Spaces:
No application file
No application file
File size: 49,096 Bytes
b7731cd |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 |
# Copyright 2001-2009 Brad Chapman.
# Revisions copyright 2009-2016 by Peter Cock.
# Revisions copyright 2009 by David Winter.
# Revisions copyright 2009-2010 by Leighton Pritchard.
# All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Code to interact with and run various EMBOSS programs (OBSOLETE).
These classes follow the AbstractCommandline interfaces for running
programs.
We have decided to remove this module in future, and instead recommend
building your command and invoking it via the subprocess module directly.
"""
from Bio.Application import _Option, _Switch, AbstractCommandline
class _EmbossMinimalCommandLine(AbstractCommandline):
"""Base Commandline object for EMBOSS wrappers (PRIVATE).
This is provided for subclassing, it deals with shared options
common to all the EMBOSS tools:
Attributes:
- auto Turn off prompts
- stdout Write standard output
- filter Read standard input, write standard output
- options Prompt for standard and additional values
- debug Write debug output to program.dbg
- verbose Report some/full command line options
- help Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
- warning Report warnings
- error Report errors
- fatal Report fatal errors
- die Report dying program messages
"""
def __init__(self, cmd=None, **kwargs):
assert cmd is not None
extra_parameters = [
_Switch(
["-auto", "auto"],
"Turn off prompts.\n\n"
"Automatic mode disables prompting, so we recommend you set this "
"argument all the time when calling an EMBOSS tool from Biopython.",
),
_Switch(["-stdout", "stdout"], "Write standard output."),
_Switch(
["-filter", "filter"], "Read standard input, write standard output."
),
_Switch(
["-options", "options"],
"Prompt for standard and additional values.\n\n"
"If you are calling an EMBOSS tool from within Biopython, "
"we DO NOT recommend using this option.",
),
_Switch(["-debug", "debug"], "Write debug output to program.dbg."),
_Switch(["-verbose", "verbose"], "Report some/full command line options"),
_Switch(
["-help", "help"],
"Report command line options.\n\n"
"More information on associated and general qualifiers "
"can be found with -help -verbose",
),
_Switch(["-warning", "warning"], "Report warnings."),
_Switch(["-error", "error"], "Report errors."),
_Switch(["-die", "die"], "Report dying program messages."),
]
try:
# Insert extra parameters - at the start just in case there
# are any arguments which must come last:
self.parameters = extra_parameters + self.parameters
except AttributeError:
# Should we raise an error? The subclass should have set this up!
self.parameters = extra_parameters
AbstractCommandline.__init__(self, cmd, **kwargs)
class _EmbossCommandLine(_EmbossMinimalCommandLine):
"""Base Commandline object for EMBOSS wrappers (PRIVATE).
This is provided for subclassing, it deals with shared options
common to all the EMBOSS tools plus:
- outfile Output filename
"""
def __init__(self, cmd=None, **kwargs):
assert cmd is not None
extra_parameters = [
_Option(["-outfile", "outfile"], "Output filename", filename=True)
]
try:
# Insert extra parameters - at the start just in case there
# are any arguments which must come last:
self.parameters = extra_parameters + self.parameters
except AttributeError:
# Should we raise an error? The subclass should have set this up!
self.parameters = extra_parameters
_EmbossMinimalCommandLine.__init__(self, cmd, **kwargs)
def _validate(self):
# Check the outfile, filter, or stdout option has been set.
# We can't simply do this via the required flag for the outfile
# output - this seems the simplest solution.
if not (self.outfile or self.filter or self.stdout):
raise ValueError(
"You must either set outfile (output filename), "
"or enable filter or stdout (output to stdout)."
)
return _EmbossMinimalCommandLine._validate(self)
class Primer3Commandline(_EmbossCommandLine):
"""Commandline object for the Primer3 interface from EMBOSS.
The precise set of supported arguments depends on your version of EMBOSS.
This version accepts arguments current at EMBOSS 6.1.0:
>>> cline = Primer3Commandline(sequence="mysequence.fas", auto=True, hybridprobe=True)
>>> cline.explainflag = True
>>> cline.osizeopt=20
>>> cline.psizeopt=200
>>> cline.outfile = "myresults.out"
>>> cline.bogusparameter = 1967 # Invalid parameter
Traceback (most recent call last):
...
ValueError: Option name bogusparameter was not found.
>>> print(cline)
eprimer3 -auto -outfile=myresults.out -sequence=mysequence.fas -hybridprobe=True -psizeopt=200 -osizeopt=20 -explainflag=True
"""
def __init__(self, cmd="eprimer3", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"],
"Sequence to choose primers from.",
is_required=True,
),
_Option(["-task", "task"], "Tell eprimer3 what task to perform."),
_Option(
["-hybridprobe", "hybridprobe"],
"Find an internal oligo to use as a hyb probe.",
),
_Option(
["-numreturn", "numreturn"], "Maximum number of primer pairs to return."
),
_Option(
["-includedregion", "includedregion"],
"Subregion of the sequence in which to pick primers.",
),
_Option(["-target", "target"], "Sequence to target for flanking primers."),
_Option(
["-excludedregion", "excludedregion"],
"Regions to exclude from primer picking.",
),
_Option(
["-forwardinput", "forwardinput"],
"Sequence of a forward primer to check.",
),
_Option(
["-reverseinput", "reverseinput"],
"Sequence of a reverse primer to check.",
),
_Option(
["-gcclamp", "gcclamp"],
"The required number of Gs and Cs at the 3' of each primer.",
),
_Option(["-osize", "osize"], "Optimum length of a primer oligo."),
_Option(["-minsize", "minsize"], "Minimum length of a primer oligo."),
_Option(["-maxsize", "maxsize"], "Maximum length of a primer oligo."),
_Option(
["-otm", "otm"],
"Melting temperature for primer oligo (OBSOLETE).\n\n"
"Option replaced in EMBOSS 6.6.0 by -opttm",
),
_Option(
["-opttm", "opttm"],
"Optimum melting temperature for a primer oligo.\n\n"
"Option added in EMBOSS 6.6.0, replacing -otm",
),
_Option(
["-mintm", "mintm"], "Minimum melting temperature for a primer oligo."
),
_Option(
["-maxtm", "maxtm"], "Maximum melting temperature for a primer oligo."
),
_Option(
["-maxdifftm", "maxdifftm"],
"Maximum difference in melting temperatures between "
"forward and reverse primers.",
),
_Option(["-ogcpercent", "ogcpercent"], "Optimum GC% for a primer."),
_Option(["-mingc", "mingc"], "Minimum GC% for a primer."),
_Option(["-maxgc", "maxgc"], "Maximum GC% for a primer."),
_Option(
["-saltconc", "saltconc"], "Millimolar salt concentration in the PCR."
),
_Option(
["-dnaconc", "dnaconc"],
"Nanomolar concentration of annealing oligos in the PCR.",
),
_Option(
["-maxpolyx", "maxpolyx"],
"Maximum allowable mononucleotide repeat length in a primer.",
),
# Primer length:
_Option(["-psizeopt", "psizeopt"], "Optimum size for the PCR product."),
_Option(
["-prange", "prange"], "Acceptable range of length for the PCR product."
),
# Primer temperature:
_Option(
["-ptmopt", "ptmopt"],
"Optimum melting temperature for the PCR product.",
),
_Option(
["-ptmmin", "ptmmin"],
"Minimum allowed melting temperature for the amplicon.",
),
_Option(
["-ptmmax", "ptmmax"],
"Maximum allowed melting temperature for the amplicon.",
),
# Note to self, should be -oexcludedregion not -oexcluderegion
_Option(
["-oexcludedregion", "oexcludedregion"],
"Do not pick internal oligos in this region.",
),
_Option(["-oligoinput", "oligoinput"], "Sequence of the internal oligo."),
# Oligo length:
_Option(["-osizeopt", "osizeopt"], "Optimum length of internal oligo."),
_Option(["-ominsize", "ominsize"], "Minimum length of internal oligo."),
_Option(["-omaxsize", "omaxsize"], "Maximum length of internal oligo."),
# Oligo GC temperature:
_Option(
["-otmopt", "otmopt"], "Optimum melting temperature of internal oligo."
),
_Option(
["-otmmin", "otmmin"], "Minimum melting temperature of internal oligo."
),
_Option(
["-otmmax", "otmmax"], "Maximum melting temperature of internal oligo."
),
# Oligo GC percent:
_Option(["-ogcopt", "ogcopt"], "Optimum GC% for internal oligo."),
_Option(["-ogcmin", "ogcmin"], "Minimum GC% for internal oligo."),
_Option(["-ogcmax", "ogcmax"], "Maximum GC% for internal oligo."),
# Oligo salt concentration:
_Option(
["-osaltconc", "osaltconc"],
"Millimolar concentration of salt in the hybridisation.",
),
_Option(
["-odnaconc", "odnaconc"],
"Nanomolar concentration of internal oligo in the hybridisation.",
),
# Oligo self complementarity
_Option(
["-oanyself", "oanyself"],
"Maximum allowable alignment score for self-complementarity.",
),
_Option(
["-oendself", "oendself"],
"Max 3'-anchored self-complementarity global alignment score.",
),
_Option(
["-opolyxmax", "opolyxmax"],
"Maximum length of mononucleotide repeat in internal oligo.",
),
_Option(
["-mispriminglibraryfile", "mispriminglibraryfile"],
"File containing library of sequences to avoid amplifying",
),
_Option(
["-maxmispriming", "maxmispriming"],
"Maximum allowed similarity of primers to sequences in "
"library specified by -mispriminglibrary",
),
_Option(
["-omishybmax", "omishybmax"],
"Maximum alignment score for hybridisation of internal oligo to "
"library specified by -mishyblibraryfile.",
),
_Option(
["-mishyblibraryfile", "mishyblibraryfile"],
"Library file of seqs to avoid internal oligo hybridisation.",
),
_Option(
["-explainflag", "explainflag"],
"Produce output tags with eprimer3 statistics",
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class PrimerSearchCommandline(_EmbossCommandLine):
"""Commandline object for the primersearch program from EMBOSS."""
def __init__(self, cmd="primersearch", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-seqall", "-sequences", "sequences", "seqall"],
"Sequence to look for the primer pairs in.",
is_required=True,
),
# When this wrapper was written primersearch used -sequences
# as the argument name. Since at least EMBOSS 5.0 (and
# perhaps earlier) this has been -seqall instead.
_Option(
["-infile", "-primers", "primers", "infile"],
"File containing the primer pairs to search for.",
filename=True,
is_required=True,
),
# When this wrapper was written primersearch used -primers
# as the argument name. Since at least EMBOSS 5.0 (and
# perhaps earlier) this has been -infile instead.
_Option(
["-mismatchpercent", "mismatchpercent"],
"Allowed percentage mismatch (any integer value, default 0).",
is_required=True,
),
_Option(
["-snucleotide", "snucleotide"], "Sequences are nucleotide (boolean)"
),
_Option(["-sprotein", "sprotein"], "Sequences are protein (boolean)"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FDNADistCommandline(_EmbossCommandLine):
"""Commandline object for the fdnadist program from EMBOSS.
fdnadist is an EMBOSS wrapper for the PHYLIP program dnadist for
calculating distance matrices from DNA sequence files.
"""
def __init__(self, cmd="fdnadist", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"],
"seq file to use (phylip)",
filename=True,
is_required=True,
),
_Option(["-method", "method"], "sub. model [f,k,j,l,s]", is_required=True),
_Option(["-gamma", "gamma"], "gamma [g, i,n]"),
_Option(
["-ncategories", "ncategories"], "number of rate catergories (1-9)"
),
_Option(["-rate", "rate"], "rate for each category"),
_Option(
["-categories", "categories"], "File of substitution rate categories"
),
_Option(["-weights", "weights"], "weights file"),
_Option(
["-gammacoefficient", "gammacoefficient"], "value for gamma (> 0.001)"
),
_Option(["-invarfrac", "invarfrac"], "proportoin of invariant sites"),
_Option(["-ttratio", "ttratio"], "ts/tv ratio"),
_Option(["-freqsfrom", "freqsfrom"], "use emprical base freqs"),
_Option(["-basefreq", "basefreq"], "specify basefreqs"),
_Option(["-lower", "lower"], "lower triangle matrix (y/N)"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FTreeDistCommandline(_EmbossCommandLine):
"""Commandline object for the ftreedist program from EMBOSS.
ftreedist is an EMBOSS wrapper for the PHYLIP program treedist used for
calculating distance measures between phylogentic trees.
"""
def __init__(self, cmd="ftreedist", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-intreefile", "intreefile"],
"tree file to score (phylip)",
filename=True,
is_required=True,
),
_Option(["-dtype", "dtype"], "distance type ([S]ymetric, [b]ranch score)"),
_Option(
["-pairing", "pairing"],
"tree pairing method ([A]djacent pairs, all [p]ossible pairs)",
),
_Option(["-style", "style"], "output style - [V]erbose, [f]ill, [s]parse"),
_Option(["-noroot", "noroot"], "treat trees as rooted [N/y]"),
_Option(
["-outgrno", "outgrno"],
"which taxon to root the trees with (starts from 0)",
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FNeighborCommandline(_EmbossCommandLine):
"""Commandline object for the fneighbor program from EMBOSS.
fneighbor is an EMBOSS wrapper for the PHYLIP program neighbor used for
calculating neighbor-joining or UPGMA trees from distance matrices.
"""
def __init__(self, cmd="fneighbor", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-datafile", "datafile"],
"dist file to use (phylip)",
filename=True,
is_required=True,
),
_Option(
["-matrixtype", "matrixtype"],
"is matrix square (S), upper (U) or lower (L)",
),
_Option(["-treetype", "treetype"], "nj or UPGMA tree (n/u)"),
_Option(["-outgrno", "outgrno"], "taxon to use as OG"),
_Option(["-jumble", "jumble"], "randommise input order (Y/n)"),
_Option(["-seed", "seed"], "provide a random seed"),
_Option(["-trout", "trout"], "write tree (Y/n)"),
_Option(["-outtreefile", "outtreefile"], "filename for output tree"),
_Option(["-progress", "progress"], "print progress (Y/n)"),
_Option(["-treeprint", "treeprint"], "print tree (Y/n)"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FSeqBootCommandline(_EmbossCommandLine):
"""Commandline object for the fseqboot program from EMBOSS.
fseqboot is an EMBOSS wrapper for the PHYLIP program seqboot used to
pseudo-sample alignment files.
"""
def __init__(self, cmd="fseqboot", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"],
"seq file to sample (phylip)",
filename=True,
is_required=True,
),
_Option(["-categories", "catergories"], "file of input categories"),
_Option(["-weights", "weights"], " weights file"),
_Option(["-test", "test"], "specify operation, default is bootstrap"),
_Option(["-regular", "regular"], "absolute number to resample"),
_Option(["-fracsample", "fracsample"], "fraction to resample"),
_Option(
["-rewriteformat", "rewriteformat"],
"output format ([P]hyilp, [n]exus, [x]ml",
),
_Option(["-seqtype", "seqtype"], "output format ([D]na, [p]rotein, [r]na"),
_Option(["-blocksize", "blocksize"], "print progress (Y/n)"),
_Option(["-reps", "reps"], "how many replicates, defaults to 100)"),
_Option(
["-justweights", "jusweights"],
"what to write out [D]atasets of just [w]eights",
),
_Option(["-seed", "seed"], "specify random seed"),
_Option(["-dotdiff", "dotdiff"], "Use dot-differencing? [Y/n]"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FDNAParsCommandline(_EmbossCommandLine):
"""Commandline object for the fdnapars program from EMBOSS.
fdnapars is an EMBOSS version of the PHYLIP program dnapars, for
estimating trees from DNA sequences using parsiomny. Calling this command
without providing a value for the option "-intreefile" will invoke
"interactive mode" (and as a result fail if called with subprocess) if
"-auto" is not set to true.
"""
def __init__(self, cmd="fdnapars", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"],
"seq file to use (phylip)",
filename=True,
is_required=True,
),
_Option(["-intreefile", "intreefile"], "Phylip tree file"),
_Option(["-weights", "weights"], "weights file"),
_Option(["-maxtrees", "maxtrees"], "max trees to save during run"),
_Option(["-thorough", "thorough"], "more thorough search (Y/n)"),
_Option(["-rearrange", "rearrange"], "Rearrange on just 1 best tree (Y/n)"),
_Option(
["-transversion", "transversion"], "Use tranversion parsimony (y/N)"
),
_Option(
["-njumble", "njumble"],
"number of times to randomise input order (default is 0)",
),
_Option(["-seed", "seed"], "provide random seed"),
_Option(["-outgrno", "outgrno"], "Specify outgroup"),
_Option(["-thresh", "thresh"], "Use threshold parsimony (y/N)"),
_Option(["-threshold", "threshold"], "Threshold value"),
_Option(["-trout", "trout"], "Write trees to file (Y/n)"),
_Option(["-outtreefile", "outtreefile"], "filename for output tree"),
_Option(["-dotdiff", "dotdiff"], "Use dot-differencing? [Y/n]"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FProtParsCommandline(_EmbossCommandLine):
"""Commandline object for the fdnapars program from EMBOSS.
fprotpars is an EMBOSS version of the PHYLIP program protpars, for
estimating trees from protein sequences using parsiomny. Calling this
command without providing a value for the option "-intreefile" will invoke
"interactive mode" (and as a result fail if called with subprocess) if
"-auto" is not set to true.
"""
def __init__(self, cmd="fprotpars", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"],
"seq file to use (phylip)",
filename=True,
is_required=True,
),
_Option(["-intreefile", "intreefile"], "Phylip tree file to score"),
_Option(
["-outtreefile", "outtreefile"],
"phylip tree output file",
filename=True,
is_required=True,
),
_Option(["-weights", "weights"], "weights file"),
_Option(["-whichcode", "whichcode"], "which genetic code, [U,M,V,F,Y]]"),
_Option(
["-njumble", "njumble"],
"number of times to randomise input order (default is 0)",
),
_Option(["-seed", "seed"], "provide random seed"),
_Option(["-outgrno", "outgrno"], "Specify outgroup"),
_Option(["-thresh", "thresh"], "Use threshold parsimony (y/N)"),
_Option(["-threshold", "threshold"], "Threshold value"),
_Option(["-trout", "trout"], "Write trees to file (Y/n)"),
_Option(["-dotdiff", "dotdiff"], "Use dot-differencing? [Y/n]"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FProtDistCommandline(_EmbossCommandLine):
"""Commandline object for the fprotdist program from EMBOSS.
fprotdist is an EMBOSS wrapper for the PHYLIP program protdist used to
estimate trees from protein sequences using parsimony
"""
def __init__(self, cmd="fprotdist", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"],
"seq file to use (phylip)",
filename=True,
is_required=True,
),
_Option(
["-ncategories", "ncategories"], "number of rate catergories (1-9)"
),
_Option(["-rate", "rate"], "rate for each category"),
_Option(["-catergories", "catergories"], "file of rates"),
_Option(["-weights", "weights"], "weights file"),
_Option(["-method", "method"], "sub. model [j,h,d,k,s,c]"),
_Option(["-gamma", "gamma"], "gamma [g, i,c]"),
_Option(
["-gammacoefficient", "gammacoefficient"], "value for gamma (> 0.001)"
),
_Option(
["-invarcoefficient", "invarcoefficient"],
"float for variation of substitution rate among sites",
),
_Option(["-aacateg", "aacateg"], "Choose the category to use [G,C,H]"),
_Option(["-whichcode", "whichcode"], "genetic code [c,m,v,f,y]"),
_Option(["-ease", "ease"], "Pob change catergory (float between -0 and 1)"),
_Option(["-ttratio", "ttratio"], "Transition/transversion ratio (0-1)"),
_Option(
["-basefreq", "basefreq"], "DNA base frequencies (space separated list)"
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FConsenseCommandline(_EmbossCommandLine):
"""Commandline object for the fconsense program from EMBOSS.
fconsense is an EMBOSS wrapper for the PHYLIP program consense used to
calculate consensus trees.
"""
def __init__(self, cmd="fconsense", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-intreefile", "intreefile"],
"file with phylip trees to make consensus from",
filename=True,
is_required=True,
),
_Option(["-method", "method"], "consensus method [s, mr, MRE, ml]"),
_Option(
["-mlfrac", "mlfrac"],
"cut-off freq for branch to appear in consensus (0.5-1.0)",
),
_Option(["-root", "root"], "treat trees as rooted (YES, no)"),
_Option(["-outgrno", "outgrno"], "OTU to use as outgroup (starts from 0)"),
_Option(["-trout", "trout"], "treat trees as rooted (YES, no)"),
_Option(
["-outtreefile", "outtreefile"], "Phylip tree output file (optional)"
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class WaterCommandline(_EmbossCommandLine):
"""Commandline object for the water program from EMBOSS."""
def __init__(self, cmd="water", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-asequence", "asequence"],
"First sequence to align",
filename=True,
is_required=True,
),
_Option(
["-bsequence", "bsequence"],
"Second sequence to align",
filename=True,
is_required=True,
),
_Option(["-gapopen", "gapopen"], "Gap open penalty", is_required=True),
_Option(
["-gapextend", "gapextend"], "Gap extension penalty", is_required=True
),
_Option(["-datafile", "datafile"], "Matrix file", filename=True),
_Switch(
["-nobrief", "nobrief"], "Display extended identity and similarity"
),
_Switch(["-brief", "brief"], "Display brief identity and similarity"),
_Option(
["-similarity", "similarity"], "Display percent identity and similarity"
),
_Option(
["-snucleotide", "snucleotide"], "Sequences are nucleotide (boolean)"
),
_Option(["-sprotein", "sprotein"], "Sequences are protein (boolean)"),
_Option(
["-aformat", "aformat"],
"Display output in a different specified output format",
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class NeedleCommandline(_EmbossCommandLine):
"""Commandline object for the needle program from EMBOSS."""
def __init__(self, cmd="needle", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-asequence", "asequence"],
"First sequence to align",
filename=True,
is_required=True,
),
_Option(
["-bsequence", "bsequence"],
"Second sequence to align",
filename=True,
is_required=True,
),
_Option(["-gapopen", "gapopen"], "Gap open penalty", is_required=True),
_Option(
["-gapextend", "gapextend"], "Gap extension penalty", is_required=True
),
_Option(["-datafile", "datafile"], "Matrix file", filename=True),
_Option(["-endweight", "endweight"], "Apply And gap penalties"),
_Option(
["-endopen", "endopen"],
"The score taken away when an end gap is created.",
),
_Option(
["-endextend", "endextend"],
"The score added to the end gap penalty for each base or "
"residue in the end gap.",
),
_Switch(
["-nobrief", "nobrief"], "Display extended identity and similarity"
),
_Switch(["-brief", "brief"], "Display brief identity and similarity"),
_Option(
["-similarity", "similarity"], "Display percent identity and similarity"
),
_Option(
["-snucleotide", "snucleotide"], "Sequences are nucleotide (boolean)"
),
_Option(["-sprotein", "sprotein"], "Sequences are protein (boolean)"),
_Option(
["-aformat", "aformat"],
"Display output in a different specified output format",
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class NeedleallCommandline(_EmbossCommandLine):
"""Commandline object for the needleall program from EMBOSS."""
def __init__(self, cmd="needleall", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-asequence", "asequence"],
"First sequence to align",
filename=True,
is_required=True,
),
_Option(
["-bsequence", "bsequence"],
"Second sequence to align",
filename=True,
is_required=True,
),
_Option(["-gapopen", "gapopen"], "Gap open penalty", is_required=True),
_Option(
["-gapextend", "gapextend"], "Gap extension penalty", is_required=True
),
_Option(["-datafile", "datafile"], "Matrix file", filename=True),
_Option(
["-minscore", "minscore"],
"Exclude alignments with scores below this threshold score.",
),
_Option(["-errorfile", "errorfile"], "Error file to be written to."),
_Option(["-endweight", "endweight"], "Apply And gap penalties"),
_Option(
["-endopen", "endopen"],
"The score taken away when an end gap is created.",
),
_Option(
["-endextend", "endextend"],
"The score added to the end gap penalty for each base or "
"residue in the end gap.",
),
_Switch(
["-nobrief", "nobrief"], "Display extended identity and similarity"
),
_Switch(["-brief", "brief"], "Display brief identity and similarity"),
_Option(
["-similarity", "similarity"], "Display percent identity and similarity"
),
_Option(
["-snucleotide", "snucleotide"], "Sequences are nucleotide (boolean)"
),
_Option(["-sprotein", "sprotein"], "Sequences are protein (boolean)"),
_Option(
["-aformat", "aformat"],
"Display output in a different specified output format",
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class StretcherCommandline(_EmbossCommandLine):
"""Commandline object for the stretcher program from EMBOSS."""
def __init__(self, cmd="stretcher", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-asequence", "asequence"],
"First sequence to align",
filename=True,
is_required=True,
),
_Option(
["-bsequence", "bsequence"],
"Second sequence to align",
filename=True,
is_required=True,
),
_Option(
["-gapopen", "gapopen"],
"Gap open penalty",
is_required=True,
checker_function=lambda value: isinstance(value, int),
),
_Option(
["-gapextend", "gapextend"],
"Gap extension penalty",
is_required=True,
checker_function=lambda value: isinstance(value, int),
),
_Option(["-datafile", "datafile"], "Matrix file", filename=True),
_Option(
["-snucleotide", "snucleotide"], "Sequences are nucleotide (boolean)"
),
_Option(["-sprotein", "sprotein"], "Sequences are protein (boolean)"),
_Option(
["-aformat", "aformat"],
"Display output in a different specified output format",
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FuzznucCommandline(_EmbossCommandLine):
"""Commandline object for the fuzznuc program from EMBOSS."""
def __init__(self, cmd="fuzznuc", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"], "Sequence database USA", is_required=True
),
_Option(
["-pattern", "pattern"],
"Search pattern, using standard IUPAC one-letter codes",
is_required=True,
),
_Option(["-pmismatch", "pmismatch"], "Number of mismatches"),
_Option(["-complement", "complement"], "Search complementary strand"),
_Option(["-rformat", "rformat"], "Specify the report format to output in."),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class FuzzproCommandline(_EmbossCommandLine):
"""Commandline object for the fuzzpro program from EMBOSS."""
def __init__(self, cmd="fuzzpro", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"], "Sequence database USA", is_required=True
),
_Option(
["-pattern", "pattern"],
"Search pattern, using standard IUPAC one-letter codes",
is_required=True,
),
_Option(["-pmismatch", "pmismatch"], "Number of mismatches"),
_Option(["-rformat", "rformat"], "Specify the report format to output in."),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class Est2GenomeCommandline(_EmbossCommandLine):
"""Commandline object for the est2genome program from EMBOSS."""
def __init__(self, cmd="est2genome", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(["-est", "est"], "EST sequence(s)", is_required=True),
_Option(["-genome", "genome"], "Genomic sequence", is_required=True),
_Option(["-match", "match"], "Score for matching two bases"),
_Option(["-mismatch", "mismatch"], "Cost for mismatching two bases"),
_Option(
["-gappenalty", "gappenalty"],
"Cost for deleting a single base in either sequence, "
"excluding introns",
),
_Option(
["-intronpenalty", "intronpenalty"],
"Cost for an intron, independent of length.",
),
_Option(
["-splicepenalty", "splicepenalty"],
"Cost for an intron, independent of length "
"and starting/ending on donor-acceptor sites",
),
_Option(
["-minscore", "minscore"],
"Exclude alignments with scores below this threshold score.",
),
_Option(
["-reverse", "reverse"], "Reverse the orientation of the EST sequence"
),
_Option(["-splice", "splice"], "Use donor and acceptor splice sites."),
_Option(
["-mode", "mode"],
"This determines the comparison mode. 'both', 'forward', or 'reverse'",
),
_Option(
["-best", "best"],
"You can print out all comparisons instead of just the best",
),
_Option(["-space", "space"], "for linear-space recursion."),
_Option(["-shuffle", "shuffle"], "Shuffle"),
_Option(["-seed", "seed"], "Random number seed"),
_Option(["-align", "align"], "Show the alignment."),
_Option(["-width", "width"], "Alignment width"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class ETandemCommandline(_EmbossCommandLine):
"""Commandline object for the etandem program from EMBOSS."""
def __init__(self, cmd="etandem", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"], "Sequence", filename=True, is_required=True
),
_Option(
["-minrepeat", "minrepeat"], "Minimum repeat size", is_required=True
),
_Option(
["-maxrepeat", "maxrepeat"], "Maximum repeat size", is_required=True
),
_Option(["-threshold", "threshold"], "Threshold score"),
_Option(["-mismatch", "mismatch"], "Allow N as a mismatch"),
_Option(["-uniform", "uniform"], "Allow uniform consensus"),
_Option(["-rformat", "rformat"], "Output report format"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class EInvertedCommandline(_EmbossCommandLine):
"""Commandline object for the einverted program from EMBOSS."""
def __init__(self, cmd="einverted", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"], "Sequence", filename=True, is_required=True
),
_Option(["-gap", "gap"], "Gap penalty", filename=True, is_required=True),
_Option(
["-threshold", "threshold"], "Minimum score threshold", is_required=True
),
_Option(["-match", "match"], "Match score", is_required=True),
_Option(["-mismatch", "mismatch"], "Mismatch score", is_required=True),
_Option(
["-maxrepeat", "maxrepeat"],
"Maximum separation between the start and end of repeat",
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class PalindromeCommandline(_EmbossCommandLine):
"""Commandline object for the palindrome program from EMBOSS."""
def __init__(self, cmd="palindrome", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"], "Sequence", filename=True, is_required=True
),
_Option(
["-minpallen", "minpallen"],
"Minimum palindrome length",
is_required=True,
),
_Option(
["-maxpallen", "maxpallen"],
"Maximum palindrome length",
is_required=True,
),
_Option(
["-gaplimit", "gaplimit"],
"Maximum gap between repeats",
is_required=True,
),
_Option(
["-nummismatches", "nummismatches"],
"Number of mismatches allowed",
is_required=True,
),
_Option(
["-overlap", "overlap"], "Report overlapping matches", is_required=True
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class TranalignCommandline(_EmbossCommandLine):
"""Commandline object for the tranalign program from EMBOSS."""
def __init__(self, cmd="tranalign", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-asequence", "asequence"],
"Nucleotide sequences to be aligned.",
filename=True,
is_required=True,
),
_Option(
["-bsequence", "bsequence"],
"Protein sequence alignment",
filename=True,
is_required=True,
),
_Option(
["-outseq", "outseq"],
"Output sequence file.",
filename=True,
is_required=True,
),
_Option(["-table", "table"], "Code to use"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class DiffseqCommandline(_EmbossCommandLine):
"""Commandline object for the diffseq program from EMBOSS."""
def __init__(self, cmd="diffseq", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-asequence", "asequence"],
"First sequence to compare",
filename=True,
is_required=True,
),
_Option(
["-bsequence", "bsequence"],
"Second sequence to compare",
filename=True,
is_required=True,
),
_Option(
["-wordsize", "wordsize"],
"Word size to use for comparisons (10 default)",
is_required=True,
),
_Option(
["-aoutfeat", "aoutfeat"],
"File for output of first sequence's features",
filename=True,
is_required=True,
),
_Option(
["-boutfeat", "boutfeat"],
"File for output of second sequence's features",
filename=True,
is_required=True,
),
_Option(["-rformat", "rformat"], "Output report file format"),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
class IepCommandline(_EmbossCommandLine):
"""Commandline for EMBOSS iep: calculated isoelectric point and charge.
Examples
--------
>>> from Bio.Emboss.Applications import IepCommandline
>>> iep_cline = IepCommandline(sequence="proteins.faa",
... outfile="proteins.txt")
>>> print(iep_cline)
iep -outfile=proteins.txt -sequence=proteins.faa
You would typically run the command line with iep_cline() or via the
Python subprocess module, as described in the Biopython tutorial.
"""
def __init__(self, cmd="iep", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"],
"Protein sequence(s) filename",
filename=True,
is_required=True,
),
_Option(
["-amino", "amino"],
"""Number of N-termini
Integer 0 (default) or more.
""",
),
_Option(
["-carboxyl", "carboxyl"],
"""Number of C-termini
Integer 0 (default) or more.
""",
),
_Option(
["-lysinemodified", "lysinemodified"],
"""Number of modified lysines
Integer 0 (default) or more.
""",
),
_Option(
["-disulphides", "disulphides"],
"""Number of disulphide bridges
Integer 0 (default) or more.
""",
),
# Should we implement the -termini switch as well?
_Option(
["-notermini", "notermini"],
"Exclude (True) or include (False) charge at N and C terminus.",
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
# seqret uses -outseq, not -outfile, so use the base class:
class SeqretCommandline(_EmbossMinimalCommandLine):
"""Commandline object for the seqret program from EMBOSS.
This tool allows you to interconvert between different sequence file
formats (e.g. GenBank to FASTA). Combining Biopython's Bio.SeqIO module
with seqret using a suitable intermediate file format can allow you to
read/write to an even wider range of file formats.
This wrapper currently only supports the core functionality, things like
feature tables (in EMBOSS 6.1.0 onwards) are not yet included.
"""
def __init__(self, cmd="seqret", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"], "Input sequence(s) filename", filename=True
),
_Option(["-outseq", "outseq"], "Output sequence file.", filename=True),
_Option(
["-sformat", "sformat"],
"Input sequence(s) format (e.g. fasta, genbank)",
),
_Option(
["-osformat", "osformat"],
"Output sequence(s) format (e.g. fasta, genbank)",
),
]
_EmbossMinimalCommandLine.__init__(self, cmd, **kwargs)
def _validate(self):
# Check the outfile, filter, or stdout option has been set.
# We can't simply do this via the required flag for the outfile
# output - this seems the simplest solution.
if not (self.outseq or self.filter or self.stdout):
raise ValueError(
"You must either set outfile (output filename), "
"or enable filter or stdout (output to stdout)."
)
if not (self.sequence or self.filter or self.stdint):
raise ValueError(
"You must either set sequence (input filename), "
"or enable filter or stdin (input from stdin)."
)
return _EmbossMinimalCommandLine._validate(self)
class SeqmatchallCommandline(_EmbossCommandLine):
"""Commandline object for the seqmatchall program from EMBOSS.
e.g.
>>> cline = SeqmatchallCommandline(sequence="opuntia.fasta", outfile="opuntia.txt")
>>> cline.auto = True
>>> cline.wordsize = 18
>>> cline.aformat = "pair"
>>> print(cline)
seqmatchall -auto -outfile=opuntia.txt -sequence=opuntia.fasta -wordsize=18 -aformat=pair
"""
def __init__(self, cmd="seqmatchall", **kwargs):
"""Initialize the class."""
self.parameters = [
_Option(
["-sequence", "sequence"],
"Readable set of sequences",
filename=True,
is_required=True,
),
_Option(
["-wordsize", "wordsize"], "Word size (Integer 2 or more, default 4)"
),
_Option(
["-aformat", "aformat"],
"Display output in a different specified output format",
),
]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
|