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