fseqboot program from EMBOSS. 576 577 fseqboot is an EMBOSS wrapper for the PHYLIP program seqboot used to 578 pseudo-sample alignment files. 579 """

580 - def __init__(self, cmd = "fseqboot", **kwargs):

581 self.parameters = [ 582 _Option(["-sequence", "sequence"], 583 "seq file to sample (phylip)", 584 filename=True, 585 is_required=True), 586 _Option(["-categories", "catergories"], 587 "file of input categories"), 588 _Option(["-weights", "weights"], 589 " weights file"), 590 _Option(["-test", "test"], 591 "specify operation, default is bootstrap"), 592 _Option(["-regular", "regular"], 593 "absolute number to resample"), 594 _Option(["-fracsample", "fracsample"], 595 "fraction to resample"), 596 _Option(["-rewriteformat", "rewriteformat"], 597 "output format ([P]hyilp, [n]exus, [x]ml"), 598 _Option(["-seqtype", "seqtype"], 599 "output format ([D]na, [p]rotein, [r]na"), 600 _Option(["-blocksize", "blocksize"], 601 "print progress (Y/n)"), 602 _Option(["-reps", "reps"], 603 "how many replicates, defaults to 100)"), 604 _Option(["-justweights", "jusweights"], 605 "what to write out [D]atasets of just [w]eights"), 606 _Option(["-seed", "seed"], 607 "specify random seed"), 608 _Option(["-dotdiff", "dotdiff"], 609 "Use dot-differencing? [Y/n]"),] 610 _EmbossCommandLine.__init__(self, cmd, **kwargs)

611 612

613 -class FDNAParsCommandline(_EmbossCommandLine):

614 """Commandline object for the fdnapars program from EMBOSS. 615 616 fdnapars is an EMBOSS version of the PHYLIP program dnapars, for 617 estimating trees from DNA sequences using parsiomny. Calling this command 618 without providing a value for the option "-intreefile" will invoke 619 "interactive mode" (and as a result fail if called with subprocess) if 620 "-auto" is not set to true. 621 """

622 - def __init__(self, cmd = "fdnapars", **kwargs):

623 self.parameters = [ 624 _Option(["-sequence", "sequence"], 625 "seq file to use (phylip)", 626 filename=True, 627 is_required=True), 628 _Option(["-intreefile", "intreefile"], 629 "Phylip tree file"), 630 _Option(["-weights", "weights"], 631 "weights file"), 632 _Option(["-maxtrees", "maxtrees"], 633 "max trees to save during run"), 634 _Option(["-thorough", "thorough"], 635 "more thorough search (Y/n)"), 636 _Option(["-rearrange", "rearrange"], 637 "Rearrange on jsut 1 best tree (Y/n)"), 638 _Option(["-transversion", "transversion"], 639 "Use tranversion parsimony (y/N)"), 640 _Option(["-njumble", "njumble"], 641 "number of times to randomise input order (default is 0)"), 642 _Option(["-seed", "seed"], 643 "provide random seed"), 644 _Option(["-outgrno", "outgrno"], 645 "Specify outgroup"), 646 _Option(["-thresh", "thresh"], 647 "Use threshold parsimony (y/N)"), 648 _Option(["-threshold", "threshold"], 649 "Threshold value"), 650 _Option(["-trout", "trout"], 651 "Write trees to file (Y/n)"), 652 _Option(["-outtreefile", "outtreefile"], 653 "filename for output tree"), 654 _Option(["-dotdiff", "dotdiff"], 655 "Use dot-differencing? [Y/n]")] 656 _EmbossCommandLine.__init__(self, cmd, **kwargs)

657 658

659 -class FProtParsCommandline(_EmbossCommandLine):

660 """Commandline object for the fdnapars program from EMBOSS. 661 662 fprotpars is an EMBOSS version of the PHYLIP program protpars, for 663 estimating trees from protein sequences using parsiomny. Calling this 664 command without providing a value for the option "-intreefile" will invoke 665 "interactive mode" (and as a result fail if called with subprocess) if 666 "-auto" is not set to true. 667 """

668 - def __init__(self, cmd = "fprotpars", **kwargs):

669 self.parameters = [ 670 _Option(["-sequence", "sequence"], 671 "seq file to use (phylip)", 672 filename=True, 673 is_required=True), 674 _Option(["-intreefile", "intreefile"], 675 "Phylip tree file to score"), 676 _Option(["-outtreefile", "outtreefile"], 677 "phylip tree output file", 678 filename=True, 679 is_required=True), 680 _Option(["-weights", "weights"], 681 "weights file"), 682 _Option(["-whichcode", "whichcode"], 683 "which genetic code, [U,M,V,F,Y]]"), 684 _Option(["-njumble", "njumble"], 685 "number of times to randomise input order (default is 0)"), 686 _Option(["-seed", "seed"], 687 "provide random seed"), 688 _Option(["-outgrno", "outgrno"], 689 "Specify outgroup"), 690 _Option(["-thresh", "thresh"], 691 "Use threshold parsimony (y/N)"), 692 _Option(["-threshold", "threshold"], 693 "Threshold value"), 694 _Option(["-trout", "trout"], 695 "Write trees to file (Y/n)"), 696 _Option(["-dotdiff", "dotdiff"], 697 "Use dot-differencing? [Y/n]")] 698 _EmbossCommandLine.__init__(self, cmd, **kwargs)

699 700

701 -class FProtDistCommandline(_EmbossCommandLine):

702 """Commandline object for the fprotdist program from EMBOSS. 703 704 fprotdist is an EMBOSS wrapper for the PHYLIP program protdist used to 705 estimate trees from protein sequences using parsimony 706 """

707 - def __init__(self, cmd = "fprotdist", **kwargs):

708 self.parameters = [ 709 _Option(["-sequence", "sequence"], 710 "seq file to use (phylip)", 711 filename=True, 712 is_required=True), 713 _Option(["-ncategories", "ncategories"], 714 "number of rate catergories (1-9)"), 715 _Option(["-rate", "rate"], 716 "rate for each category"), 717 _Option(["-catergories","catergories"], 718 "file of rates"), 719 _Option(["-weights", "weights"], 720 "weights file"), 721 _Option(["-method", "method"], 722 "sub. model [j,h,d,k,s,c]"), 723 _Option(["-gamma", "gamma"], 724 "gamma [g, i,c]"), 725 _Option(["-gammacoefficient", "gammacoefficient"], 726 "value for gamma (> 0.001)"), 727 _Option(["-invarcoefficient", "invarcoefficient"], 728 "float for variation of substitution rate among sites"), 729 _Option(["-aacateg", "aacateg"], 730 "Choose the category to use [G,C,H]"), 731 _Option(["-whichcode", "whichcode"], 732 "genetic code [c,m,v,f,y]"), 733 _Option(["-ease", "ease"], 734 "Pob change catergory (float between -0 and 1)"), 735 _Option(["-ttratio", "ttratio"], 736 "Transition/transversion ratio (0-1)"), 737 _Option(["-basefreq", "basefreq"], 738 "DNA base frequencies (space separated list)")] 739 _EmbossCommandLine.__init__(self, cmd, **kwargs)

740 741

742 -class FConsenseCommandline(_EmbossCommandLine):

743 """Commandline object for the fconsense program from EMBOSS. 744 745 fconsense is an EMBOSS wrapper for the PHYLIP program consense used to 746 calculate consensus trees. 747 """

748 - def __init__(self, cmd = "fconsense", **kwargs):

749 self.parameters = [ 750 _Option(["-intreefile", "intreefile"], 751 "file with phylip trees to make consensus from", 752 filename=True, 753 is_required=True), 754 _Option(["-method", "method"], 755 "consensus method [s, mr, MRE, ml]"), 756 _Option(["-mlfrac", "mlfrac"], 757 "cut-off freq for a branch to appear in consensus (0.5-1.0)"), 758 _Option(["-root", "root"], 759 "treat trees as rooted (YES, no)"), 760 _Option(["-outgrno", "outgrno"], 761 "OTU to use as outgroup (starts from 0)"), 762 _Option(["-trout", "trout"], 763 "treat trees as rooted (YES, no)"), 764 _Option(["-outtreefile", "outtreefile"], 765 "Phylip tree output file (optional)")] 766 _EmbossCommandLine.__init__(self, cmd, **kwargs)

767 768

769 -class WaterCommandline(_EmbossCommandLine):

770 """Commandline object for the water program from EMBOSS. 771 """

772 - def __init__(self, cmd="water", **kwargs):

773 self.parameters = [ 774 _Option(["-asequence","asequence"], 775 "First sequence to align", 776 filename=True, 777 is_required=True), 778 _Option(["-bsequence","bsequence"], 779 "Second sequence to align", 780 filename=True, 781 is_required=True), 782 _Option(["-gapopen","gapopen"], 783 "Gap open penalty", 784 is_required=True), 785 _Option(["-gapextend","gapextend"], 786 "Gap extension penalty", 787 is_required=True), 788 _Option(["-datafile","datafile"], 789 "Matrix file", 790 filename=True), 791 _Switch(["-nobrief", "nobrief"], 792 "Display extended identity and similarity"), 793 _Switch(["-brief", "brief"], 794 "Display brief identity and similarity"), 795 _Option(["-similarity","similarity"], 796 "Display percent identity and similarity"), 797 _Option(["-snucleotide","snucleotide"], 798 "Sequences are nucleotide (boolean)"), 799 _Option(["-sprotein","sprotein"], 800 "Sequences are protein (boolean)"), 801 _Option(["-aformat","aformat"], 802 "Display output in a different specified output format")] 803 _EmbossCommandLine.__init__(self, cmd, **kwargs)

804 805

806 -class NeedleCommandline(_EmbossCommandLine):

807 """Commandline object for the needle program from EMBOSS. 808 """

809 - def __init__(self, cmd="needle", **kwargs):

810 self.parameters = [ 811 _Option(["-asequence","asequence"], 812 "First sequence to align", 813 filename=True, 814 is_required=True), 815 _Option(["-bsequence","bsequence"], 816 "Second sequence to align", 817 filename=True, 818 is_required=True), 819 _Option(["-gapopen","gapopen"], 820 "Gap open penalty", 821 is_required=True), 822 _Option(["-gapextend","gapextend"], 823 "Gap extension penalty", 824 is_required=True), 825 _Option(["-datafile","datafile"], 826 "Matrix file", 827 filename=True), 828 _Option(["-endweight", "endweight"], 829 "Apply And gap penalties"), 830 _Option(["-endopen", "endopen"], 831 "The score taken away when an end gap is created."), 832 _Option(["-endextend", "endextend"], 833 "The score added to the end gap penality for each base or " 834 "residue in the end gap."), 835 _Switch(["-nobrief", "nobrief"], 836 "Display extended identity and similarity"), 837 _Switch(["-brief", "brief"], 838 "Display brief identity and similarity"), 839 _Option(["-similarity","similarity"], 840 "Display percent identity and similarity"), 841 _Option(["-snucleotide","snucleotide"], 842 "Sequences are nucleotide (boolean)"), 843 _Option(["-sprotein","sprotein"], 844 "Sequences are protein (boolean)"), 845 _Option(["-aformat","aformat"], 846 "Display output in a different specified output format")] 847 _EmbossCommandLine.__init__(self, cmd, **kwargs)

848 849

850 -class NeedleallCommandline(_EmbossCommandLine):

851 """Commandline object for the needleall program from EMBOSS. 852 """

853 - def __init__(self, cmd="needleall", **kwargs):

854 self.parameters = [ 855 _Option(["-asequence","asequence"], 856 "First sequence to align", 857 filename=True, 858 is_required=True), 859 _Option(["-bsequence","bsequence"], 860 "Second sequence to align", 861 filename=True, 862 is_required=True), 863 _Option(["-gapopen","gapopen"], 864 "Gap open penalty", 865 is_required=True), 866 _Option(["-gapextend","gapextend"], 867 "Gap extension penalty", 868 is_required=True), 869 _Option(["-datafile","datafile"], 870 "Matrix file", 871 filename=True), 872 _Option(["-minscore","minscore"], 873 "Exclude alignments with scores below this threshold score."), 874 _Option(["-errorfile", "errorfile"], 875 "Error file to be written to."), 876 _Option(["-endweight", "endweight"], 877 "Apply And gap penalties"), 878 _Option(["-endopen", "endopen"], 879 "The score taken away when an end gap is created."), 880 _Option(["-endextend", "endextend"], 881 "The score added to the end gap penality for each base or " 882 "residue in the end gap."), 883 _Switch(["-nobrief", "nobrief"], 884 "Display extended identity and similarity"), 885 _Switch(["-brief", "brief"], 886 "Display brief identity and similarity"), 887 _Option(["-similarity","similarity"], 888 "Display percent identity and similarity"), 889 _Option(["-snucleotide","snucleotide"], 890 "Sequences are nucleotide (boolean)"), 891 _Option(["-sprotein","sprotein"], 892 "Sequences are protein (boolean)"), 893 _Option(["-aformat","aformat"], 894 "Display output in a different specified output format")] 895 _EmbossCommandLine.__init__(self, cmd, **kwargs)

896 897

898 -class StretcherCommandline(_EmbossCommandLine):

899 """Commandline object for the stretcher program from EMBOSS. 900 """

901 - def __init__(self, cmd="stretcher", **kwargs):

902 self.parameters = [ 903 _Option(["-asequence","asequence"], 904 "First sequence to align", 905 filename=True, 906 is_required=True), 907 _Option(["-bsequence","bsequence"], 908 "Second sequence to align", 909 filename=True, 910 is_required=True), 911 _Option(["-gapopen","gapopen"], 912 "Gap open penalty", 913 is_required=True, 914 checker_function=lambda value: isinstance(value, int)), 915 _Option(["-gapextend","gapextend"], 916 "Gap extension penalty", 917 is_required=True, 918 checker_function=lambda value: isinstance(value, int)), 919 _Option(["-datafile","datafile"], 920 "Matrix file", 921 filename=True), 922 _Option(["-snucleotide","snucleotide"], 923 "Sequences are nucleotide (boolean)"), 924 _Option(["-sprotein","sprotein"], 925 "Sequences are protein (boolean)"), 926 _Option(["-aformat","aformat"], 927 "Display output in a different specified output format")] 928 _EmbossCommandLine.__init__(self, cmd, **kwargs)

929 930

931 -class FuzznucCommandline(_EmbossCommandLine):

932 """Commandline object for the fuzznuc program from EMBOSS. 933 """

934 - def __init__(self, cmd="fuzznuc", **kwargs):

935 self.parameters = [ 936 _Option(["-sequence","sequence"], 937 "Sequence database USA", 938 is_required=True), 939 _Option(["-pattern","pattern"], 940 "Search pattern, using standard IUPAC one-letter codes", 941 is_required=True), 942 _Option(["-mismatch","mismatch"], 943 "Number of mismatches", 944 is_required=True), 945 _Option(["-complement","complement"], 946 "Search complementary strand"), 947 _Option(["-rformat","rformat"], 948 "Specify the report format to output in.")] 949 _EmbossCommandLine.__init__(self, cmd, **kwargs)

950 951

952 -class Est2GenomeCommandline(_EmbossCommandLine):

953 """Commandline object for the est2genome program from EMBOSS. 954 """

955 - def __init__(self, cmd="est2genome", **kwargs):

956 self.parameters = [ 957 _Option(["-est","est"], 958 "EST sequence(s)", 959 is_required=True), 960 _Option(["-genome","genome"], 961 "Genomic sequence", 962 is_required=True), 963 _Option(["-match","match"], 964 "Score for matching two bases"), 965 _Option(["-mismatch","mismatch"], 966 "Cost for mismatching two bases"), 967 _Option(["-gappenalty","gappenalty"], 968 "Cost for deleting a single base in either sequence, " 969 "excluding introns"), 970 _Option(["-intronpenalty","intronpenalty"], 971 "Cost for an intron, independent of length."), 972 _Option(["-splicepenalty","splicepenalty"], 973 "Cost for an intron, independent of length " 974 "and starting/ending on donor-acceptor sites"), 975 _Option(["-minscore","minscore"], 976 "Exclude alignments with scores below this threshold score."), 977 _Option(["-reverse","reverse"], 978 "Reverse the orientation of the EST sequence"), 979 _Option(["-splice","splice"], 980 "Use donor and acceptor splice sites."), 981 _Option(["-mode","mode"], 982 "This determines the comparion mode. 'both', 'forward' " 983 "'reverse'"), 984 _Option(["-best","best"], 985 "You can print out all comparisons instead of just the best"), 986 _Option(["-space","space"], 987 "for linear-space recursion."), 988 _Option(["-shuffle","shuffle"], 989 "Shuffle"), 990 _Option(["-seed","seed"], 991 "Random number seed"), 992 _Option(["-align","align"], 993 "Show the alignment."), 994 _Option(["-width","width"], 995 "Alignment width") 996 ] 997 _EmbossCommandLine.__init__(self, cmd, **kwargs)

998 999

1000 -class ETandemCommandline(_EmbossCommandLine):

1001 """Commandline object for the etandem program from EMBOSS. 1002 """

1003 - def __init__(self, cmd="etandem", **kwargs):

1004 self.parameters = [ 1005 _Option(["-sequence","sequence"], 1006 "Sequence", 1007 filename=True, 1008 is_required=True), 1009 _Option(["-minrepeat","minrepeat"], 1010 "Minimum repeat size", 1011 is_required=True), 1012 _Option(["-maxrepeat","maxrepeat"], 1013 "Maximum repeat size", 1014 is_required=True), 1015 _Option(["-threshold","threshold"], 1016 "Threshold score"), 1017 _Option(["-mismatch","mismatch"], 1018 "Allow N as a mismatch"), 1019 _Option(["-uniform","uniform"], 1020 "Allow uniform consensus"), 1021 _Option(["-rformat","rformat"], 1022 "Output report format")] 1023 _EmbossCommandLine.__init__(self, cmd, **kwargs)

1024 1025

1026 -class EInvertedCommandline(_EmbossCommandLine):

1027 """Commandline object for the einverted program from EMBOSS. 1028 """

1029 - def __init__(self, cmd="einverted", **kwargs):

1030 self.parameters = [ 1031 _Option(["-sequence","sequence"], 1032 "Sequence", 1033 filename=True, 1034 is_required=True), 1035 _Option(["-gap","gap"], 1036 "Gap penalty", 1037 filename=True, 1038 is_required=True), 1039 _Option(["-threshold","threshold"], 1040 "Minimum score threshold", 1041 is_required=True), 1042 _Option(["-match","match"], 1043 "Match score", 1044 is_required=True), 1045 _Option(["-mismatch","mismatch"], 1046 "Mismatch score", 1047 is_required=True), 1048 _Option(["-maxrepeat","maxrepeat"], 1049 "Maximum separation between the start and end of repeat"), 1050 ] 1051 _EmbossCommandLine.__init__(self, cmd, **kwargs)

1052 1053

1054 -class PalindromeCommandline(_EmbossCommandLine):

1055 """Commandline object for the palindrome program from EMBOSS. 1056 """

1057 - def __init__(self, cmd="palindrome", **kwargs):

1058 self.parameters = [ 1059 _Option(["-sequence","sequence"], 1060 "Sequence", 1061 filename=True, 1062 is_required=True), 1063 _Option(["-minpallen","minpallen"], 1064 "Minimum palindrome length", 1065 is_required=True), 1066 _Option(["-maxpallen","maxpallen"], 1067 "Maximum palindrome length", 1068 is_required=True), 1069 _Option(["-gaplimit","gaplimit"], 1070 "Maximum gap between repeats", 1071 is_required=True), 1072 _Option(["-nummismatches","nummismatches"], 1073 "Number of mismatches allowed", 1074 is_required=True), 1075 _Option(["-overlap","overlap"], 1076 "Report overlapping matches", 1077 is_required=True), 1078 ] 1079 _EmbossCommandLine.__init__(self, cmd, **kwargs)

1080 1081

1082 -class TranalignCommandline(_EmbossCommandLine):

1083 """Commandline object for the tranalign program from EMBOSS. 1084 """

1085 - def __init__(self, cmd="tranalign", **kwargs):

1086 self.parameters = [ 1087 _Option(["-asequence","asequence"], 1088 "Nucleotide sequences to be aligned.", 1089 filename=True, 1090 is_required=True), 1091 _Option(["-bsequence","bsequence"], 1092 "Protein sequence alignment", 1093 filename=True, 1094 is_required=True), 1095 _Option(["-outseq","outseq"], 1096 "Output sequence file.", 1097 filename=True, 1098 is_required=True), 1099 _Option(["-table","table"], 1100 "Code to use")] 1101 _EmbossCommandLine.__init__(self, cmd, **kwargs)

1102 1103

1104 -class DiffseqCommandline(_EmbossCommandLine):

1105 """Commandline object for the diffseq program from EMBOSS. 1106 """

1107 - def __init__(self, cmd="diffseq", **kwargs):

1108 self.parameters = [ 1109 _Option(["-asequence","asequence"], 1110 "First sequence to compare", 1111 filename=True, 1112 is_required=True), 1113 _Option(["-bsequence","bsequence"], 1114 "Second sequence to compare", 1115 filename=True, 1116 is_required=True), 1117 _Option(["-wordsize","wordsize"], 1118 "Word size to use for comparisons (10 default)", 1119 is_required=True), 1120 _Option(["-aoutfeat","aoutfeat"], 1121 "File for output of first sequence's features", 1122 filename=True, 1123 is_required=True), 1124 _Option(["-boutfeat","boutfeat"], 1125 "File for output of second sequence's features", 1126 filename=True, 1127 is_required=True), 1128 _Option(["-rformat","rformat"], 1129 "Output report file format") 1130 ] 1131 _EmbossCommandLine.__init__(self, cmd, **kwargs)

1132 1133

1134 -class IepCommandline(_EmbossCommandLine):

1135 """Commandline for EMBOSS iep: calculated isoelectric point and charge. 1136 1137 Example: 1138 1139 >>> from Bio.Emboss.Applications import IepCommandline 1140 >>> iep_cline = IepCommandline(sequence="proteins.faa", 1141 ... outfile="proteins.txt") 1142 >>> print iep_cline 1143 iep -outfile=proteins.txt -sequence=proteins.faa 1144 1145 You would typically run the command line with iep_cline() or via the 1146 Python subprocess module, as described in the Biopython tutorial. 1147 """

1148 - def __init__(self, cmd="iep", **kwargs):

1149 self.parameters = [ 1150 _Option(["-sequence","sequence"], 1151 "Protein sequence(s) filename", 1152 filename=True, 1153 is_required=True), 1154 _Option(["-amino","amino"], 1155 """Number of N-termini 1156 1157 Integer 0 (default) or more. 1158 """), 1159 _Option(["-carboxyl","carboxyl"], 1160 """Number of C-termini 1161 1162 Integer 0 (default) or more. 1163 """), 1164 _Option(["-lysinemodified","lysinemodified"], 1165 """Number of modified lysines 1166 1167 Integer 0 (default) or more. 1168 """), 1169 _Option(["-disulphides","disulphides"], 1170 """Number of disulphide bridges 1171 1172 Integer 0 (default) or more. 1173 """), 1174 #Should we implement the -termini switch as well? 1175 _Option(["-notermini","notermini"], 1176 "Exclude (True) or include (False) charge at N and C terminus."), 1177 ] 1178 _EmbossCommandLine.__init__(self, cmd, **kwargs)

1179 1180 1181 #seqret uses -outseq, not -outfile, so use the base class:

1182 -class SeqretCommandline(_EmbossMinimalCommandLine):

1183 """Commandline object for the seqret program from EMBOSS. 1184 1185 This tool allows you to interconvert between different sequence file 1186 formats (e.g. GenBank to FASTA). Combining Biopython's Bio.SeqIO module 1187 with seqret using a suitable intermediate file format can allow you to 1188 read/write to an even wider range of file formats. 1189 1190 This wrapper currently only supports the core functionality, things like 1191 feature tables (in EMBOSS 6.1.0 onwards) are not yet included. 1192 """

1193 - def __init__(self, cmd="seqret", **kwargs):

1194 self.parameters = [ 1195 _Option(["-sequence","sequence"], 1196 "Input sequence(s) filename", 1197 filename=True), 1198 _Option(["-outseq","outseq"], 1199 "Output sequence file.", 1200 filename=True), 1201 _Option(["-sformat","sformat"], 1202 "Input sequence(s) format (e.g. fasta, genbank)"), 1203 _Option(["-osformat","osformat"], 1204 "Output sequence(s) format (e.g. fasta, genbank)"), 1205 ] 1206 _EmbossMinimalCommandLine.__init__(self, cmd, **kwargs)

1207

1208 - def _validate(self):

1209 #Check the outfile, filter, or stdout option has been set. 1210 #We can't simply do this via the required flag for the outfile 1211 #output - this seems the simplest solution. 1212 if not (self.outseq or self.filter or self.stdout): 1213 raise ValueError("You must either set outfile (output filename), " 1214 "or enable filter or stdout (output to stdout).") 1215 if not (self.sequence or self.filter or self.stdint): 1216 raise ValueError("You must either set sequence (input filename), " 1217 "or enable filter or stdin (input from stdin).") 1218 return _EmbossMinimalCommandLine._validate(self)

1219 1220

1221 -class SeqmatchallCommandline(_EmbossCommandLine):

1222 """ Commandline object for the seqmatchall program from EMBOSS 1223 1224 e.g. 1225 >>> cline = SeqmatchallCommandline(sequence="opuntia.fasta", outfile="opuntia.txt") 1226 >>> cline.auto = True 1227 >>> cline.wordsize = 18 1228 >>> cline.aformat = "pair" 1229 >>> print cline 1230 seqmatchall -auto -outfile=opuntia.txt -sequence=opuntia.fasta -wordsize=18 -aformat=pair 1231 1232 """

1233 - def __init__(self, cmd="seqmatchall", **kwargs):

1234 self.parameters = [ 1235 _Option(["-sequence", "sequence"], 1236 "Readable set of sequences", 1237 filename=True, 1238 is_required=True), 1239 _Option(["-wordsize", "wordsize"], 1240 "Word size (Integer 2 or more, default 4)"), 1241 _Option(["-aformat","aformat"], 1242 "Display output in a different specified output format"), 1243 ] 1244 _EmbossCommandLine.__init__(self, cmd, **kwargs)

1245 1246

1247 -def _test():

1248 """Run the Bio.Emboss.Applications module doctests.""" 1249 import doctest 1250 doctest.testmod()

1251 1252 if __name__ == "__main__": 1253 #Run the doctests 1254 _test() 1255

Source Code for Module Bio.Emboss.Applications