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

  1  """Code to interact with and run various EMBOSS programs. 
  2   
  3  These classes follow the AbstractCommandline interfaces for running 
  4  programs. 
  5  """ 
  6   
  7  from Bio import Application 
  8  from Bio.Application import _Option 
  9   
10 -class Primer3Commandline(Application.AbstractCommandline):
11 """Commandline object for the Primer3 interface from EMBOSS. 12 """
13 - def __init__(self, cmd = "eprimer3"):
14 Application.AbstractCommandline.__init__(self) 15 self.program_name = cmd 16 17 self.parameters = \ 18 [_Option(["-sequence"], ["input"], None, 1, 19 "Sequence to choose primers from"), 20 _Option(["-outfile"], ["output", "file"], None, 1, 21 "Output file name"), 22 _Option(["-task"], ["input"], None, 0), 23 _Option(["-numreturn"], ["input"], None, 0), 24 _Option(["-includedregion"], ["input"], None, 0), 25 _Option(["-target"], ["input"], None, 0), 26 _Option(["-excludedregion"], ["input"], None, 0), 27 _Option(["-forwardinput"], ["input"], None, 0), 28 _Option(["-reverseinput"], ["input"], None, 0), 29 _Option(["-gcclamp"], ["input"], None, 0), 30 _Option(["-osize"], ["input"], None, 0), 31 _Option(["-minsize"], ["input"], None, 0), 32 _Option(["-maxsize"], ["input"], None, 0), 33 _Option(["-otm"], ["input"], None, 0), 34 _Option(["-mintm"], ["input"], None, 0), 35 _Option(["-maxtm"], ["input"], None, 0), 36 _Option(["-maxdifftm"], ["input"], None, 0), 37 _Option(["-ogcpercent"], ["input"], None, 0), 38 _Option(["-mingc"], ["input"], None, 0), 39 _Option(["-maxgc"], ["input"], None, 0), 40 _Option(["-saltconc"], ["input"], None, 0), 41 _Option(["-dnaconc"], ["input"], None, 0), 42 _Option(["-maxployx"], ["input"], None, 0), 43 _Option(["-productosize"], ["input"], None, 0), 44 _Option(["-productsizerange"], ["input"], None, 0), 45 _Option(["-productotm"], ["input"], None, 0), 46 _Option(["-productmintm"], ["input"], None, 0), 47 _Option(["-productmaxtm"], ["input"], None, 0), 48 _Option(["-oligoexcluderegion"], ["input"], None, 0), 49 _Option(["-oligoinput"], ["input"], None, 0), 50 _Option(["-oligosize"], ["input"], None, 0), 51 _Option(["-oligominsize"], ["input"], None, 0), 52 _Option(["-oligomaxsize"], ["input"], None, 0), 53 _Option(["-oligotm"], ["input"], None, 0), 54 _Option(["-oligomintm"], ["input"], None, 0), 55 _Option(["-oligomaxtm"], ["input"], None, 0), 56 _Option(["-oligoogcpercent"], ["input"], None, 0), 57 _Option(["-oligomingc"], ["input"], None, 0), 58 _Option(["-oligomaxgc"], ["input"], None, 0), 59 _Option(["-oligosaltconc"], ["input"], None, 0), 60 _Option(["-oligodnaconc"], ["input"], None, 0), 61 _Option(["-oligoselfany"], ["input"], None, 0), 62 _Option(["-oligoselfend"], ["input"], None, 0), 63 _Option(["-oligomaxpolyx"], ["input"], None, 0), 64 _Option(["-mispriminglibraryfile"], ["input"], None, 0), 65 _Option(["-maxmispriming"], ["input"], None, 0), 66 _Option(["-oligomishyblibraryfile"], ["input"], None, 0), 67 _Option(["-oligomaxmishyb"], ["input"], None, 0),]
68
69 -class PrimerSearchCommandline(Application.AbstractCommandline):
70 """Commandline object for the primersearch program from EMBOSS. 71 """
72 - def __init__(self, cmd = "primersearch"):
73 Application.AbstractCommandline.__init__(self) 74 self.program_name = cmd 75 76 self.parameters = \ 77 [_Option(["-sequences"], ["input"], None, 1, 78 "Sequence to look for the primer pairs in."), 79 _Option(["-primers"], ["input", "file"], None, 1, 80 "File containing the primer pairs to search for."), 81 _Option(["-out"], ["output", "file"], None, 1, 82 "Name of the output file."), 83 _Option(["-mismatchpercent"], ["input"], None, 1, 84 "Allowed percentage mismatch.")]
85
86 -class EProtDistCommandline(Application.AbstractCommandline):
87 """Commandline object for the eprotdist program from EMBOSS. 88 89 This is an EMBOSS wrapper around protdist from PHYLIP. 90 """
91 - def __init__(self, cmd = "eprotdist"):
92 Application.AbstractCommandline.__init__(self) 93 self.program_name = cmd 94 95 self.parameters = \ 96 [_Option(["-msf"], ["input"], None, 1, 97 "File containing sequences"), 98 _Option(["-outfile"], ["output"], None, 1, 99 "Output file name"), 100 _Option(["-method"], ["input"], None, 1, 101 "Choose the method to use"), 102 _Option(["-categ"], ["input"], None, 0, 103 "Choose the categorie to use"), 104 _Option(["-gencode"], ["input"], None, 0, 105 "Which genetic code"), 106 _Option(["-prob"], ["input"], None, 0, 107 "Prob change category (1.0=easy)"), 108 _Option(["-tranrate"], ["input"], None, 0, 109 "Transition/transversion ratio"), 110 _Option(["-freqa"], ["input"], None, 0, 111 "Frequency for A"), 112 _Option(["-freqc"], ["input"], None, 0, 113 "Frequency for C"), 114 _Option(["-freqg"], ["input"], None, 0, 115 "Frequency for G"), 116 _Option(["-freqt"], ["input"], None, 0, 117 "Frequency for T"), 118 _Option(["-printdata"], ["input"], None, 0, 119 "Print out the data at start of run"), 120 _Option(["-progress"], ["input"], None, 0, 121 "Print indications of progress of run"), 122 _Option(["-basefrequency"], ["input"], None, 0, 123 "Use empirical base frequencies")]
124
125 -class ENeighborCommandline(Application.AbstractCommandline):
126 """Commandline object for the eneighbor program from EMBOSS. 127 128 This is an EMBOSS wrapper around neighbor from PHYLIP. 129 """
130 - def __init__(self, cmd = "eneighbor"):
131 Application.AbstractCommandline.__init__(self) 132 self.program_name = cmd 133 134 self.parameters = \ 135 [_Option(["-infile"], ["input"], None, 1, 136 "infile value"), 137 _Option(["-outfile"], ["output"], None, 1, 138 "Output file name"), 139 _Option(["-trout"], ["input"], None, 1, 140 "Create a tree file"), 141 _Option(["-treefile"], ["input"], None, 1, 142 "Tree file name"), 143 _Option(["-nj"], ["input"], None, 1, 144 "Neighbor-joining"), 145 _Option(["-noog"], ["input"], None, 1, 146 "Outgroup root"), 147 _Option(["-outgnum"], ["input"], None, 0, 148 "number of the outgroup"), 149 _Option(["-randseed"], ["input"], None, 0, 150 "Random number seed (must be odd)"), 151 _Option(["-datasets"], ["input"], None, 0, 152 "How many data sets"), 153 _Option(["-drawtree"], ["input"], None, 0, 154 "Draw tree"), 155 _Option(["-lt"], ["input"], None, 0, 156 "Lower-triangular data matrix"), 157 _Option(["-ut"], ["input"], None, 0, 158 "Upper-triangular data matrix"), 159 _Option(["-sr"], ["input"], None, 0, 160 "Subreplicates"), 161 _Option(["-random"], ["input"], None, 0, 162 "Randomize input order of species"), 163 _Option(["-multsets"], ["input"], None, 0, 164 "Analyze multiple data sets"), 165 _Option(["-printdata"], ["input"], None, 0, 166 "Print out the data at start of run"), 167 _Option(["-progress"], ["input"], None, 0, 168 "Print indications of progress of run")]
169
170 -class EProtParsCommandline(Application.AbstractCommandline):
171 """Commandline object for the eprotpars program from EMBOSS. 172 173 This is an EMBOSS wrapper around protpars from PHYLIP. 174 """
175 - def __init__(self, cmd = "eprotpars"):
176 Application.AbstractCommandline.__init__(self) 177 self.program_name = cmd 178 179 self.parameters = \ 180 [_Option(["-msf"], ["input", "file"], None, 1, 181 "Sequences file to be read in"), 182 _Option(["-outfile"], ["output", "file"], None, 1, 183 "Output file"), 184 _Option(["-besttree"], ["input"], None, 0, 185 "Search for the best tree"), 186 _Option(["-random"], ["input"], None, 0, 187 "Randomize input order of species"), 188 _Option(["-norandom"], ["input"], None, 0, 189 "Do not randomize input order of species"), 190 _Option(["-randseed"], ["input"], None, 0, 191 "Random number seed (must be odd)"), 192 _Option(["-randtimes"], ["input"], None, 0, 193 "How many times to randomize"), 194 _Option(["-og"], ["input"], None, 0, 195 "Use an outgroup root"), 196 _Option(["-noog"], ["input"], None, 0, 197 "Do not use an outgroup root"), 198 _Option(["-outgnum"], ["input"], None, 0, 199 "Number of the outgroup"), 200 _Option(["-thresh"], ["input"], None, 0, 201 "Use Threshold parsimony"), 202 _Option(["-valthresh"], ["input"], None, 0, 203 "threshold value"), 204 _Option(["-printdata"], ["input"], None, 0, 205 "Print out the data at start of run"), 206 _Option(["-progress"], ["input"], None, 0, 207 "Print indications of progress of run"), 208 _Option(["-steps"], ["input"], None, 0, 209 "Print out steps in each site"), 210 _Option(["-seqatnodes"], ["input"], None, 0, 211 "Print sequences at all nodes of tree"), 212 _Option(["-drawtree"], ["input"], None, 0, 213 "Draw tree"), 214 _Option(["-trout"], ["input"], None, 0, 215 "Create a tree file"), 216 _Option(["-notrout"], ["input"], None, 0, 217 "Do not create a tree file"), 218 _Option(["-treefile"], ["output", "file"], None, 0, 219 "Output treefile name")]
220
221 -class EConsenseCommandline(Application.AbstractCommandline):
222 """Commandline object for the econsense program from EMBOSS. 223 224 This is an EMBOSS wrapper around consense from PHYLIP. 225 """
226 - def __init__(self, cmd = "econsense"):
227 Application.AbstractCommandline.__init__(self) 228 self.program_name = cmd 229 230 self.parameters = \ 231 [_Option(["-infile"], ["input", "file"], None, 1, 232 "file to read in (New Hampshire standard form)"), 233 _Option(["-outfile"], ["output", "file"], None, 1, 234 "Output file name"), 235 _Option(["-notrout"], ["input"], None, 0, 236 "Do not create a tree file"), 237 _Option(["-trout"], ["input"], None, 0, 238 "Create a tree file"), 239 _Option(["-treefile"], ["output", "file"], None, 0, 240 "tree file name"), 241 _Option(["-noog"], ["input"], None, 0, 242 "Do not use an outgroup"), 243 _Option(["-og"], ["input"], None, 0, 244 "Use an outgroup"), 245 _Option(["-outgnum"], ["input"], None, 0, 246 "number of the outgroup"), 247 _Option(["-nodrawtree"], ["input"], None, 0, 248 "Do not draw a tree"), 249 _Option(["-drawtree"], ["input"], None, 0, 250 "Draw tree"), 251 _Option(["-root"], ["input"], None, 0, 252 "Trees to be treated as Rooted"), 253 _Option(["-progress"], ["input"], None, 0, 254 "Print indications of the progress of run"), 255 _Option(["-noprintsets"], ["input"], None, 0, 256 "Do not print out the sets of species"), 257 _Option(["-printsets"], ["input"], None, 0, 258 "Print out the sets of species")]
259
260 -class ESeqBootCommandline(Application.AbstractCommandline):
261 """Commandline object for the eseqboot program from EMBOSS. 262 263 This is an EMBOSS wrapper around seqboot from PHYLIP. 264 """
265 - def __init__(self, cmd = "eseqboot"):
266 Application.AbstractCommandline.__init__(self) 267 self.program_name = cmd 268 269 self.parameters = \ 270 [_Option(["-datafile"], ["input", "file"], None, 1, 271 "Input file"), 272 _Option(["-outfile"], ["output", "file"], None, 1, 273 "Output file name"), 274 _Option(["-randseed"], ["input"], None, 1, 275 "Random number seed (must be odd)"), 276 _Option(["-method"], ["input"], None, 1, 277 "Choose the method"), 278 _Option(["-test"], ["input"], None, 1, 279 "Choose test"), 280 _Option(["-reps"], ["input"], None, 1, 281 "How many replicates"), 282 _Option(["-inter"], ["input"], None, 0, 283 "Interleaved input"), 284 _Option(["-enzymes"], ["input"], None, 0, 285 "Present in input file"), 286 _Option(["-all"], ["input"], None, 0, 287 "All alleles present at each locus"), 288 _Option(["-printdata"], ["input"], None, 0, 289 "Print out the data at start of run"), 290 _Option(["-progress"], ["input"], None, 0, 291 "Print indications of progress of run")]
292
293 -class WaterCommandline(Application.AbstractCommandline):
294 """Commandline object for the water program from EMBOSS. 295 """
296 - def __init__(self, cmd = "water"):
297 Application.AbstractCommandline.__init__(self) 298 self.program_name = cmd 299 300 self.parameters = \ 301 [_Option(["-asequence"], ["input", "file"], None, 1, 302 "First sequence to align"), 303 _Option(["-bsequence"], ["input", "file"], None, 1, 304 "Second sequence to align"), 305 _Option(["-gapopen"], ["input"], None, 1, 306 "Gap open penalty"), 307 _Option(["-gapextend"], ["input"], None, 1, 308 "Gap extension penalty"), 309 _Option(["-outfile"], ["output", "file"], None, 1, 310 "Output file for the alignment"), 311 _Option(["-datafile"], ["input", "file"], None, 0, 312 "Matrix file"), 313 _Option(["-similarity"], ["input"], None, 0, 314 "Display percent identity and similarity"), 315 _Option(["-nosimilarity"], ["input"], None, 0, 316 "Do not display percent identity and similarity"), 317 _Option(["-aformat"], ["input"], None, 0, 318 "Display output in a different specified output format")]
319
320 -class FuzznucCommandline(Application.AbstractCommandline):
321 """Commandline object for the fuzznuc program from EMBOSS. 322 """
323 - def __init__(self, cmd = "fuzznuc"):
324 Application.AbstractCommandline.__init__(self) 325 self.program_name = cmd 326 327 self.parameters = [ 328 _Option(["-sequence"], ["input"], None, 1, 329 "Sequence database USA"), 330 _Option(["-pattern"], ["input"], None, 1, 331 "Search pattern, using standard IUPAC one-letter codes"), 332 _Option(["-mismatch"], ["input"], None, 1, 333 "Number of mismatches"), 334 _Option(["-outfile"], ["output", "file"], None, 1, 335 "Output report file name"), 336 _Option(["-complement"], ["input"], None, 0, 337 "Search complementary strand"), 338 _Option(["-rformat"], ["input"], None, 0, 339 "Specify the report format to output in.")]
340
341 -class Est2GenomeCommandline(Application.AbstractCommandline):
342 """Commandline object for the est2genome program from EMBOSS. 343 """
344 - def __init__(self, cmd = "est2genome"):
345 Application.AbstractCommandline.__init__(self) 346 self.program_name = cmd 347 348 self.parameters = [ 349 _Option(["-est"], ["input"], None, 1, 350 "EST sequence(s)"), 351 _Option(["-genome"], ["input"], None, 1, 352 "Genomic sequence"), 353 _Option(["-outfile"], ["output", "file"], None, 1, 354 "Output file name"), 355 _Option(["-match"], ["input"], None, 0, 356 "Score for matching two bases"), 357 _Option(["-mismatch"], ["input"], None, 0, 358 "Cost for mismatching two bases"), 359 _Option(["-gappenalty"], ["input"], None, 0, 360 "Cost for deleting a single base in either sequence, " + \ 361 "excluding introns"), 362 _Option(["-intronpenalty"], ["input"], None, 0, 363 "Cost for an intron, independent of length."), 364 _Option(["-splicepenalty"], ["input"], None, 0, 365 "Cost for an intron, independent of length " + \ 366 "and starting/ending on donor-acceptor sites"), 367 _Option(["-minscore"], ["input"], None, 0, 368 "Exclude alignments with scores below this threshold score."), 369 _Option(["-reverse"], ["input"], None, 0, 370 "Reverse the orientation of the EST sequence"), 371 _Option(["-splice"], ["input"], None, 0, 372 "Use donor and acceptor splice sites."), 373 _Option(["-mode"], ["input"], None, 0, 374 "This determines the comparion mode. 'both', 'forward' " + \ 375 "'reverse'"), 376 _Option(["-best"], ["input"], None, 0, 377 "You can print out all comparisons instead of just the best"), 378 _Option(["-space"], ["input"], None, 0, 379 "for linear-space recursion."), 380 _Option(["-shuffle"], ["input"], None, 0, 381 "Shuffle"), 382 _Option(["-seed"], ["input"], None, 0, 383 "Random number seed"), 384 _Option(["-align"], ["input"], None, 0, 385 "Show the alignment."), 386 _Option(["-width"], ["input"], None, 0, 387 "Alignment width") 388 ]
389
390 -class ETandemCommandline(Application.AbstractCommandline):
391 """Commandline object for the etandem program from EMBOSS. 392 """
393 - def __init__(self, cmd = "etandem"):
394 Application.AbstractCommandline.__init__(self) 395 self.program_name = cmd 396 397 self.parameters = [ 398 _Option(["-sequence"], ["input", "file"], None, 1, 399 "Sequence"), 400 _Option(["-minrepeat"], ["input"], None, 1, 401 "Minimum repeat size"), 402 _Option(["-maxrepeat"], ["input"], None, 1, 403 "Maximum repeat size"), 404 _Option(["-outfile"], ["output", "file"] , None, 1, 405 "Output report file name"), 406 _Option(["-threshold"], ["input"], None, 0, 407 "Threshold score"), 408 _Option(["-mismatch"], ["input"], None, 0, 409 "Allow N as a mismatch"), 410 _Option(["-uniform"], ["input"], None, 0, 411 "Allow uniform consensus"), 412 _Option(["-rformat"], ["output"], None, 0, 413 "Output report format")]
414
415 -class EInvertedCommandline(Application.AbstractCommandline):
416 """Commandline object for the einverted program from EMBOSS. 417 """
418 - def __init__(self, cmd = "einverted"):
419 Application.AbstractCommandline.__init__(self) 420 self.program_name = cmd 421 422 self.parameters = [ 423 _Option(["-sequence"], ["input", "file"], None, 1, 424 "Sequence"), 425 _Option(["-gap"], ["input", "file"], None, 1, 426 "Gap penalty"), 427 _Option(["-threshold"], ["input"], None, 1, 428 "Minimum score threshold"), 429 _Option(["-match"], ["input"], None, 1, 430 "Match score"), 431 _Option(["-mismatch"], ["input"], None, 1, 432 "Mismatch score"), 433 _Option(["-outfile"], ["output", "file"] , None, 1, 434 "Output report file name"), 435 _Option(["-maxrepeat"], ["input"], None, 0, 436 "Maximum separation between the start and end of repeat"), 437 ]
438
439 -class PalindromeCommandline(Application.AbstractCommandline):
440 """Commandline object for the palindrome program from EMBOSS. 441 """
442 - def __init__(self, cmd = "palindrome"):
443 Application.AbstractCommandline.__init__(self) 444 self.program_name = cmd 445 446 self.parameters = [ 447 _Option(["-sequence"], ["input", "file"], None, 1, 448 "Sequence"), 449 _Option(["-minpallen"], ["input"], None, 1, 450 "Minimum palindrome length"), 451 _Option(["-maxpallen"], ["input"], None, 1, 452 "Maximum palindrome length"), 453 _Option(["-gaplimit"], ["input"], None, 1, 454 "Maximum gap between repeats"), 455 _Option(["-nummismatches"], ["input"], None, 1, 456 "Number of mismatches allowed"), 457 _Option(["-overlap"], ["input"], None, 1, 458 "Report overlapping matches"), 459 _Option(["-outfile"], ["output", "file"] , None, 1, 460 "Output report file name"), 461 ]
462
463 -class TranalignCommandline(Application.AbstractCommandline):
464 """Commandline object for the tranalign program from EMBOSS. 465 """
466 - def __init__(self, cmd = "tranalign"):
467 Application.AbstractCommandline.__init__(self) 468 self.program_name = cmd 469 470 self.parameters = [ 471 _Option(["-asequence"], ["input", "file"], None, 1, 472 "Nucleotide sequences to be aligned."), 473 _Option(["-bsequence"], ["input", "file"], None, 1, 474 "Protein sequence alignment"), 475 _Option(["-outseq"], ["output", "file"], None, 1, 476 "Output sequence file."), 477 _Option(["-table"], ["input"], None, 0, 478 "Code to use")]
479
480 -class DiffseqCommandline(Application.AbstractCommandline):
481 """Commandline object for the diffseq program from EMBOSS. 482 """
483 - def __init__(self, cmd = "diffseq"):
484 Application.AbstractCommandline.__init__(self) 485 self.program_name = cmd 486 487 self.parameters = [ 488 _Option(["-asequence"], ["input", "file"], None, 1, 489 "First sequence to compare"), 490 _Option(["-bsequence"], ["input", "file"], None, 1, 491 "Second sequence to compare"), 492 _Option(["-wordsize"], ["input"], None, 1, 493 "Word size to use for comparisons (10 default)"), 494 _Option(["-outfile"], ["output", "file"], None, 1, 495 "Output report file name"), 496 _Option(["-aoutfeat"], ["output", "file"], None, 1, 497 "File for output of first sequence's features"), 498 _Option(["-boutfeat"], ["output", "file"], None, 1, 499 "File for output of second sequence's features"), 500 _Option(["-rformat"], ["output"], None, 0, 501 "Output report file format") 502 ]
503