/usr/lib/python2.7/dist-packages/cogent/core/sequence.py is in python-cogent 1.9-9.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 | #!/usr/bin/env python
"""Contains classes that represent biological sequence data. These
provide generic biological sequence manipulation functions, plus functions
that are critical for the EVOLVE calculations.
WARNING: Do not import sequence classes directly! It is expected that you will
access them through the moltype module. Sequence classes depend on information
from the MolType that is _only_ available after MolType has been imported.
Sequences are intended to be immutable. This is not enforced by the code for
performance reasons, but don't alter the MolType or the sequence data after
creation.
"""
from __future__ import division
from annotation import Map, Feature, _Annotatable
from cogent.util.transform import keep_chars, for_seq, per_shortest, \
per_longest
from cogent.util.misc import DistanceFromMatrix
from cogent.core.genetic_code import DEFAULT as DEFAULT_GENETIC_CODE, \
GeneticCodes
from cogent.parse import gff
from cogent.format.fasta import fasta_from_sequences
from cogent.core.info import Info as InfoClass
from numpy import array, zeros, put, nonzero, take, ravel, compress, \
logical_or, logical_not, arange
from numpy.random import permutation
from operator import eq, ne
from random import shuffle
import re
import warnings
__author__ = "Rob Knight, Gavin Huttley, and Peter Maxwell"
__copyright__ = "Copyright 2007-2016, The Cogent Project"
__credits__ = ["Rob Knight", "Peter Maxwell", "Gavin Huttley",
"Matthew Wakefield", "Daniel McDonald"]
__license__ = "GPL"
__version__ = "1.9"
__maintainer__ = "Rob Knight"
__email__ = "rob@spot.colorado.edu"
__status__ = "Production"
ARRAY_TYPE = type(array(1))
#standard distance functions: left because generally useful
frac_same = for_seq(f=eq, aggregator=sum, normalizer=per_shortest)
frac_diff = for_seq(f=ne, aggregator=sum, normalizer=per_shortest)
class SequenceI(object):
"""Abstract class containing Sequence interface.
Specifies methods that Sequence delegates to its MolType, and methods for
detecting gaps.
"""
#String methods delegated to self._seq -- remember to override if self._seq
#isn't a string in your base class, but it's probably better to make
#self._seq a property that contains the string.
LineWrap = None #used for formatting FASTA strings
def __str__(self):
"""__str__ returns self._seq unmodified."""
return self._seq
def toFasta(self, make_seqlabel=None):
"""Return string of self in FASTA format, no trailing newline
Arguments:
- make_seqlabel: callback function that takes the seq object and
returns a label str
"""
return fasta_from_sequences([self], make_seqlabel = make_seqlabel,
line_wrap=self.LineWrap)
def translate(self, *args, **kwargs):
"""translate() delegates to self._seq."""
return self._seq.translate(*args, **kwargs)
def count(self, item):
"""count() delegates to self._seq."""
return self._seq.count(item)
def __cmp__(self, other):
"""__cmp__ compares based on the sequence string."""
return cmp(self._seq, other)
def __hash__(self):
"""__hash__ behaves like the sequence string for dict lookup."""
return hash(self._seq)
def __contains__(self, other):
"""__contains__ checks whether other is in the sequence string."""
return other in self._seq
def shuffle(self):
"""returns a randomized copy of the Sequence object"""
randomized_copy_list = list(self)
shuffle(randomized_copy_list)
return self.__class__(''.join(randomized_copy_list), Info=self.Info)
def complement(self):
"""Returns complement of self, using data from MolType.
Always tries to return same type as item: if item looks like a dict,
will return list of keys.
"""
return self.__class__(self.MolType.complement(self), Info=self.Info)
def stripDegenerate(self):
"""Removes degenerate bases by stripping them out of the sequence."""
return self.__class__(self.MolType.stripDegenerate(self), Info=self.Info)
def stripBad(self):
"""Removes any symbols not in the alphabet."""
return self.__class__(self.MolType.stripBad(self), Info=self.Info)
def stripBadAndGaps(self):
"""Removes any symbols not in the alphabet, and any gaps."""
return self.__class__(self.MolType.stripBadAndGaps(self), Info=self.Info)
def rc(self):
"""Returns reverse complement of self w/ data from MolType.
Always returns same type self.
"""
return self.__class__(self.MolType.rc(self), Info=self.Info)
def isGapped(self):
"""Returns True if sequence contains gaps."""
return self.MolType.isGapped(self)
def isGap(self, char=None):
"""Returns True if char is a gap.
If char is not supplied, tests whether self is gaps only.
"""
if char is None: #no char - so test if self is all gaps
return len(self) == self.countGaps()
else:
return self.MolType.isGap(char)
def isDegenerate(self):
"""Returns True if sequence contains degenerate characters."""
return self.MolType.isDegenerate(self)
def isValid(self):
"""Returns True if sequence contains no items absent from alphabet."""
return self.MolType.isValid(self)
def isStrict(self):
"""Returns True if sequence contains only monomers."""
return self.MolType.isStrict(self)
def firstGap(self):
"""Returns the index of the first gap in the sequence, or None."""
return self.MolType.firstGap(self)
def firstDegenerate(self):
"""Returns the index of first degenerate symbol in sequence, or None."""
return self.MolType.firstDegenerate(self)
def firstInvalid(self):
"""Returns the index of first invalid symbol in sequence, or None."""
return self.MolType.firstInvalid(self)
def firstNonStrict(self):
"""Returns the index of first non-strict symbol in sequence, or None."""
return self.MolType.firstNonStrict(self)
def disambiguate(self, method='strip'):
"""Returns a non-degenerate sequence from a degenerate one.
method can be 'strip' (deletes any characters not in monomers or gaps)
or 'random'(assigns the possibilities at random, using equal
frequencies).
"""
return self.__class__(self.MolType.disambiguate(self, method), \
Info=self.Info)
def degap(self):
"""Deletes all gap characters from sequence."""
return self.__class__(self.MolType.degap(self), Info=self.Info)
def gapList(self):
"""Returns list of indices of all gaps in the sequence, or []."""
return self.MolType.gapList(self)
def gapVector(self):
"""Returns vector of True or False according to which pos are gaps."""
return self.MolType.gapVector(self)
def gapMaps(self):
"""Returns dicts mapping between gapped and ungapped positions."""
return self.MolType.gapMaps(self)
def countGaps(self):
"""Counts the gaps in the specified sequence."""
return self.MolType.countGaps(self)
def countDegenerate(self):
"""Counts the degenerate bases in the specified sequence."""
return self.MolType.countDegenerate(self)
def possibilities(self):
"""Counts number of possible sequences matching the sequence.
Uses self.Degenerates to decide how many possibilites there are at
each position in the sequence.
"""
return self.MolType.possibilities(self)
def MW(self, method='random', delta=None):
"""Returns the molecular weight of (one strand of) the sequence.
If the sequence is ambiguous, uses method (random or strip) to
disambiguate the sequence.
If delta is passed in, adds delta per strand (default is None, which
uses the alphabet default. Typically, this adds 18 Da for terminal
water. However, note that the default nucleic acid weight assumes
5' monophosphate and 3' OH: pass in delta=18.0 if you want 5' OH as
well.
Note that this method only calculates the MW of the coding strand. If
you want the MW of the reverse strand, add self.rc().MW(). DO NOT
just multiply the MW by 2: the results may not be accurate due to
strand bias, e.g. in mitochondrial genomes.
"""
return self.MolType.MW(self, method, delta)
def canMatch(self, other):
"""Returns True if every pos in self could match same pos in other.
Truncates at length of shorter sequence.
Gaps are only allowed to match other gaps.
"""
return self.MolType.canMatch(self, other)
def canMismatch(self, other):
"""Returns True if any position in self could mismatch with other.
Truncates at length of shorter sequence.
Gaps are always counted as matches.
"""
return self.MolType.canMismatch(self, other)
def mustMatch(self, other):
"""Returns True if all positions in self must match positions in other."""
return self.MolType.mustMatch(self, other)
def canPair(self, other):
"""Returns True if self and other could pair.
Pairing occurs in reverse order, i.e. last position of other with
first position of self, etc.
Truncates at length of shorter sequence.
Gaps are only allowed to pair with other gaps, and are counted as 'weak'
(same category as GU and degenerate pairs).
NOTE: second must be able to be reverse
"""
return self.MolType.canPair(self, other)
def canMispair(self, other):
"""Returns True if any position in self could mispair with other.
Pairing occurs in reverse order, i.e. last position of other with
first position of self, etc.
Truncates at length of shorter sequence.
Gaps are always counted as possible mispairs, as are weak pairs like GU.
"""
return self.MolType.canMispair(self, other)
def mustPair(self, other):
"""Returns True if all positions in self must pair with other.
Pairing occurs in reverse order, i.e. last position of other with
first position of self, etc.
"""
return not self.MolType.canMispair(self, other)
def diff(self, other):
"""Returns number of differences between self and other.
NOTE: truncates at the length of the shorter sequence. Case-sensitive.
"""
return self.distance(other)
def distance(self, other, function=None):
"""Returns distance between self and other using function(i,j).
other must be a sequence.
function should be a function that takes two items and returns a
number. To turn a 2D matrix into a function, use
cogent.util.miscs.DistanceFromMatrix(matrix).
NOTE: Truncates at the length of the shorter sequence.
Note that the function acts on two _elements_ of the sequences, not
the two sequences themselves (i.e. the behavior will be the same for
every position in the sequences, such as identity scoring or a function
derived from a distance matrix as suggested above). One limitation of
this approach is that the distance function cannot use properties of
the sequences themselves: for example, it cannot use the lengths of the
sequences to normalize the scores as percent similarities or percent
differences.
If you want functions that act on the two sequences themselves, there
is no particular advantage in making these functions methods of the
first sequences by passing them in as parameters like the function
in this method. It makes more sense to use them as standalone functions.
The factory function cogent.util.transform.for_seq is useful for
converting per-element functions into per-sequence functions, since it
takes as parameters a per-element scoring function, a score aggregation
function, and a normalization function (which itself takes the two
sequences as parameters), returning a single function that combines
these functions and that acts on two complete sequences.
"""
if function is None:
#use identity scoring function
function = lambda a, b : a != b
distance = 0
for first, second in zip(self, other):
distance += function(first, second)
return distance
def matrixDistance(self, other, matrix):
"""Returns distance between self and other using a score matrix.
WARNING: the matrix must explicitly contain scores for the case where
a position is the same in self and other (e.g. for a distance matrix,
an identity between U and U might have a score of 0). The reason the
scores for the 'diagonals' need to be passed explicitly is that for
some kinds of distance matrices, e.g. log-odds matrices, the 'diagonal'
scores differ from each other. If these elements are missing, this
function will raise a KeyError at the first position that the two
sequences are identical.
"""
return self.distance(other, DistanceFromMatrix(matrix))
def fracSame(self, other):
"""Returns fraction of positions where self and other are the same.
Truncates at length of shorter sequence.
Note that fracSame and fracDiff are both 0 if one sequence is empty.
"""
return frac_same(self, other)
def fracDiff(self, other):
"""Returns fraction of positions where self and other differ.
Truncates at length of shorter sequence.
Note that fracSame and fracDiff are both 0 if one sequence is empty.
"""
return frac_diff(self, other)
def fracSameGaps(self, other):
"""Returns fraction of positions where self and other share gap states.
In other words, if self and other are both all gaps, or both all
non-gaps, or both have gaps in the same places, fracSameGaps will
return 1.0. If self is all gaps and other has no gaps, fracSameGaps
will return 0.0. Returns 0 if one sequence is empty.
Uses self's gap characters for both sequences.
"""
if not self or not other:
return 0.0
is_gap = self.MolType.Gaps.__contains__
return sum([is_gap(i) == is_gap(j) for i,j in zip(self, other)]) \
/min(len(self),len(other))
def fracDiffGaps(self, other):
"""Returns frac. of positions where self and other's gap states differ.
In other words, if self and other are both all gaps, or both all
non-gaps, or both have gaps in the same places, fracDiffGaps will
return 0.0. If self is all gaps and other has no gaps, fracDiffGaps
will return 1.0.
Returns 0 if one sequence is empty.
Uses self's gap characters for both sequences.
"""
if not self or not other:
return 0.0
return 1.0 - self.fracSameGaps(other)
def fracSameNonGaps(self, other):
"""Returns fraction of non-gap positions where self matches other.
Doesn't count any position where self or other has a gap.
Truncates at the length of the shorter sequence.
Returns 0 if one sequence is empty.
"""
if not self or not other:
return 0.0
is_gap = self.MolType.Gaps.__contains__
count = 0
identities = 0
for i, j in zip(self, other):
if is_gap(i) or is_gap(j):
continue
count += 1
if i == j:
identities += 1
if count:
return identities/count
else: #there were no positions that weren't gaps
return 0
def fracDiffNonGaps(self, other):
"""Returns fraction of non-gap positions where self differs from other.
Doesn't count any position where self or other has a gap.
Truncates at the length of the shorter sequence.
Returns 0 if one sequence is empty. Note that this means that
fracDiffNonGaps is _not_ the same as 1 - fracSameNonGaps, since both
return 0 if one sequence is empty.
"""
if not self or not other:
return 0.0
is_gap = self.MolType.Gaps.__contains__
count = 0
diffs = 0
for i, j in zip(self, other):
if is_gap(i) or is_gap(j):
continue
count += 1
if i != j:
diffs += 1
if count:
return diffs/count
else: #there were no positions that weren't gaps
return 0
def fracSimilar(self, other, similar_pairs):
"""Returns fraction of positions where self[i] is similar to other[i].
similar_pairs must be a dict such that d[(i,j)] exists if i and j are
to be counted as similar. Use PairsFromGroups in cogent.util.misc to
construct such a dict from a list of lists of similar residues.
Truncates at the length of the shorter sequence.
Note: current implementation re-creates the distance function each
time, so may be expensive compared to creating the distance function
using for_seq separately.
Returns 0 if one sequence is empty.
"""
if not self or not other:
return 0.0
return for_seq(f = lambda x, y: (x,y) in similar_pairs, \
normalizer=per_shortest)(self, other)
def withTerminiUnknown(self):
"""Returns copy of sequence with terminal gaps remapped as missing."""
gaps = self.gapVector()
first_nongap = last_nongap = None
for i, state in enumerate(gaps):
if not state:
if first_nongap is None:
first_nongap = i
last_nongap = i
missing = self.MolType.Missing
if first_nongap is None: #sequence was all gaps
result = self.__class__([missing for i in len(self)],Info=self.Info)
else:
prefix = missing*first_nongap
mid = str(self[first_nongap:last_nongap+1])
suffix = missing*(len(self)-last_nongap-1)
result = self.__class__(prefix + mid + suffix, Info=self.Info)
return result
class Sequence(_Annotatable, SequenceI):
"""Holds the standard Sequence object. Immutable."""
MolType = None #connected to ACSII when moltype is imported
def __init__(self, Seq='',Name=None, Info=None, check=True, \
preserve_case=False, gaps_allowed=True, wildcards_allowed=True):
"""Initialize a sequence.
Arguments:
Seq: the raw sequence string, default is ''
Name: the sequence name
check: if True (the default), validates against the MolType
"""
if Name is None and hasattr(Seq, 'Name'):
Name = Seq.Name
self.Name = Name
orig_seq = Seq
if isinstance(Seq, Sequence):
Seq = Seq._seq
elif isinstance(Seq, ModelSequence):
Seq = str(Seq)
elif type(Seq) is not str:
try:
Seq = ''.join(Seq)
except TypeError:
Seq = ''.join(map(str, Seq))
Seq = self._seq_filter(Seq)
if not preserve_case and not Seq.isupper():
Seq = Seq.upper()
self._seq = Seq
if check:
self.MolType.verifySequence(self._seq, gaps_allowed, \
wildcards_allowed)
if not isinstance(Info, InfoClass):
try:
Info = InfoClass(Info)
except TypeError:
Info = InfoClass()
if hasattr(orig_seq, 'Info'):
try:
Info.update(orig_seq.Info)
except:
pass
self.Info = Info
if isinstance(orig_seq, _Annotatable):
self.copyAnnotations(orig_seq)
def _seq_filter(self, seq):
"""Returns filtered seq; used to do DNA/RNA conversions."""
return seq
def getColourScheme(self, colours):
return {}
#dict([(motif,colours.black) for motif in self.MolType])
def getColorScheme(self, colors): #alias to support US spelling
return self.getColourScheme(colours=colors)
def copyAnnotations(self, other):
self.annotations = other.annotations[:]
def annotateFromGff(self, f):
first_seqname = None
for (seqname, source, feature, start, end, score, strand,
frame, attributes, comments) in gff.GffParser(f):
if first_seqname is None:
first_seqname = seqname
else:
assert seqname == first_seqname, (seqname, first_seqname)
feat_label = gff.parse_attributes(attributes)
self.addFeature(feature, feat_label, [(start, end)])
def withMaskedAnnotations(self, annot_types, mask_char=None, shadow=False):
"""returns a sequence with annot_types regions replaced by mask_char
if shadow is False, otherwise all other regions are masked.
Arguments:
- annot_types: annotation type(s)
- mask_char: must be a character valid for the seq MolType. The
default value is the most ambiguous character, eg. '?' for DNA
- shadow: whether to mask the annotated regions, or everything but
the annotated regions"""
if mask_char is None:
ambigs = [(len(v), c) for c,v in self.MolType.Ambiguities.items()]
ambigs.sort()
mask_char = ambigs[-1][1]
assert mask_char in self.MolType, 'Invalid mask_char %s' % mask_char
annotations = []
annot_types = [annot_types, [annot_types]][isinstance(annot_types, str)]
for annot_type in annot_types:
annotations += self.getAnnotationsMatching(annot_type)
region = self.getRegionCoveringAll(annotations)
if shadow:
region = region.getShadow()
i = 0
segments = []
for b, e in region.getCoordinates():
segments.append(self._seq[i:b])
segments.append(mask_char * (e-b))
i = e
segments.append(self._seq[i:])
new = self.__class__(''.join(segments), Name=self.Name, check=False,
Info=self.Info)
new.annotations = self.annotations[:]
return new
def gappedByMapSegmentIter(self, map, allow_gaps=True, recode_gaps=False):
for span in map.spans:
if span.lost:
if allow_gaps:
unknown = span.terminal or recode_gaps
seg = "-?"[unknown] * span.length
else:
raise ValueError('Gap(s) in map %s' % map)
else:
seg = self._seq[span.Start:span.End]
if span.Reverse:
complement = self.MolType.complement
seg = [complement(base) for base in seg[::-1]]
seg = ''.join(seg)
yield seg
def gappedByMapMotifIter(self, map):
for segment in self.gappedByMapSegmentIter(map):
for motif in segment:
yield motif
def gappedByMap(self, map, recode_gaps=False):
segments = self.gappedByMapSegmentIter(map, True, recode_gaps)
new = self.__class__(''.join(segments),
Name=self.Name, check=False, Info=self.Info)
annots = self._slicedAnnotations(new, map)
new.annotations = annots
return new
def _mapped(self, map):
# Called by generic __getitem__
segments = self.gappedByMapSegmentIter(map, allow_gaps=False)
new = self.__class__(''.join(segments), self.Name, Info=self.Info)
return new
def __add__(self, other):
"""Adds two sequences (other can be a string as well)."""
if hasattr(other, 'MolType'):
if self.MolType != other.MolType:
raise ValueError, "MolTypes don't match: (%s,%s)" % \
(self.MolType, other.MolType)
other_seq = other._seq
else:
other_seq = other
new_seq = self.__class__(self._seq + other_seq)
# Annotations which extend past the right end of the left sequence
# or past the left end of the right sequence are dropped because
# otherwise they will annotate the wrong part of the constructed
# sequence.
left = [a for a in self._shiftedAnnotations(new_seq, 0)
if a.map.End <= len(self)]
if hasattr(other, '_shiftedAnnotations'):
right = [a for a in other._shiftedAnnotations(new_seq, len(self))
if a.map.Start >= len(self)]
new_seq.annotations = left + right
else:
new_seq.annotations = left
return new_seq
def __repr__(self):
myclass = '%s' % self.__class__.__name__
myclass = myclass.split('.')[-1]
if len(self) > 10:
seq = str(self._seq[:7]) + '... %s' % len(self)
else:
seq = str(self._seq)
return "%s(%s)" % (myclass, seq)
def getTracks(self, policy):
return policy.tracksForSequence(self)
def getName(self):
"""Return the sequence name -- should just use Name instead."""
return self.Name
def __len__(self):
return len(self._seq)
def __iter__(self):
return iter(self._seq)
def gettype(self):
"""Return the sequence type."""
return self.MolType.label
def resolveambiguities(self):
"""Returns a list of tuples of strings."""
ambigs = self.MolType.resolveAmbiguity
return [ambigs(motif) for motif in self._seq]
def slidingWindows(self, window, step, start=None, end=None):
"""Generator function that yield new sequence objects
of a given length at a given interval.
Arguments:
- window: The length of the returned sequence
- step: The interval between the start of the returned
sequence objects
- start: first window start position
- end: last window start position
"""
start = [start, 0][start is None]
end = [end, len(self)-window+1][end is None]
end = min(len(self)-window+1, end)
if start < end and len(self)-end >= window-1:
for pos in xrange(start, end, step):
yield self[pos:pos+window]
def getInMotifSize(self, motif_length=1, log_warnings=True):
"""returns sequence as list of non-overlapping motifs
Arguments:
- motif_length: length of the motifs
- log_warnings: whether to notify of an incomplete terminal motif"""
seq = self._seq
if motif_length == 1:
return seq
else:
length = len(seq)
remainder = length % motif_length
if remainder and log_warnings:
warnings.warn('Dropped remainder "%s" from end of sequence' %
seq[-remainder:])
return [seq[i:i+motif_length]
for i in range(0, length-remainder, motif_length)]
def parseOutGaps(self):
gapless = []
segments = []
nongap = re.compile('([^%s]+)' % re.escape("-"))
for match in nongap.finditer(self._seq):
segments.append(match.span())
gapless.append(match.group())
map = Map(segments, parent_length=len(self)).inverse()
seq = self.__class__(
''.join(gapless),
Name = self.getName(), Info=self.Info)
if self.annotations:
seq.annotations = [a.remappedTo(seq, map) for a in self.annotations]
return (map, seq)
class ProteinSequence(Sequence):
"""Holds the standard Protein sequence. MolType set in moltype module."""
pass
class ProteinWithStopSequence(Sequence):
"""Holds the standard Protein sequence, allows for stop codon
MolType set in moltype module
"""
pass
class NucleicAcidSequence(Sequence):
"""Base class for DNA and RNA sequences. Abstract."""
PROTEIN = None #will set in moltype
CodonAlphabet = None #will set in moltype
def reversecomplement(self):
"""Converts a nucleic acid sequence to its reverse complement.
Synonymn for rc."""
return self.rc()
def rc(self):
"""Converts a nucleic acid sequence to its reverse complement."""
complement = self.MolType.rc(self)
rc = self.__class__(complement, Name=self.Name, Info=self.Info)
self._annotations_nucleic_reversed_on(rc)
return rc
def _gc_from_arg(self, gc):
# codon_alphabet is being deprecated in favor of genetic codes.
if gc is None:
gc = DEFAULT_GENETIC_CODE
elif isinstance(gc, (int, basestring)):
gc = GeneticCodes[gc]
return gc
def hasTerminalStop(self, gc=None, allow_partial=False):
"""Return True if the sequence has a terminal stop codon.
Arguments:
- gc: genetic code object
- allow_partial: if True and the sequence length is not dividisble
by 3, ignores the 3' terminal incomplete codon
"""
gc = self._gc_from_arg(gc)
codons = self._seq
divisible_by_3 = len(codons) % 3 == 0
if not allow_partial and not divisible_by_3:
raise ValueError("seq length not divisible by 3")
if not divisible_by_3:
return False
return codons and gc.isStop(codons[-3:])
def withoutTerminalStopCodon(self, gc=None, allow_partial=False):
"""Removes a terminal stop codon from the sequence
Arguments:
- gc: genetic code object
- allow_partial: if True and the sequence length is not divisible
by 3, ignores the 3' terminal incomplete codon
"""
gc = self._gc_from_arg(gc)
codons = self._seq
divisible_by_3 = len(codons) % 3 == 0
if not allow_partial and not divisible_by_3:
raise ValueError("seq length not divisible by 3")
if divisible_by_3 and codons and gc.isStop(codons[-3:]):
codons = codons[:-3]
return self.__class__(codons, Name=self.Name, Info=self.Info)
def getTranslation(self, gc=None):
gc = self._gc_from_arg(gc)
codon_alphabet = self.CodonAlphabet(gc).withGapMotif()
# translate the codons
translation = []
for posn in range(0, len(self._seq)-2, 3):
orig_codon = self._seq[posn:posn+3]
resolved = codon_alphabet.resolveAmbiguity(orig_codon)
trans = []
for codon in resolved:
if codon == '---':
aa = '-'
else:
assert '-' not in codon
aa = gc[codon]
if aa == '*':
continue
trans.append(aa)
if not trans:
raise ValueError(orig_codon)
aa = self.PROTEIN.whatAmbiguity(trans)
translation.append(aa)
translation = self.PROTEIN.makeSequence(
Seq=''.join(translation), Name=self.Name)
return translation
def getOrfPositions(self, gc=None, atg=False):
gc = self._gc_from_arg(gc)
orfs = []
start = None
protein = self.getTranslation(gc=gc)
for (posn, aa) in enumerate(protein):
posn *= 3
if aa == '*':
if start is not None:
orfs.append((start,posn))
start = None
else:
if start is None:
if (not atg) or gc.isStart(self[posn:posn+3]):
start = posn
if start is not None:
orfs.append((start, posn+3))
return orfs
def toRna(self):
"""Returns copy of self as RNA."""
return RnaSequence(self)
def toDna(self):
"""Returns copy of self as DNA."""
return DnaSequence(self)
class DnaSequence(NucleicAcidSequence):
def getColourScheme(self, colours):
return {
'A': colours.black,
'T': colours.red,
'C': colours.blue,
'G': colours.green,
}
def _seq_filter(self, seq):
"""Converts U to T."""
return seq.replace('u','t').replace('U','T')
class RnaSequence(NucleicAcidSequence):
def getColourScheme(self, colours):
return {
'A': colours.black,
'U': colours.red,
'C': colours.blue,
'G': colours.green,
}
def _seq_filter(self, seq):
"""Converts T to U."""
return seq.replace('t','u').replace('T','U')
class ABSequence(Sequence):
"""Used for two-state modeling; MolType set in moltypes."""
pass
class ByteSequence(Sequence):
"""Used for storing arbitrary bytes."""
def __init__(self, Seq='', Name=None, Info=None, check=False, \
preserve_case=True):
return super(ByteSequence, self).__init__(Seq, Name=Name, Info=Info, \
check=check, preserve_case=preserve_case)
class ModelSequenceBase(object):
"""Holds the information for a non-degenerate sequence. Mutable.
A ModelSequence is an array of indices of symbols, where those symbols are
defined by an Alphabet. This representation of Sequence is convenient for
counting symbol frequencies or tuple frequencies, remapping data (e.g. for
reverse-complement), looking up model parameters, etc. Its main drawback is
that the sequences can no longer be treated as strings, and conversion
to/from strings can be fairly time-consuming. Also, any symbol not in the
Alphabet cannot be represented at all.
A sequence can have a Name, which will be used for output in formats
such as FASTA.
A sequence Class has an alphabet (which can be overridden in instances
where necessary), a delimiter used for string conversions, a LineWrap
for wrapping characters into lines for e.g. FASTA output.
Note that a ModelSequence _must_ have an Alphabet, not a MolType,
because it is often important to store just a subset of the possible
characters (e.g. the non-degenerate bases) for modeling purposes.
"""
Alphabet = None #REPLACE IN SUBCLASSES
MolType = None #REPLACE IN SUBCLASSES
Delimiter = '' #Used for string conversions
LineWrap = 80 #Wrap sequences at 80 characters by default.
def __init__(self, data='', Alphabet=None, Name=None, Info=None, \
check='ignored'):
"""Initializes sequence from data and alphabet.
WARNING: Does not validate the data or alphabet for compatibility.
This is for speed. Use isValid() to check whether the data
is consistent with the alphabet.
WARNING: If data has name and/or Info, gets ref to same object rather
than copying in each case.
"""
if Name is None and hasattr(data, 'Name'):
Name = data.Name
if Info is None and hasattr(data, 'Info'):
Info = data.Info
#set the label
self.Name = Name
#override the class alphabet if supplied
if Alphabet is not None:
self.Alphabet = Alphabet
#if we haven't already set self._data (e.g. in a subclass __init__),
#guess the data type and set it here
if not hasattr(self, '_data'):
#if data is a sequence, copy its data and alphabet
if isinstance(data, ModelSequence):
self._data = data._data
self.Alphabet = data.Alphabet
#if it's an array
elif type(data) == ARRAY_TYPE:
self._data = data
else: #may be set in subclass init
self._from_sequence(data)
self.MolType = self.Alphabet.MolType
self.Info = Info
def __getitem__(self, *args):
"""__getitem__ returns char or slice, as same class."""
if len(args) == 1 and not isinstance(args[0], slice):
result = array([self._data[args[0]]])
else:
result = self._data.__getitem__(*args)
return self.__class__(result)
def __cmp__(self, other):
"""__cmp__ compares based on string"""
return cmp(str(self), other)
def _from_sequence(self, data):
"""Fills self using the values in data, via the Alphabet."""
if self.Alphabet:
self._data = array(self.Alphabet.toIndices(data), \
self.Alphabet.ArrayType)
else:
self._data = array(data)
def __str__(self):
"""Uses alphabet to convert self to string, using delimiter."""
if hasattr(self.Alphabet, 'toString'):
return self.Alphabet.toString(self._data)
else:
return self.Delimiter.join(map(str, \
self.Alphabet.fromIndices(self._data)))
def __len__(self):
"""Returns length of data."""
return len(self._data)
def toFasta(self, make_seqlabel=None):
"""Return string of self in FASTA format, no trailing newline
Arguments:
- make_seqlabel: callback function that takes the seq object and
returns a label str
"""
return fasta_from_sequences([self], make_seqlabel = make_seqlabel,
line_wrap=self.LineWrap)
def toPhylip(self, name_len=28, label_len=30):
"""Return string of self in one line for PHYLIP, no newline.
Default: max name length is 28, label length is 30.
"""
return str(self.Name)[:name_len].ljust(label_len) + str(self)
def isValid(self):
"""Checks that no items in self are out of the Alphabet range."""
return self._data == self._data.clip(m, 0, len(self.Alphabet)-1)
def toKwords(self, k, overlapping=True):
"""Turns sequence into sequence of its k-words.
Just returns array, not Sequence object."""
alpha_len = len(self.Alphabet)
seq = self._data
seq_len = len(seq)
if overlapping:
num_words = seq_len - k + 1
else:
num_words, remainder = divmod(seq_len, k)
last_index = num_words * k
result = zeros(num_words)
for i in range(k):
if overlapping:
curr_slice = seq[i:i+num_words]
else:
curr_slice = seq[i:last_index+i:k]
result *= alpha_len
result += curr_slice
return result
def __iter__(self):
"""iter returns characters of self, rather than slices."""
if hasattr(self.Alphabet, 'toString'):
return iter(self.Alphabet.toString(self._data))
else:
return iter(self.Alpabet.fromIndices(self._data))
def tostring(self):
"""tostring delegates to self._data."""
return self._data.tostring()
def gaps(self):
"""Returns array containing 1 where self has gaps, 0 elsewhere.
WARNING: Only checks for standard gap character (for speed), and
does not check for ambiguous gaps, etc.
"""
return self._data == self.Alphabet.GapIndex
def nongaps(self):
"""Returns array contining 0 where self has gaps, 1 elsewhere.
WARNING: Only checks for standard gap character (for speed), and
does not check for ambiguous gaps, etc.
"""
return self._data != self.Alphabet.GapIndex
def regap(self, other, strip_existing_gaps=False):
"""Inserts elements of self into gaps specified by other.
WARNING: Only checks for standard gap character (for speed), and
does not check for ambiguous gaps, etc.
"""
if strip_existing_gaps:
s = self.degap()
else:
s = self
c = self.__class__
a = self.Alphabet.Gapped
result = zeros(len(other),a.ArrayType)+a.GapIndex
put(result, nonzero(other.nongaps()), s._data)
return c(result)
def degap(self):
"""Returns ungapped copy of self, not changing alphabet."""
if not hasattr(self.Alphabet, 'Gap') or self.Alphabet.Gap is None:
return self.copy()
d = take(self._data, nonzero(logical_not(self.gapArray()))[0])
return self.__class__(d, Alphabet=self.Alphabet, Name=self.Name, \
Info=self.Info)
def copy(self):
"""Returns copy of self, always separate object."""
return self.__class__(self._data.copy(), Alphabet=self.Alphabet, \
Name=self.Name, Info=self.Info)
def __contains__(self, item):
"""Returns true if item in self (converts to strings)."""
return item in str(self)
def disambiguate(self, *args, **kwargs):
"""Disambiguates self using strings/moltype. Should recode if demand."""
return self.__class__(self.MolType.disambiguate(str(self), \
*args,**kwargs))
def distance(self, other, function=None, use_indices=False):
"""Returns distance between self and other using function(i,j).
other must be a sequence.
function should be a function that takes two items and returns a
number. To turn a 2D matrix into a function, use
cogent.util.miscs.DistanceFromMatrix(matrix).
use_indices: if False, maps the indices onto items (e.g. assumes
function relates the characters). If True, uses the indices directly.
NOTE: Truncates at the length of the shorter sequence.
Note that the function acts on two _elements_ of the sequences, not
the two sequences themselves (i.e. the behavior will be the same for
every position in the sequences, such as identity scoring or a function
derived from a distance matrix as suggested above). One limitation of
this approach is that the distance function cannot use properties of
the sequences themselves: for example, it cannot use the lengths of the
sequences to normalize the scores as percent similarities or percent
differences.
If you want functions that act on the two sequences themselves, there
is no particular advantage in making these functions methods of the
first sequences by passing them in as parameters like the function
in this method. It makes more sense to use them as standalone functions.
The factory function cogent.util.transform.for_seq is useful for
converting per-element functions into per-sequence functions, since it
takes as parameters a per-element scoring function, a score aggregation
function, and a normalization function (which itself takes the two
sequences as parameters), returning a single function that combines
these functions and that acts on two complete sequences.
"""
if function is None:
#use identity scoring
shortest = min(len(self), len(other))
if not hasattr(other, '_data'):
other = self.__class__(other)
distance = (self._data[:shortest] != other._data[:shortest]).sum()
else:
distance = 0
if use_indices:
self_seq = self._data
if hasattr(other, '_data'):
other_seq = other._data
else:
self_seq = self.Alphabet.fromIndices(self._data)
if hasattr(other, '_data'):
other_seq = other.Alphabet.fromIndices(other._data)
else:
other_seq = other
for first, second in zip(self_seq, other_seq):
distance += function(first, second)
return distance
def matrixDistance(self, other, matrix, use_indices=False):
"""Returns distance between self and other using a score matrix.
if use_indices is True (default is False), assumes that matrix is
an array using the same indices that self uses.
WARNING: the matrix must explicitly contain scores for the case where
a position is the same in self and other (e.g. for a distance matrix,
an identity between U and U might have a score of 0). The reason the
scores for the 'diagonals' need to be passed explicitly is that for
some kinds of distance matrices, e.g. log-odds matrices, the 'diagonal'
scores differ from each other. If these elements are missing, this
function will raise a KeyError at the first position that the two
sequences are identical.
"""
return self.distance(other, DistanceFromMatrix(matrix))
def shuffle(self):
"""Returns shuffled copy of self"""
return self.__class__(permutation(self._data), Info=self.Info)
def gapArray(self):
"""Returns array of 0/1 indicating whether each position is a gap."""
gap_indices = []
a = self.Alphabet
for c in self.MolType.Gaps:
if c in a:
gap_indices.append(a.index(c))
gap_vector = None
for i in gap_indices:
if gap_vector is None:
gap_vector = self._data == i
else:
gap_vector = logical_or(gap_vector, self._data == i)
return gap_vector
def gapIndices(self):
"""Returns array of indices of gapped positions in self."""
return self.gapArray().nonzero()[0]
def fracSameGaps(self, other):
"""Returns fraction of positions where gaps match other's gaps.
"""
if not other:
return 0
self_gaps = self.gapArray()
if hasattr(other, 'gapArray'):
other_gaps = other.gapArray()
elif hasattr(other, 'gapVector'):
other_gaps = array(other.gapVector())
else:
other_gaps = array(self.MolType.gapVector(other))
min_len = min(len(self), len(other))
self_gaps, other_gaps = self_gaps[:min_len], other_gaps[:min_len]
return (self_gaps == other_gaps).sum()/float(min_len)
class ModelSequence(ModelSequenceBase, SequenceI):
"""ModelSequence provides an array-based implementation of Sequence.
Use ModelSequenceBase if you need a stripped-down, fast implementation.
ModelSequence implements everything that SequenceI implements.
See docstrings for ModelSequenceBase and SequenceI for information about
these respective classes.
"""
def stripBad(self):
"""Returns copy of self with bad chars excised"""
valid_indices = self._data < len(self.Alphabet)
result = compress(valid_indices, self._data)
return self.__class__(result, Info=self.Info)
def stripBadAndGaps(self):
"""Returns copy of self with bad chars and gaps excised."""
gap_indices = map(self.Alphabet.index, self.MolType.Gaps)
valid_indices = self._data < len(self.Alphabet)
for i in gap_indices:
valid_indices -= self._data == i
result = compress(valid_indices, self._data)
return self.__class__(result, Info=self.Info)
def stripDegenerate(self):
"""Returns copy of self without degenerate symbols.
NOTE: goes via string intermediate because some of the algorithms
for resolving degenerates are complex. This could be optimized if
speed becomes critical.
"""
return self.__class__(self.MolType.stripDegenerate(str(self)), \
Info=self.Info)
def countGaps(self):
"""Returns count of gaps in self."""
return self.gapArray().sum()
def gapVector(self):
"""Returns list of bool containing whether each pos is a gap."""
return map(bool, self.gapArray())
def gapList(self):
"""Returns list of gap indices."""
return list(self.gapIndices())
def gapMaps(self):
"""Returns dicts mapping gapped/ungapped positions."""
nongaps = logical_not(self.gapArray())
indices = arange(len(self)).compress(nongaps)
new_indices = arange(len(indices))
return dict(zip(new_indices, indices)), dict(zip(indices, new_indices))
def firstGap(self):
"""Returns position of first gap, or None."""
a = self.gapIndices()
try:
return a[0]
except IndexError:
return None
def isGapped(self):
"""Returns True of sequence contains gaps."""
return len(self.gapIndices())
def MW(self, *args, **kwargs):
"""Returns molecular weight.
Works via string intermediate: could optimize using array of MW if
speed becomes important.
"""
return self.MolType.MW(str(self), *args, **kwargs)
def fracSimilar(self, other, similar_pairs):
"""Returns fraction of positions where self[i] is similar to other[i].
similar_pairs must be a dict such that d[(i,j)] exists if i and j are
to be counted as similar. Use PairsFromGroups in cogent.util.misc to
construct such a dict from a list of lists of similar residues.
Truncates at the length of the shorter sequence.
Note: current implementation re-creates the distance function each
time, so may be expensive compared to creating the distance function
using for_seq separately.
Returns 0 if one sequence is empty.
NOTE: goes via string intermediate, could optimize using array if
speed becomes important. Note that form of similar_pairs input would
also have to change.
"""
if not self or not other:
return 0.0
return for_seq(f = lambda x, y: (x,y) in similar_pairs, \
normalizer=per_shortest)(str(self), str(other))
class ModelNucleicAcidSequence(ModelSequence):
"""Abstract class defining ops for codons, translation, etc."""
def toCodons(self):
"""Returns copy of self in codon alphabet. Assumes ungapped."""
alpha_len = len(self.Alphabet)
return ModelCodonSequence(alpha_len*(\
alpha_len*self._data[::3] + self._data[1::3]) + self._data[2::3], \
Name=self.Name, Alphabet=self.Alphabet.Triples)
def complement(self):
"""Returns complement of sequence"""
return self.__class__(self.Alphabet._complement_array.take(self._data),\
Info=self.Info)
def rc(self):
"""Returns reverse-complement of sequence"""
comp = self.Alphabet._complement_array.take(self._data)
return self.__class__(comp[::-1], Info=self.Info)
def toRna(self):
"""Returns self as RNA"""
return ModelRnaSequence(self._data)
def toDna(self):
"""Returns self as DNA"""
return ModelDnaSequence(self._data)
class ModelRnaSequence(ModelNucleicAcidSequence):
MolType = None #set to RNA in moltype.py
Alphabet = None #set to RNA.Alphabets.DegenGapped in moltype.py
def __init__(self, data='', *args, **kwargs):
"""Returns new ModelRnaSequence, converting T -> U"""
if hasattr(data, 'upper'):
data = data.upper().replace('T','U')
return super(ModelNucleicAcidSequence, self).__init__(data, \
*args, **kwargs)
class ModelDnaSequence(ModelNucleicAcidSequence):
MolType = None #set to DNA in moltype.py
Alphabet = None #set to DNA.Alphabets.DegenGapped in moltype.py
def __init__(self, data='', *args, **kwargs):
"""Returns new ModelRnaSequence, converting U -> T"""
if hasattr(data, 'upper'):
data = data.upper().replace('U','T')
return super(ModelNucleicAcidSequence, self).__init__(data, \
*args, **kwargs)
class ModelCodonSequence(ModelSequence):
"""Abstract base class for codon sequences, incl. string conversion."""
SequenceClass = ModelNucleicAcidSequence
def __str__(self):
"""Joins triplets together as string."""
return self.Delimiter.join(map(''.join, \
self.Alphabet.fromIndices(self._data)))
def _from_string(self, s):
"""Reads from a raw string, rather than a DnaSequence."""
s = s.upper().replace('U','T') #convert to uppercase DNA
d = self.SequenceClass(s, \
Alphabet=self.Alphabet.SubEnumerations[0])
self._data = d.toCodons()._data
def __init__(self, data='', Alphabet=None, Name=None, Info=None):
"""Override __init__ to handle init from string."""
if isinstance(data, str):
self._from_string(data)
ModelSequence.__init__(self, data, Alphabet, Name, Info=Info)
def toCodons(self):
"""Converts self to codons -- in practice, just returns self.
Supports interface of other NucleicAcidSequences."""
return self
def toDna(self):
"""Returns a ModelDnaSequence from the data in self"""
unpacked = self.Alphabet.unpackArrays(self._data)
result = zeros((len(self._data),3))
for i, v in enumerate(unpacked):
result[:,i] = v
return ModelDnaSequence(ravel(result), Name=self.Name)
def toRna(self):
"""Returns a ModelDnaSequence from the data in self."""
unpacked = self.Alphabet.unpackArrays(self._data)
result = zeros((len(self._data),3))
for i, v in enumerate(unpacked):
result[:,i] = v
return ModelRnaSequence(ravel(result), Name=self.Name)
class ModelDnaCodonSequence(ModelCodonSequence):
"""Holds non-degenerate DNA codon sequence."""
Alphabet = None #set to DNA.Alphabets.Base.Triples in moltype.py
SequenceClass = ModelDnaSequence
class ModelRnaCodonSequence(ModelCodonSequence):
"""Holds non-degenerate DNA codon sequence."""
Alphabet = None #set to RNA.Alphabets.Base.Triples in motype.py
SequenceClass = ModelRnaSequence
def _from_string(self, s):
"""Reads from a raw string, rather than a DnaSequence."""
s = s.upper().replace('T','U') #convert to uppercase DNA
d = self.SequenceClass(s, \
Alphabet=self.Alphabet.SubEnumerations[0])
self._data = d.toCodons()._data
class ModelProteinSequence(ModelSequence):
MolType = None #set to PROTEIN in moltype.py
Alphabet = None #set to PROTEIN.Alphabets.DegenGapped in moltype.py
class ModelProteinWithStopSequence(ModelSequence):
MolType = None #set to PROTEIN_WITH_STOP in moltype.py
Alphabet= None #set to PROTEIN_WITH_STOP.Alphabets.DegenGapped in moltype.py
|