Spaces:
No application file
No application file
File size: 84,776 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 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 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 |
# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved.
# Revisions copyright 2014-2015 by Joe Cora (standard data)
#
# 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.
"""Nexus class. Parse the contents of a NEXUS file.
Based upon 'NEXUS: An extensible file format for systematic information'
Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621
"""
from functools import reduce
import copy
import math
import random
import sys
import warnings
from Bio import File
from Bio.Data import IUPACData
from Bio.Seq import Seq
from Bio import BiopythonDeprecationWarning
from Bio.Nexus.StandardData import StandardData
from Bio.Nexus.Trees import Tree
INTERLEAVE = 70
SPECIAL_COMMANDS = [
"charstatelabels",
"charlabels",
"taxlabels",
"taxset",
"charset",
"charpartition",
"taxpartition",
"matrix",
"tree",
"utree",
"translate",
"codonposset",
"title",
]
KNOWN_NEXUS_BLOCKS = ["trees", "data", "characters", "taxa", "sets", "codons"]
PUNCTUATION = "()[]{}\\,;:=*\\'\"`+-<>"
MRBAYESSAFE = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890_"
WHITESPACE = " \t\n"
# SPECIALCOMMENTS = ['!','&','%','/','\\','@'] # original list of special comments
SPECIALCOMMENTS = [
"&"
] # supported special comment ('tree' command), all others are ignored
CHARSET = "chars"
TAXSET = "taxa"
CODONPOSITIONS = "codonpositions"
DEFAULTNEXUS = (
"#NEXUS\nbegin data; dimensions ntax=0 nchar=0; format datatype=dna; end; "
)
class NexusError(Exception):
"""Provision for the management of Nexus exceptions."""
pass
class CharBuffer:
"""Helps reading NEXUS-words and characters from a buffer (semi-PRIVATE).
This class is not intended for public use (any more).
"""
def __init__(self, string):
"""Initialize the class."""
if string:
self.buffer = list(string)
else:
self.buffer = []
def peek(self):
"""Return the first character from the buffer."""
if self.buffer:
return self.buffer[0]
else:
return None
def peek_nonwhitespace(self):
"""Return the first character from the buffer, do not include spaces."""
b = "".join(self.buffer).strip()
if b:
return b[0]
else:
return None
def __next__(self):
"""Iterate over NEXUS characters in the file."""
if self.buffer:
return self.buffer.pop(0)
else:
return None
def next_nonwhitespace(self):
"""Check for next non whitespace character in NEXUS file."""
while True:
p = next(self)
if p is None:
break
if p not in WHITESPACE:
return p
return None
def skip_whitespace(self):
"""Skip whitespace characters in NEXUS file."""
while self.buffer[0] in WHITESPACE:
self.buffer = self.buffer[1:]
def next_until(self, target):
"""Iterate over the NEXUS file until a target character is reached."""
for t in target:
try:
pos = self.buffer.index(t)
except ValueError:
pass
else:
found = "".join(self.buffer[:pos])
self.buffer = self.buffer[pos:]
return found
else:
return None
def peek_word(self, word):
"""Return a word stored in the buffer."""
return "".join(self.buffer[: len(word)]) == word
def next_word(self):
"""Return the next NEXUS word from a string.
This deals with single and double quotes, whitespace and punctuation.
"""
word = []
quoted = False
# get first character
first = self.next_nonwhitespace()
if not first:
# return empty if only whitespace left
return None
word.append(first)
if first == "'":
quoted = "'"
elif first == '"':
quoted = '"'
elif first in PUNCTUATION:
# if it's non-quote punctuation, return immediately
return first
while True:
c = self.peek()
if c == quoted: # a quote?
word.append(next(self)) # store quote
if self.peek() == quoted: # double quote
next(self) # skip second quote
elif quoted: # second single quote ends word
break
elif quoted:
# if quoted, then add anything
word.append(next(self))
elif not c or c in PUNCTUATION or c in WHITESPACE:
# if not quoted and special character, stop
break
else:
word.append(next(self)) # standard character
return "".join(word)
def rest(self):
"""Return the rest of the string without parsing."""
return "".join(self.buffer)
class StepMatrix:
"""Calculate a stepmatrix for weighted parsimony.
See :
COMBINATORIAL WEIGHTS IN PHYLOGENETIC ANALYSIS - A STATISTICAL PARSIMONY PROCEDURE
Wheeler (1990), Cladistics 6:269-275.
"""
def __init__(self, symbols, gap):
"""Initialize the class."""
self.data = {}
self.symbols = sorted(symbols)
if gap:
self.symbols.append(gap)
for x in self.symbols:
for y in [s for s in self.symbols if s != x]:
self.set(x, y, 0)
def set(self, x, y, value):
"""Set a given value in the matrix's position."""
if x > y:
x, y = y, x
self.data[x + y] = value
def add(self, x, y, value):
"""Add the given value to existing, in matrix's position."""
if x > y:
x, y = y, x
self.data[x + y] += value
def sum(self):
"""Calculate the associations, makes matrix of associations."""
return reduce(lambda x, y: x + y, self.data.values())
def transformation(self):
"""Calculate the transformation matrix.
Normalizes the columns of the matrix of associations.
"""
total = self.sum()
if total != 0:
for k in self.data:
self.data[k] /= total
return self
def weighting(self):
"""Calculate the Phylogenetic weight matrix.
Constructed from the logarithmic transformation of the
transformation matrix.
"""
for k in self.data:
if self.data[k] != 0:
self.data[k] = -math.log(self.data[k])
return self
def smprint(self, name="your_name_here"):
"""Print a stepmatrix."""
matrix = "usertype %s stepmatrix=%d\n" % (name, len(self.symbols))
matrix += f" {' '.join(self.symbols)}\n"
for x in self.symbols:
matrix += "[%s]".ljust(8) % x
for y in self.symbols:
if x == y:
matrix += " . "
else:
if x > y:
x1, y1 = y, x
else:
x1, y1 = x, y
if self.data[x1 + y1] == 0:
matrix += "inf. "
else:
matrix += "%2.2f".ljust(10) % (self.data[x1 + y1])
matrix += "\n"
matrix += ";\n"
return matrix
def safename(name, mrbayes=False):
"""Return a taxon identifier according to NEXUS standard.
Wrap quotes around names with punctuation or whitespace, and double
single quotes.
mrbayes=True: write names without quotes, whitespace or punctuation
for the mrbayes software package.
"""
if mrbayes:
safe = name.replace(" ", "_")
safe = "".join(c for c in safe if c in MRBAYESSAFE)
else:
safe = name.replace("'", "''")
if set(safe).intersection(set(WHITESPACE + PUNCTUATION)):
safe = "'" + safe + "'"
return safe
def quotestrip(word):
"""Remove quotes and/or double quotes around identifiers."""
if not word:
return None
while (word.startswith("'") and word.endswith("'")) or (
word.startswith('"') and word.endswith('"')
):
word = word[1:-1]
return word
def get_start_end(sequence, skiplist=("-", "?")):
"""Return position of first and last character which is not in skiplist.
Skiplist defaults to ['-','?'].
"""
length = len(sequence)
if length == 0:
return None, None
end = length - 1
while end >= 0 and (sequence[end] in skiplist):
end -= 1
start = 0
while start < length and (sequence[start] in skiplist):
start += 1
if start == length and end == -1: # empty sequence
return -1, -1
else:
return start, end
def _sort_keys_by_values(p):
"""Return a sorted list of keys of p sorted by values of p (PRIVATE)."""
return sorted((pn for pn in p if p[pn]), key=lambda pn: p[pn])
def _make_unique(values):
"""Check all values in list are unique and return a pruned and sorted list (PRIVATE)."""
return sorted(set(values))
def _unique_label(previous_labels, label):
"""Return a unique name if label is already in previous_labels (PRIVATE)."""
while label in previous_labels:
label_split = label.split(".")
if label_split[-1].startswith("copy"):
copy_num = 1
if label_split[-1] != "copy":
copy_num = int(label_split[-1][4:]) + 1
new_label = f"{'.'.join(label_split[:-1])}.copy{copy_num}"
label = new_label
else:
label += ".copy"
return label
def _seqmatrix2strmatrix(matrix):
"""Convert a Seq-object matrix to a plain sequence-string matrix (PRIVATE)."""
return {t: str(matrix[t]) for t in matrix}
def _compact4nexus(orig_list):
r"""Compact lists for Nexus output (PRIVATE).
Example
-------
>>> _compact4nexus([1, 2, 3, 5, 6, 7, 8, 12, 15, 18, 20])
'2-4 6-9 13-19\\3 21'
Transform [1 2 3 5 6 7 8 12 15 18 20] (baseindex 0, used in the Nexus class)
into '2-4 6-9 13-19\\3 21' (baseindex 1, used in programs like Paup or MrBayes.).
"""
if not orig_list:
return ""
orig_list = sorted(set(orig_list))
shortlist = []
clist = orig_list[:]
clist.append(clist[-1] + 0.5) # dummy value makes it easier
while len(clist) > 1:
step = 1
for i, x in enumerate(clist):
if x == clist[0] + i * step: # are we still in the right step?
continue
elif i == 1 and len(clist) > 3 and clist[i + 1] - x == x - clist[0]:
# second element, and possibly at least 3 elements to link,
# and the next one is in the right step
step = x - clist[0]
else: # pattern broke, add all values before current position to new list
sub = clist[:i]
if len(sub) == 1:
shortlist.append(str(sub[0] + 1))
else:
if step == 1:
shortlist.append("%d-%d" % (sub[0] + 1, sub[-1] + 1))
else:
shortlist.append("%d-%d\\%d" % (sub[0] + 1, sub[-1] + 1, step))
clist = clist[i:]
break
return " ".join(shortlist)
def combine(matrices):
"""Combine matrices in [(name,nexus-instance),...] and return new nexus instance.
combined_matrix=combine([(name1,nexus_instance1),(name2,nexus_instance2),...]
Character sets, character partitions and taxon sets are prefixed, readjusted
and present in the combined matrix.
"""
if not matrices:
return None
name = matrices[0][0]
combined = copy.deepcopy(matrices[0][1]) # initiate with copy of first matrix
mixed_datatypes = len({n[1].datatype for n in matrices}) > 1
if mixed_datatypes:
# dealing with mixed matrices is application specific.
# You take care of that yourself!
combined.datatype = "None"
# raise NexusError('Matrices must be of same datatype')
combined.charlabels = None
combined.statelabels = None
combined.interleave = False
combined.translate = None
# rename taxon sets and character sets and name them with prefix
for cn, cs in combined.charsets.items():
combined.charsets[f"{name}.{cn}"] = cs
del combined.charsets[cn]
for tn, ts in combined.taxsets.items():
combined.taxsets[f"{name}.{tn}"] = ts
del combined.taxsets[tn]
# previous partitions usually don't make much sense in combined matrix
# just initiate one new partition parted by single matrices
combined.charpartitions = {"combined": {name: list(range(combined.nchar))}}
for n, m in matrices[1:]: # add all other matrices
both = [t for t in combined.taxlabels if t in m.taxlabels]
combined_only = [t for t in combined.taxlabels if t not in both]
m_only = [t for t in m.taxlabels if t not in both]
for t in both:
# concatenate sequences and unify gap and missing character symbols
combined.matrix[t] += Seq(
str(m.matrix[t])
.replace(m.gap, combined.gap)
.replace(m.missing, combined.missing)
)
# replace date of missing taxa with symbol for missing data
for t in combined_only:
combined.matrix[t] += Seq(combined.missing * m.nchar)
for t in m_only:
combined.matrix[t] = Seq(combined.missing * combined.nchar) + Seq(
str(m.matrix[t])
.replace(m.gap, combined.gap)
.replace(m.missing, combined.missing)
)
combined.taxlabels.extend(m_only) # new taxon list
for cn, cs in m.charsets.items(): # adjust character sets for new matrix
combined.charsets[f"{n}.{cn}"] = [x + combined.nchar for x in cs]
if m.taxsets:
if not combined.taxsets:
combined.taxsets = {}
# update taxon sets
combined.taxsets.update({f"{n}.{tn}": ts for tn, ts in m.taxsets.items()})
# update new charpartition
combined.charpartitions["combined"][n] = list(
range(combined.nchar, combined.nchar + m.nchar)
)
# update charlabels
if m.charlabels:
if not combined.charlabels:
combined.charlabels = {}
combined.charlabels.update(
{combined.nchar + i: label for i, label in m.charlabels.items()}
)
combined.nchar += m.nchar # update nchar and ntax
combined.ntax += len(m_only)
# some prefer partitions, some charsets:
# make separate charset for ecah initial dataset
for c in combined.charpartitions["combined"]:
combined.charsets[c] = combined.charpartitions["combined"][c]
return combined
def _kill_comments_and_break_lines(text):
r"""Delete []-delimited comments out of a file and break into lines separated by ';' (PRIVATE).
stripped_text=_kill_comments_and_break_lines(text):
Nested and multiline comments are allowed. [ and ] symbols within single
or double quotes are ignored, newline ends a quote, all symbols with quotes are
treated the same (thus not quoting inside comments like [this character ']' ends a comment])
Special [&...] and [\...] comments remain untouched, if not inside standard comment.
Quotes inside special [& and [\ are treated as normal characters,
but no nesting inside these special comments allowed (like [& [\ ]]).
';' is deleted from end of line.
NOTE: this function is very slow for large files, and obsolete when using C extension cnexus
"""
if not text:
return ""
contents = iter(text)
newtext = []
newline = []
quotelevel = ""
speciallevel = False
commlevel = 0
# Parse with one character look ahead (for special comments)
t2 = next(contents)
while True:
t = t2
try:
t2 = next(contents)
except StopIteration:
t2 = None
if t is None:
break
if t == quotelevel and not (commlevel or speciallevel):
# matching quote ends quotation
quotelevel = ""
elif (
not quotelevel
and not (commlevel or speciallevel)
and (t == '"' or t == "'")
):
# single or double quote starts quotation
quotelevel = t
elif not quotelevel and t == "[":
# opening bracket outside a quote
if t2 in SPECIALCOMMENTS and commlevel == 0 and not speciallevel:
speciallevel = True
else:
commlevel += 1
elif not quotelevel and t == "]":
# closing bracket ioutside a quote
if speciallevel:
speciallevel = False
else:
commlevel -= 1
if commlevel < 0:
raise NexusError("Nexus formatting error: unmatched ]")
continue
if commlevel == 0:
# copy if we're not in comment
if t == ";" and not quotelevel:
newtext.append("".join(newline))
newline = []
else:
newline.append(t)
# level of comments should be 0 at the end of the file
if newline:
newtext.append("\n".join(newline))
if commlevel > 0:
raise NexusError("Nexus formatting error: unmatched [")
return newtext
def _adjust_lines(lines):
"""Adjust linebreaks to match ';', strip leading/trailing whitespace (PRIVATE).
list_of_commandlines=_adjust_lines(input_text)
Lines are adjusted so that no linebreaks occur within a commandline
(except matrix command line)
"""
formatted_lines = []
for line in lines:
# Convert line endings
line = line.replace("\r\n", "\n").replace("\r", "\n").strip()
if line.lower().startswith("matrix"):
formatted_lines.append(line)
else:
line = line.replace("\n", " ")
if line:
formatted_lines.append(line)
return formatted_lines
def _replace_parenthesized_ambigs(seq, rev_ambig_values):
"""Replace ambigs in xxx(ACG)xxx format by IUPAC ambiguity code (PRIVATE)."""
opening = seq.find("(")
while opening > -1:
closing = seq.find(")")
if closing < 0:
raise NexusError("Missing closing parenthesis in: " + seq)
elif closing < opening:
raise NexusError("Missing opening parenthesis in: " + seq)
ambig = "".join(sorted(seq[opening + 1 : closing]))
ambig_code = rev_ambig_values[ambig.upper()]
if ambig != ambig.upper():
ambig_code = ambig_code.lower()
seq = seq[:opening] + ambig_code + seq[closing + 1 :]
opening = seq.find("(")
return seq
class Commandline:
"""Represent a commandline as command and options."""
def __init__(self, line, title):
"""Initialize the class."""
self.options = {}
options = []
self.command = None
try:
# Assume matrix (all other command lines have been stripped of \n)
self.command, options = line.strip().split("\n", 1)
except ValueError: # Not matrix
# self.command,options=line.split(' ',1) # no: could be tab or spaces (translate...)
self.command = line.split()[0]
options = " ".join(line.split()[1:])
self.command = self.command.strip().lower()
if self.command in SPECIAL_COMMANDS:
# special command that need newlines and order of options preserved
self.options = options.strip()
else:
if len(options) > 0:
try:
options = options.replace("=", " = ").split()
valued_indices = [
(n - 1, n, n + 1)
for n in range(len(options))
if options[n] == "=" and n != 0 and n != len(options)
]
indices = []
for sl in valued_indices:
indices.extend(sl)
token_indices = [n for n in range(len(options)) if n not in indices]
for opt in valued_indices:
# self.options[options[opt[0]].lower()] = options[opt[2]].lower()
self.options[options[opt[0]].lower()] = options[opt[2]]
for token in token_indices:
self.options[options[token].lower()] = None
except ValueError:
raise NexusError(f"Incorrect formatting in line: {line}") from None
class Block:
"""Represent a NEXUS block with block name and list of commandlines."""
def __init__(self, title=None):
"""Initialize the class."""
self.title = title
self.commandlines = []
class Nexus:
"""Create the Nexus class, main class for the management of Nexus files."""
def __init__(self, input=None):
"""Initialize the class."""
self.ntax = 0 # number of taxa
self.nchar = 0 # number of characters
self.unaltered_taxlabels = (
[]
) # taxlabels as the appear in the input file (incl. duplicates, etc.)
self.taxlabels = [] # labels for taxa, ordered by their id
self.charlabels = None # ... and for characters
self.statelabels = None # ... and for states
self.datatype = "dna" # (standard), dna, rna, nucleotide, protein
self.respectcase = False # case sensitivity
self.missing = "?" # symbol for missing characters
self.gap = "-" # symbol for gap
self.symbols = None # set of symbols
self.equate = None # set of symbol synonyms
self.matchchar = None # matching char for matrix representation
self.labels = None # left, right, no
self.transpose = False # whether matrix is transposed
self.interleave = False # whether matrix is interleaved
self.tokens = False # unsupported
self.eliminate = None # unsupported
self.matrix = None # ...
self.unknown_blocks = [] # blocks we don't care about
self.taxsets = {}
self.charsets = {}
self.charpartitions = {}
self.taxpartitions = {}
self.trees = [] # list of Trees (instances of Tree class)
self.translate = None # Dict to translate taxon <-> taxon numbers
self.structured = [] # structured input representation
self.set = {} # dict of the set command to set various options
self.options = {} # dict of the options command in the data block
self.codonposset = (
None # name of the charpartition that defines codon positions
)
# some defaults
self.options["gapmode"] = "missing"
if input:
self.read(input)
else:
self.read(DEFAULTNEXUS)
def get_original_taxon_order(self):
"""Included for backwards compatibility (DEPRECATED)."""
warnings.warn(
"The get_original_taxon_order method has been deprecated "
"and will likely be removed from Biopython in the near "
"future. Please use the original_taxon_order attribute "
"instead.",
BiopythonDeprecationWarning,
)
return self.taxlabels
def set_original_taxon_order(self, value):
"""Included for backwards compatibility (DEPRECATED)."""
warnings.warn(
"The set_original_taxon_order method has been deprecated "
"and will likely be removed from Biopython in the near "
"future. Please use the original_taxon_order attribute "
"instead.",
BiopythonDeprecationWarning,
)
self.taxlabels = value
original_taxon_order = property(get_original_taxon_order, set_original_taxon_order)
def read(self, input):
"""Read and parse NEXUS input (a filename, file-handle, or string)."""
# 1. Assume we have the name of a file in the execution dir or a
# file-like object.
# Note we need to add parsing of the path to dir/filename
try:
with File.as_handle(input) as fp:
file_contents = fp.read()
self.filename = getattr(fp, "name", "Unknown_nexus_file")
except (TypeError, OSError, AttributeError):
# 2. Assume we have a string from a fh.read()
if isinstance(input, str):
file_contents = input
self.filename = "input_string"
else:
raise NexusError(f"Unrecognized input: {input[:100]} ...") from None
file_contents = file_contents.strip()
if file_contents.startswith("#NEXUS"):
file_contents = file_contents[6:]
commandlines = _get_command_lines(file_contents)
# get rid of stupid 'NEXUS token - in merged treefiles, this might appear multiple times'
for i, cl in enumerate(commandlines):
try:
if cl[:6].upper() == "#NEXUS":
commandlines[i] = cl[6:].strip()
except IndexError:
pass
# now loop through blocks (we parse only data in known blocks, thus ignoring non-block commands
nexus_block_gen = self._get_nexus_block(commandlines)
while True:
try:
title, contents = next(nexus_block_gen)
except StopIteration:
break
if title in KNOWN_NEXUS_BLOCKS:
self._parse_nexus_block(title, contents)
else:
self._unknown_nexus_block(title, contents)
def _get_nexus_block(self, file_contents):
"""Return a generator for looping through Nexus blocks (PRIVATE)."""
inblock = False
blocklines = []
while file_contents:
cl = file_contents.pop(0)
if cl.lower().startswith("begin"):
if not inblock:
inblock = True
title = cl.split()[1].lower()
else:
raise NexusError(f"Illegal block nesting in block {title}")
elif cl.lower().startswith("end"):
if inblock:
inblock = False
yield title, blocklines
blocklines = []
else:
raise NexusError("Unmatched 'end'.")
elif inblock:
blocklines.append(cl)
def _unknown_nexus_block(self, title, contents):
block = Block()
block.commandlines.append(contents)
block.title = title
self.unknown_blocks.append(block)
def _parse_nexus_block(self, title, contents):
"""Parse a known Nexus Block (PRIVATE)."""
# attached the structured block representation
self._apply_block_structure(title, contents)
# now check for taxa,characters,data blocks. If this stuff is defined more than once
# the later occurrences will override the previous ones.
block = self.structured[-1]
for line in block.commandlines:
try:
getattr(self, "_" + line.command)(line.options)
except AttributeError:
raise NexusError(f"Unknown command: {line.command} ") from None
def _title(self, options):
pass
def _link(self, options):
pass
def _dimensions(self, options):
if "ntax" in options:
self.ntax = eval(options["ntax"])
if "nchar" in options:
self.nchar = eval(options["nchar"])
def _format(self, options):
# print options
# we first need to test respectcase, then symbols (which depends on respectcase)
# then datatype (which, if standard, depends on symbols and respectcase in order to generate
# dicts for ambiguous values
if "respectcase" in options:
self.respectcase = True
# adjust symbols to for respectcase
if "symbols" in options:
self.symbols = "".join(options["symbols"].split())
if (self.symbols.startswith('"') and self.symbols.endswith('"')) or (
self.symbols.startswith("'") and self.symbols.endswith("'")
):
self.symbols = self.symbols[1:-1]
if not self.respectcase:
self.symbols = list(self.symbols.upper())
# self.symbols = self.symbols.lower() + self.symbols.upper()
# self.symbols = list(set(self.symbols))
if "datatype" in options:
self.datatype = options["datatype"].lower()
if self.datatype == "dna" or self.datatype == "nucleotide":
self.ambiguous_values = IUPACData.ambiguous_dna_values.copy()
self.unambiguous_letters = IUPACData.unambiguous_dna_letters
elif self.datatype == "rna":
self.ambiguous_values = IUPACData.ambiguous_rna_values.copy()
self.unambiguous_letters = IUPACData.unambiguous_rna_letters
elif self.datatype == "protein":
self.ambiguous_values = {
"B": "DN",
"Z": "EQ",
"X": IUPACData.protein_letters,
}
# that's how PAUP handles it
self.unambiguous_letters = IUPACData.protein_letters + "*" # stop-codon
elif self.datatype == "standard":
self.ambiguous_values = {}
if not self.symbols:
# PARSER BUG ##
# This error arises when symbols are absent or when
# whitespace is located within the SYMBOLS command values.
# The Nexus parser quits reading the SYMBOLS line upon
# finding a whitespace character.
raise NexusError(
"Symbols must be defined when using standard datatype. "
"Please remove any whitespace (spaces, tabs, etc.) "
"between values for symbols as this confuses the Nexus parser."
)
self.unambiguous_letters = "".join(self.symbols)
if not self.respectcase:
self.unambiguous_letters += self.unambiguous_letters.lower()
else:
raise NexusError("Unsupported datatype: " + self.datatype)
self.valid_characters = (
"".join(self.ambiguous_values) + self.unambiguous_letters
)
if not self.respectcase:
self.valid_characters = (
self.valid_characters.lower() + self.valid_characters.upper()
)
# we have to sort the reverse ambig coding dict key characters:
# to be sure that it's 'ACGT':'N' and not 'GTCA':'N'
rev = {v: k for k, v in self.ambiguous_values.items() if k != "X"}
self.rev_ambiguous_values = {}
for k, v in rev.items():
key = sorted(c for c in k)
self.rev_ambiguous_values["".join(key)] = v
# overwrite symbols for datatype rna,dna,nucleotide
if self.datatype in ["dna", "nucleotide"]:
self.symbols = IUPACData.ambiguous_dna_letters
if self.missing not in self.ambiguous_values:
self.ambiguous_values[self.missing] = (
self.unambiguous_letters + self.gap
)
self.ambiguous_values[self.gap] = self.gap
elif self.datatype == "rna":
self.symbols = IUPACData.ambiguous_rna_letters
if self.missing not in self.ambiguous_values:
self.ambiguous_values[self.missing] = (
self.unambiguous_letters + self.gap
)
self.ambiguous_values[self.gap] = self.gap
# elif self.datatype == 'standard':
# if not self.symbols:
# self.symbols = ['0', '1']
if "missing" in options:
self.missing = options["missing"][0]
if "gap" in options:
self.gap = options["gap"][0]
if "equate" in options:
self.equate = options["equate"]
if "matchchar" in options:
self.matchchar = options["matchchar"][0]
if "labels" in options:
self.labels = options["labels"]
if "interleave" in options:
if options["interleave"] is None or options["interleave"].lower() == "yes":
self.interleave = True
if "tokens" in options:
self.tokens = True
if "notokens" in options:
self.tokens = False
def _set(self, options):
self.set = options
def _options(self, options):
self.options = options
def _eliminate(self, options):
self.eliminate = options
def _taxlabels(self, options):
"""Get taxon labels (PRIVATE).
As the taxon names are already in the matrix, this is superfluous
except for transpose matrices, which are currently unsupported anyway.
Thus, we ignore the taxlabels command to make handling of duplicate
taxon names easier.
"""
pass
# self.taxlabels = []
# opts = CharBuffer(options)
# while True:
# taxon = quotestrip(opts.next_word())
# if not taxon:
# break
# self.taxlabels.append(taxon)
def _check_taxlabels(self, taxon):
"""Check for presence of taxon in self.taxlabels (PRIVATE)."""
# According to NEXUS standard, underscores shall be treated as spaces...,
# so checking for identity is more difficult
nextaxa = {t.replace(" ", "_"): t for t in self.taxlabels}
nexid = taxon.replace(" ", "_")
return nextaxa.get(nexid)
def _charlabels(self, options):
"""Get labels for characters (PRIVATE)."""
self.charlabels = {}
opts = CharBuffer(options)
while True:
# get id and state
w = opts.next_word()
if (
w is None
): # McClade saves and reads charlabel-lists with terminal comma?!
break
identifier = self._resolve(w, set_type=CHARSET)
state = quotestrip(opts.next_word())
self.charlabels[identifier] = state
# check for comma or end of command
c = opts.next_nonwhitespace()
if c is None:
break
elif c != ",":
raise NexusError(f"Missing ',' in line {options}.")
def _charstatelabels(self, options):
self.charlabels = {}
self.statelabels = {}
opts = CharBuffer(options)
# Make sure symbols are defined
if not self.symbols:
raise NexusError("Symbols must be defined when using character states")
while True:
# get id and character name
w = opts.next_word()
# McClade saves and reads charlabel-lists with terminal comma?!
if w is None:
break
identifier = self._resolve(w, set_type=CHARSET)
character = quotestrip(opts.next_word())
self.charlabels[identifier] = character
self.statelabels[identifier] = []
# check for comma, slash or end of command
c = opts.next_nonwhitespace()
if c is None:
break
elif c != ",":
# Check if states are defined, otherwise report error
if c != "/":
raise NexusError(f"Missing ',' in line {options}.")
# Get the first state
state = quotestrip(opts.next_word())
if state is None:
raise NexusError(f"Missing character state in line {options}.")
while True:
# Make sure current state does not exceed number of
# available symbols
if len(self.statelabels[identifier]) > len(self.symbols):
raise NexusError(
"Character states exceed number of available symbols in line %s."
% options
)
# Add the character state to the statelabels
self.statelabels[identifier].append(state)
# Check for another state or comma to end states (last
# character should not have comma at end of states - but
# we'll ignore)
state = quotestrip(opts.next_word())
if state is None:
return
elif state == ",":
break
def _statelabels(self, options):
# self.charlabels = options
# print("Command statelabels is not supported and will be ignored.")
pass
def _matrix(self, options):
"""Create a matrix for NEXUS object (PRIVATE)."""
if not self.ntax or not self.nchar:
raise NexusError("Dimensions must be specified before matrix!")
self.matrix = {}
taxcount = 0
first_matrix_block = True
# eliminate empty lines and leading/trailing whitespace
lines = [_.strip() for _ in options.split("\n") if _.strip() != ""]
lineiter = iter(lines)
while True:
try:
line = next(lineiter)
except StopIteration:
if taxcount < self.ntax:
raise NexusError("Not enough taxa in matrix.") from None
elif taxcount > self.ntax:
raise NexusError("Too many taxa in matrix.") from None
else:
break
# count the taxa and check for interleaved matrix
taxcount += 1
if taxcount > self.ntax:
if not self.interleave:
raise NexusError(
"Too many taxa in matrix - should matrix be interleaved?"
)
else:
taxcount = 1
first_matrix_block = False
# get taxon name and sequence
linechars = CharBuffer(line)
id = quotestrip(linechars.next_word())
line = linechars.rest().strip()
chars = ""
if self.interleave:
# interleaved matrix
if line:
chars = "".join(line.split())
else:
chars = "".join(next(lineiter).split())
else:
# non-interleaved matrix
chars = "".join(line.split())
while len(chars) < self.nchar:
line = next(lineiter)
chars += "".join(line.split())
# Reformat sequence for non-standard datatypes
if self.datatype != "standard":
iupac_seq = Seq(
_replace_parenthesized_ambigs(chars, self.rev_ambiguous_values)
)
# first taxon has the reference sequence if matchhar is used
if taxcount == 1:
refseq = iupac_seq
else:
if self.matchchar:
while True:
p = iupac_seq.find(self.matchchar)
if p == -1:
break
iupac_seq = Seq(
iupac_seq[:p] + refseq[p] + iupac_seq[p + 1 :]
)
# Check for invalid characters
for i, c in enumerate(iupac_seq):
if (
c not in self.valid_characters
and c != self.gap
and c != self.missing
):
raise NexusError(
"Taxon %s: Illegal character %s in sequence %s "
"(check dimensions/interleaving)" % (id, c, iupac_seq)
)
else:
iupac_seq = StandardData(chars)
# Check for invalid characters
for i, c in enumerate(iupac_seq):
# Go through each coding for each character
for coding in c["d"]:
if coding not in self.valid_characters:
if coding != self.gap and coding != self.missing:
raise NexusError(
"Taxon %s: Illegal character %s in sequence %s "
"(check dimensions/interleaving)"
% (id, coding, iupac_seq)
)
# add sequence to matrix
if first_matrix_block:
self.unaltered_taxlabels.append(id)
id = _unique_label(list(self.matrix.keys()), id)
self.matrix[id] = iupac_seq
self.taxlabels.append(id)
else:
# taxon names need to be in the same order in each interleaved block
id = _unique_label(self.taxlabels[: taxcount - 1], id)
taxon_present = self._check_taxlabels(id)
if taxon_present:
self.matrix[taxon_present] += iupac_seq
else:
raise NexusError(
"Taxon %s not in first block of interleaved "
"matrix. Check matrix dimensions and interleave." % id
)
# check all sequences for length according to nchar
for taxon in self.matrix:
if len(self.matrix[taxon]) != self.nchar:
raise NexusError(
"Matrix Nchar %d does not match data length (%d) for taxon %s"
% (self.nchar, len(self.matrix[taxon]), taxon)
)
# check that taxlabels is identical with matrix.keys. If not, it's a problem
matrixkeys = sorted(self.matrix)
taxlabelssort = sorted(self.taxlabels[:])
if matrixkeys != taxlabelssort:
raise ValueError(
"ERROR: TAXLABELS must be identical with MATRIX. "
"Please Report this as a bug, and send in data file."
)
def _translate(self, options):
"""Translate a Nexus file (PRIVATE)."""
self.translate = {}
opts = CharBuffer(options)
while True:
try:
# get id and state
identifier = int(opts.next_word())
label = quotestrip(opts.next_word())
self.translate[identifier] = label
# check for comma or end of command
c = opts.next_nonwhitespace()
if c is None:
break
elif c != ",":
raise NexusError(f"Missing ',' in line {options}.")
except NexusError:
raise
except Exception: # TODO: ValueError?
raise NexusError(f"Format error in line {options}.") from None
def _utree(self, options):
"""Use 'utree' to denote an unrooted tree (ex: clustalx) (PRIVATE)."""
self._tree(options)
def _tree(self, options):
opts = CharBuffer(options)
if opts.peek_nonwhitespace() == "*":
# a star can be used to make it the default tree in some software packages
dummy = opts.next_nonwhitespace()
name = opts.next_word()
if opts.next_nonwhitespace() != "=":
raise NexusError(f"Syntax error in tree description: {options[:50]}")
rooted = False
weight = 1.0
while opts.peek_nonwhitespace() == "[":
opts.next_nonwhitespace() # discard opening bracket
symbol = next(opts)
if symbol != "&":
raise NexusError(
"Illegal special comment [%s...] in tree description: %s"
% (symbol, options[:50])
)
special = next(opts)
value = opts.next_until("]")
next(opts) # discard closing bracket
if special == "R":
rooted = True
elif special == "U":
rooted = False
elif special == "W":
weight = float(value)
tree = Tree(name=name, weight=weight, rooted=rooted, tree=opts.rest().strip())
# if there's an active translation table, translate
if self.translate:
for n in tree.get_terminals():
try:
tree.node(n).data.taxon = safename(
self.translate[int(tree.node(n).data.taxon)]
)
except (ValueError, KeyError):
raise NexusError(
"Unable to substitute %s using 'translate' data."
% tree.node(n).data.taxon
) from None
self.trees.append(tree)
def _apply_block_structure(self, title, lines):
"""Apply Block structure to the NEXUS file (PRIVATE)."""
block = Block("")
block.title = title
for line in lines:
block.commandlines.append(Commandline(line, title))
self.structured.append(block)
def _taxset(self, options):
"""Create unique taxset (PRIVATE)."""
name, taxa = self._get_indices(options, set_type=TAXSET)
self.taxsets[name] = _make_unique(taxa)
def _charset(self, options):
"""Create unique character set (PRIVATE)."""
name, sites = self._get_indices(options, set_type=CHARSET)
self.charsets[name] = _make_unique(sites)
def _taxpartition(self, options):
"""Collect taxpartition from a NEXUS file (PRIVATE)."""
taxpartition = {}
quotelevel = False
opts = CharBuffer(options)
name = self._name_n_vector(opts)
if not name:
raise NexusError(f"Formatting error in taxpartition: {options} ")
# now collect thesubbpartitions and parse them
# subpartitons separated by commas - which unfortunately could be part of a quoted identifier...
# this is rather unelegant, but we have to avoid double-parsing and potential change of special nexus-words
sub = ""
while True:
w = next(opts)
if w is None or (w == "," and not quotelevel):
subname, subindices = self._get_indices(
sub, set_type=TAXSET, separator=":"
)
taxpartition[subname] = _make_unique(subindices)
sub = ""
if w is None:
break
else:
if w == "'":
quotelevel = not quotelevel
sub += w
self.taxpartitions[name] = taxpartition
def _codonposset(self, options):
"""Read codon positions from a codons block as written from McClade (PRIVATE).
Here codonposset is just a fancy name for a character partition with
the name CodonPositions and the partitions N,1,2,3
"""
prev_partitions = list(self.charpartitions.keys())
self._charpartition(options)
# mcclade calls it CodonPositions, but you never know...
codonname = [n for n in self.charpartitions if n not in prev_partitions]
if codonname == [] or len(codonname) > 1:
raise NexusError(f"Formatting Error in codonposset: {options} ")
else:
self.codonposset = codonname[0]
def _codeset(self, options):
pass
def _charpartition(self, options):
"""Collect character partition from NEXUS file (PRIVATE)."""
charpartition = {}
quotelevel = False
opts = CharBuffer(options)
name = self._name_n_vector(opts)
if not name:
raise NexusError(f"Formatting error in charpartition: {options} ")
# now collect the subpartitions and parse them
# subpartitions separated by commas - which unfortunately could be part
# of a quoted identifier...
sub = ""
while True:
w = next(opts)
if w is None or (w == "," and not quotelevel):
subname, subindices = self._get_indices(
sub, set_type=CHARSET, separator=":"
)
charpartition[subname] = _make_unique(subindices)
sub = ""
if w is None:
break
else:
if w == "'":
quotelevel = not quotelevel
sub += w
self.charpartitions[name] = charpartition
def _get_indices(self, options, set_type=CHARSET, separator="="):
r"""Parse the taxset/charset specification (PRIVATE).
e.g. '1 2 3 - 5 dog cat 10 - 20 \\ 3'
--> [0,1,2,3,4,'dog','cat',9,12,15,18]
"""
opts = CharBuffer(options)
name = self._name_n_vector(opts, separator=separator)
indices = self._parse_list(opts, set_type=set_type)
if indices is None:
raise NexusError(f"Formatting error in line: {options} ")
return name, indices
def _name_n_vector(self, opts, separator="="):
"""Extract name and check that it's not in vector format (PRIVATE)."""
rest = opts.rest()
name = opts.next_word()
# we ignore * before names
if name == "*":
name = opts.next_word()
if not name:
raise NexusError(f"Formatting error in line: {rest} ")
name = quotestrip(name)
if opts.peek_nonwhitespace == "(":
open = opts.next_nonwhitespace()
qualifier = open.next_word()
close = opts.next_nonwhitespace()
if qualifier.lower() == "vector":
raise NexusError(f"Unsupported VECTOR format in line {opts}")
elif qualifier.lower() != "standard":
raise NexusError(f"Unknown qualifier {qualifier} in line {opts}")
if opts.next_nonwhitespace() != separator:
raise NexusError(f"Formatting error in line: {rest} ")
return name
def _parse_list(self, options_buffer, set_type):
r"""Parse a NEXUS list (PRIVATE).
e.g. [1, 2, 4-8\\2, dog, cat] --> [1,2,4,6,8,17,21],
(assuming dog is taxon no. 17 and cat is taxon no. 21).
"""
plain_list = []
if options_buffer.peek_nonwhitespace():
try:
# capture all possible exceptions and treat them as formatting
# errors, if they are not NexusError
while True:
identifier = options_buffer.next_word() # next list element
if not identifier: # end of list?
break
start = self._resolve(identifier, set_type=set_type)
if options_buffer.peek_nonwhitespace() == "-": # followed by -
end = start
step = 1
# get hyphen and end of range
hyphen = options_buffer.next_nonwhitespace()
end = self._resolve(
options_buffer.next_word(), set_type=set_type
)
if set_type == CHARSET:
if (
options_buffer.peek_nonwhitespace() == "\\"
): # followed by \
backslash = options_buffer.next_nonwhitespace()
step = int(
options_buffer.next_word()
) # get backslash and step
plain_list.extend(range(start, end + 1, step))
else:
if isinstance(start, list) or isinstance(end, list):
raise NexusError(
"Name if character sets not allowed in range definition: %s"
% identifier
)
start = self.taxlabels.index(start)
end = self.taxlabels.index(end)
taxrange = self.taxlabels[start : end + 1]
plain_list.extend(taxrange)
else:
if isinstance(start, list):
# start was the name of charset or taxset
plain_list.extend(start)
else:
# start was an ordinary identifier
plain_list.append(start)
except NexusError:
raise
except Exception: # FIXME - this seems unwise
return None
return plain_list
def _resolve(self, identifier, set_type=None):
"""Translate identifier in list into character/taxon index (PRIVATE).
Characters (which are referred to by their index in Nexus.py):
Plain numbers are returned minus 1 (Nexus indices to python indices)
Text identifiers are translated into their indices (if plain character identifiers),
the first hit in charlabels is returned (charlabels don't need to be unique)
or the range of indices is returned (if names of character sets).
Taxa (which are referred to by their unique name in Nexus.py):
Plain numbers are translated in their taxon name, underscores and spaces are considered equal.
Names are returned unchanged (if plain taxon identifiers), or the names in
the corresponding taxon set is returned.
"""
identifier = quotestrip(identifier)
if not set_type:
raise NexusError("INTERNAL ERROR: Need type to resolve identifier.")
if set_type == CHARSET:
try:
n = int(identifier)
except ValueError:
if self.charlabels and identifier in self.charlabels.values():
for k in self.charlabels:
if self.charlabels[k] == identifier:
return k
elif self.charsets and identifier in self.charsets:
return self.charsets[identifier]
else:
raise NexusError(
f"Unknown character identifier: {identifier}"
) from None
else:
if n <= self.nchar:
return n - 1
else:
raise NexusError(
"Illegal character identifier: %d>nchar (=%d)."
% (identifier, self.nchar)
)
elif set_type == TAXSET:
try:
n = int(identifier)
except ValueError:
taxlabels_id = self._check_taxlabels(identifier)
if taxlabels_id:
return taxlabels_id
elif self.taxsets and identifier in self.taxsets:
return self.taxsets[identifier]
else:
raise NexusError(
f"Unknown taxon identifier: {identifier}"
) from None
else:
if n > 0 and n <= self.ntax:
return self.taxlabels[n - 1]
else:
raise NexusError(
"Illegal taxon identifier: %d>ntax (=%d)."
% (identifier, self.ntax)
)
else:
raise NexusError(f"Unknown set specification: {set_type}.")
def _stateset(self, options):
# Not implemented
pass
def _changeset(self, options):
# Not implemented
pass
def _treeset(self, options):
# Not implemented
pass
def _treepartition(self, options):
# Not implemented
pass
def write_nexus_data_partitions(
self,
matrix=None,
filename=None,
blocksize=None,
interleave=False,
exclude=(),
delete=(),
charpartition=None,
comment="",
mrbayes=False,
):
"""Write a nexus file for each partition in charpartition.
Only non-excluded characters and non-deleted taxa are included,
just the data block is written.
"""
if not matrix:
matrix = self.matrix
if not matrix:
return
if not filename:
filename = self.filename
if charpartition:
pfilenames = {}
for p in charpartition:
total_exclude = list(exclude)
total_exclude.extend(
c for c in range(self.nchar) if c not in charpartition[p]
)
total_exclude = _make_unique(total_exclude)
pcomment = comment + "\nPartition: " + p + "\n"
dot = filename.rfind(".")
if dot > 0:
pfilename = filename[:dot] + "_" + p + ".data"
else:
pfilename = filename + "_" + p
pfilenames[p] = pfilename
self.write_nexus_data(
filename=pfilename,
matrix=matrix,
blocksize=blocksize,
interleave=interleave,
exclude=total_exclude,
delete=delete,
comment=pcomment,
append_sets=False,
mrbayes=mrbayes,
)
return pfilenames
else:
fn = self.filename + ".data"
self.write_nexus_data(
filename=fn,
matrix=matrix,
blocksize=blocksize,
interleave=interleave,
exclude=exclude,
delete=delete,
comment=comment,
append_sets=False,
mrbayes=mrbayes,
)
return fn
def write_nexus_data(
self,
filename=None,
matrix=None,
exclude=(),
delete=(),
blocksize=None,
interleave=False,
interleave_by_partition=False,
comment=None,
omit_NEXUS=False,
append_sets=True,
mrbayes=False,
codons_block=True,
):
"""Write a nexus file with data and sets block to a file or handle.
Character sets and partitions are appended by default, and are
adjusted according to excluded characters (i.e. character sets
still point to the same sites (not necessarily same positions),
without including the deleted characters.
- filename - Either a filename as a string (which will be opened,
written to and closed), or a handle object (which will
be written to but NOT closed).
- interleave_by_partition - Optional name of partition (string)
- omit_NEXUS - Boolean. If true, the '#NEXUS' line normally at the
start of the file is omitted.
Returns the filename/handle used to write the data.
"""
if not matrix:
matrix = self.matrix
if not matrix:
return
if not filename:
filename = self.filename
if [t for t in delete if not self._check_taxlabels(t)]:
raise NexusError(
"Unknown taxa: %s"
% ", ".join(set(delete).difference(set(self.taxlabels)))
)
if interleave_by_partition:
if interleave_by_partition not in self.charpartitions:
raise NexusError(f"Unknown partition: {interleave_by_partition!r}")
else:
partition = self.charpartitions[interleave_by_partition]
# we need to sort the partition names by starting position
# before we exclude characters
names = _sort_keys_by_values(partition)
newpartition = {}
for p in partition:
newpartition[p] = [c for c in partition[p] if c not in exclude]
# how many taxa and how many characters are left?
undelete = [
taxon for taxon in self.taxlabels if taxon in matrix and taxon not in delete
]
cropped_matrix = _seqmatrix2strmatrix(
self.crop_matrix(matrix, exclude=exclude, delete=delete)
)
ntax_adjusted = len(undelete)
nchar_adjusted = len(cropped_matrix[undelete[0]])
if not undelete or (undelete and undelete[0] == ""):
return
with File.as_handle(filename, mode="w") as fh:
if not omit_NEXUS:
fh.write("#NEXUS\n")
if comment:
fh.write("[" + comment + "]\n")
fh.write("begin data;\n")
fh.write("dimensions ntax=%d nchar=%d;\n" % (ntax_adjusted, nchar_adjusted))
fh.write("format datatype=" + self.datatype)
if self.respectcase:
fh.write(" respectcase")
if self.missing:
fh.write(" missing=" + self.missing)
if self.gap:
fh.write(" gap=" + self.gap)
if self.matchchar:
fh.write(" matchchar=" + self.matchchar)
if self.labels:
fh.write(" labels=" + self.labels)
if self.equate:
fh.write(" equate=" + self.equate)
if interleave or interleave_by_partition:
fh.write(" interleave")
fh.write(";\n")
# if self.taxlabels:
# fh.write('taxlabels '+' '.join(self.taxlabels)+';\n')
if self.charlabels:
newcharlabels = self._adjust_charlabels(exclude=exclude)
clkeys = sorted(newcharlabels)
fh.write(
"charlabels "
+ ", ".join(f"{k + 1} {safename(newcharlabels[k])}" for k in clkeys)
+ ";\n"
)
fh.write("matrix\n")
if not blocksize:
if interleave:
blocksize = 70
else:
blocksize = self.nchar
# delete deleted taxa and ecxclude excluded characters...
namelength = max(len(safename(t, mrbayes=mrbayes)) for t in undelete)
if interleave_by_partition:
# interleave by partitions, but adjust partitions with regard
# to excluded characters
seek = 0
for p in names:
fh.write(f"[{interleave_by_partition}: {p}]\n")
if len(newpartition[p]) > 0:
for taxon in undelete:
fh.write(
safename(taxon, mrbayes=mrbayes).ljust(namelength + 1)
)
fh.write(
cropped_matrix[taxon][
seek : seek + len(newpartition[p])
]
+ "\n"
)
fh.write("\n")
else:
fh.write("[empty]\n\n")
seek += len(newpartition[p])
elif interleave:
for seek in range(0, nchar_adjusted, blocksize):
for taxon in undelete:
fh.write(safename(taxon, mrbayes=mrbayes).ljust(namelength + 1))
fh.write(cropped_matrix[taxon][seek : seek + blocksize] + "\n")
fh.write("\n")
else:
for taxon in undelete:
if blocksize < nchar_adjusted:
fh.write(safename(taxon, mrbayes=mrbayes) + "\n")
else:
fh.write(safename(taxon, mrbayes=mrbayes).ljust(namelength + 1))
taxon_seq = cropped_matrix[taxon]
for seek in range(0, nchar_adjusted, blocksize):
fh.write(taxon_seq[seek : seek + blocksize] + "\n")
del taxon_seq
fh.write(";\nend;\n")
if append_sets:
if codons_block:
fh.write(
self.append_sets(
exclude=exclude,
delete=delete,
mrbayes=mrbayes,
include_codons=False,
)
)
fh.write(
self.append_sets(
exclude=exclude,
delete=delete,
mrbayes=mrbayes,
codons_only=True,
)
)
else:
fh.write(
self.append_sets(
exclude=exclude, delete=delete, mrbayes=mrbayes
)
)
return filename
def append_sets(
self,
exclude=(),
delete=(),
mrbayes=False,
include_codons=True,
codons_only=False,
):
"""Return a sets block."""
if not self.charsets and not self.taxsets and not self.charpartitions:
return ""
if codons_only:
setsb = ["\nbegin codons"]
else:
setsb = ["\nbegin sets"]
# - now if characters have been excluded, the character sets need to be adjusted,
# so that they still point to the right character positions
# calculate a list of offsets: for each deleted character, the following character position
# in the new file will have an additional offset of -1
offset = 0
offlist = []
for c in range(self.nchar):
if c in exclude:
offset += 1
offlist.append(
-1
) # dummy value as these character positions are excluded
else:
offlist.append(c - offset)
# now adjust each of the character sets
if not codons_only:
for n, ns in self.charsets.items():
cset = [offlist[c] for c in ns if c not in exclude]
if cset:
setsb.append(f"charset {safename(n)} = {_compact4nexus(cset)}")
for n, s in self.taxsets.items():
tset = [safename(t, mrbayes=mrbayes) for t in s if t not in delete]
if tset:
setsb.append(f"taxset {safename(n)} = {' '.join(tset)}")
for n, p in self.charpartitions.items():
if not include_codons and n == CODONPOSITIONS:
continue
elif codons_only and n != CODONPOSITIONS:
continue
# as characters have been excluded, the partitions must be adjusted
# if a partition is empty, it will be omitted from the charpartition command
# (although paup allows charpartition part=t1:,t2:,t3:1-100)
names = _sort_keys_by_values(p)
newpartition = {}
for sn in names:
nsp = [offlist[c] for c in p[sn] if c not in exclude]
if nsp:
newpartition[sn] = nsp
if newpartition:
if include_codons and n == CODONPOSITIONS:
command = "codonposset"
else:
command = "charpartition"
setsb.append(
"%s %s = %s"
% (
command,
safename(n),
", ".join(
f"{sn}: {_compact4nexus(newpartition[sn])}"
for sn in names
if sn in newpartition
),
)
)
# now write charpartititions, much easier than charpartitions
for n, p in self.taxpartitions.items():
names = _sort_keys_by_values(p)
newpartition = {}
for sn in names:
nsp = [t for t in p[sn] if t not in delete]
if nsp:
newpartition[sn] = nsp
if newpartition:
setsb.append(
"taxpartition %s = %s"
% (
safename(n),
", ".join(
"%s: %s"
% (
safename(sn),
" ".join(safename(x) for x in newpartition[sn]),
)
for sn in names
if sn in newpartition
),
)
)
# add 'end' and return everything
setsb.append("end;\n")
if len(setsb) == 2: # begin and end only
return ""
else:
return ";\n".join(setsb)
def export_fasta(self, filename=None, width=70):
"""Write matrix into a fasta file."""
if not filename:
if "." in self.filename and self.filename.split(".")[-1].lower() in [
"paup",
"nexus",
"nex",
"dat",
]:
filename = ".".join(self.filename.split(".")[:-1]) + ".fas"
else:
filename = self.filename + ".fas"
with open(filename, "w") as fh:
for taxon in self.taxlabels:
fh.write(">" + safename(taxon) + "\n")
for i in range(0, len(str(self.matrix[taxon])), width):
fh.write(str(self.matrix[taxon])[i : i + width] + "\n")
return filename
def export_phylip(self, filename=None):
"""Write matrix into a PHYLIP file.
Note that this writes a relaxed PHYLIP format file, where the names
are not truncated, nor checked for invalid characters.
"""
if not filename:
if "." in self.filename and self.filename.split(".")[-1].lower() in [
"paup",
"nexus",
"nex",
"dat",
]:
filename = ".".join(self.filename.split(".")[:-1]) + ".phy"
else:
filename = self.filename + ".phy"
with open(filename, "w") as fh:
fh.write("%d %d\n" % (self.ntax, self.nchar))
for taxon in self.taxlabels:
fh.write(f"{safename(taxon)} {str(self.matrix[taxon])}\n")
return filename
def constant(self, matrix=None, delete=(), exclude=()):
"""Return a list with all constant characters."""
if not matrix:
matrix = self.matrix
undelete = [t for t in self.taxlabels if t in matrix and t not in delete]
if not undelete:
return None
elif len(undelete) == 1:
return [x for x in range(len(matrix[undelete[0]])) if x not in exclude]
# get the first sequence and expand all ambiguous values
constant = [
(x, self.ambiguous_values.get(n.upper(), n.upper()))
for x, n in enumerate(str(matrix[undelete[0]]))
if x not in exclude
]
for taxon in undelete[1:]:
newconstant = []
for site in constant:
# print("%d (paup=%d)" % (site[0],site[0]+1), end="")
seqsite = matrix[taxon][site[0]].upper()
# print(seqsite,"checked against",site[1],"\t", end="")
if (
seqsite == self.missing
or (
seqsite == self.gap
and self.options["gapmode"].lower() == "missing"
)
or seqsite == site[1]
):
# missing or same as before -> ok
newconstant.append(site)
elif (
seqsite in site[1]
or site[1] == self.missing
or (
self.options["gapmode"].lower() == "missing"
and site[1] == self.gap
)
):
# subset of an ambig or only missing in previous -> take subset
newconstant.append(
(site[0], self.ambiguous_values.get(seqsite, seqsite))
)
elif seqsite in self.ambiguous_values:
# is it an ambig: check the intersection with prev. values
intersect = set(self.ambiguous_values[seqsite]).intersection(
set(site[1])
)
if intersect:
newconstant.append((site[0], "".join(intersect)))
# print("ok")
# else:
# print("failed")
# else:
# print("failed")
constant = newconstant
cpos = [s[0] for s in constant]
return cpos
def cstatus(self, site, delete=(), narrow=True):
"""Summarize character.
narrow=True: paup-mode (a c ? --> ac; ? ? ? --> ?)
narrow=false: (a c ? --> a c g t -; ? ? ? --> a c g t -)
"""
undelete = [t for t in self.taxlabels if t not in delete]
if not undelete:
return None
cstatus = []
for t in undelete:
c = self.matrix[t][site].upper()
if self.options.get("gapmode") == "missing" and c == self.gap:
c = self.missing
if narrow and c == self.missing:
if c not in cstatus:
cstatus.append(c)
else:
cstatus.extend(b for b in self.ambiguous_values[c] if b not in cstatus)
if self.missing in cstatus and narrow and len(cstatus) > 1:
cstatus = [_ for _ in cstatus if _ != self.missing]
cstatus.sort()
return cstatus
def weighted_stepmatrix(self, name="your_name_here", exclude=(), delete=()):
"""Calculate a stepmatrix for weighted parsimony.
See Wheeler (1990), Cladistics 6:269-275 and
Felsenstein (1981), Biol. J. Linn. Soc. 16:183-196
"""
m = StepMatrix(self.unambiguous_letters, self.gap)
for site in [s for s in range(self.nchar) if s not in exclude]:
cstatus = self.cstatus(site, delete)
for i, b1 in enumerate(cstatus[:-1]):
for b2 in cstatus[i + 1 :]:
m.add(b1.upper(), b2.upper(), 1)
return m.transformation().weighting().smprint(name=name)
def crop_matrix(self, matrix=None, delete=(), exclude=()):
"""Return a matrix without deleted taxa and excluded characters."""
if not matrix:
matrix = self.matrix
if [t for t in delete if not self._check_taxlabels(t)]:
raise NexusError(
f"Unknown taxa: {', '.join(set(delete).difference(self.taxlabels))}"
)
if exclude != []:
undelete = [t for t in self.taxlabels if t in matrix and t not in delete]
if not undelete:
return {}
m = [str(matrix[k]) for k in undelete]
sitesm = [s for i, s in enumerate(zip(*m)) if i not in exclude]
if sitesm == []:
return {t: Seq("") for t in undelete}
else:
m = [Seq(s) for s in ("".join(x) for x in zip(*sitesm))]
return dict(zip(undelete, m))
else:
return {
t: matrix[t] for t in self.taxlabels if t in matrix and t not in delete
}
def bootstrap(self, matrix=None, delete=(), exclude=()):
"""Return a bootstrapped matrix."""
if not matrix:
matrix = self.matrix
seqobjects = isinstance(
matrix[list(matrix.keys())[0]], Seq
) # remember if Seq objects
cm = self.crop_matrix(delete=delete, exclude=exclude) # crop data out
if not cm: # everything deleted?
return {}
elif not cm[list(cm.keys())[0]]: # everything excluded?
return cm
undelete = [t for t in self.taxlabels if t in cm]
if seqobjects:
sitesm = list(zip(*(str(cm[t]) for t in undelete)))
else:
sitesm = list(zip(*(cm[t] for t in undelete)))
bootstrapsitesm = [
sitesm[random.randint(0, len(sitesm) - 1)] for _ in range(len(sitesm))
]
bootstrapseqs = ["".join(x) for x in zip(*bootstrapsitesm)]
if seqobjects:
bootstrapseqs = [Seq(s) for s in bootstrapseqs]
return dict(zip(undelete, bootstrapseqs))
def add_sequence(self, name, sequence):
"""Add a sequence (string) to the matrix."""
if not name:
raise NexusError("New sequence must have a name")
diff = self.nchar - len(sequence)
if diff < 0:
self.insert_gap(self.nchar, -diff)
elif diff > 0:
sequence += self.missing * diff
if name in self.taxlabels:
unique_name = _unique_label(self.taxlabels, name)
# print("WARNING: Sequence name %s is already present. Sequence was added as %s." % (name,unique_name))
else:
unique_name = name
if unique_name in self.matrix:
raise ValueError(
"ERROR. There is a discrepancy between taxlabels "
"and matrix keys. Report this as a bug."
)
self.matrix[unique_name] = Seq(sequence)
self.ntax += 1
self.taxlabels.append(unique_name)
self.unaltered_taxlabels.append(name)
def insert_gap(self, pos, n=1, leftgreedy=False):
"""Add a gap into the matrix and adjust charsets and partitions.
pos=0: first position
pos=nchar: last position
"""
def _adjust(set, x, d, leftgreedy=False):
"""Adjust character sets if gaps are inserted (PRIVATE).
Takes care of new gaps within a coherent character set.
"""
# if 3 gaps are inserted at pos. 9 in a set that looks like 1 2 3 8 9 10 11 13 14 15
# then the adjusted set will be 1 2 3 8 9 10 11 12 13 14 15 16 17 18
# but inserting into position 8 it will stay like 1 2 3 11 12 13 14 15 16 17 18
set.sort()
addpos = 0
for i, c in enumerate(set):
if c >= x:
set[i] = c + d
# if we add gaps within a group of characters, we want the gap position included in this group
if c == x:
if leftgreedy or (i > 0 and set[i - 1] == c - 1):
addpos = i
if addpos > 0:
set[addpos:addpos] = list(range(x, x + d))
return set
if pos < 0 or pos > self.nchar:
raise NexusError("Illegal gap position: %d" % pos)
if n == 0:
return
sitesm = list(zip(*(str(self.matrix[t]) for t in self.taxlabels)))
sitesm[pos:pos] = [["-"] * len(self.taxlabels)] * n
mapped = ["".join(x) for x in zip(*sitesm)]
listed = [(taxon, Seq(mapped[i])) for i, taxon in enumerate(self.taxlabels)]
self.matrix = dict(listed)
self.nchar += n
# now adjust character sets
for i, s in self.charsets.items():
self.charsets[i] = _adjust(s, pos, n, leftgreedy=leftgreedy)
for p in self.charpartitions:
for sp, s in self.charpartitions[p].items():
self.charpartitions[p][sp] = _adjust(s, pos, n, leftgreedy=leftgreedy)
# now adjust character state labels
self.charlabels = self._adjust_charlabels(insert=[pos] * n)
return self.charlabels
def _adjust_charlabels(self, exclude=None, insert=None):
"""Return adjusted indices of self.charlabels if characters are excluded or inserted (PRIVATE)."""
if exclude and insert:
raise NexusError("Can't exclude and insert at the same time")
if not self.charlabels:
return None
labels = sorted(self.charlabels)
newcharlabels = {}
if exclude:
exclude.sort()
exclude.append(sys.maxsize)
excount = 0
for c in labels:
if c not in exclude:
while c > exclude[excount]:
excount += 1
newcharlabels[c - excount] = self.charlabels[c]
elif insert:
insert.sort()
insert.append(sys.maxsize)
icount = 0
for c in labels:
while c >= insert[icount]:
icount += 1
newcharlabels[c + icount] = self.charlabels[c]
else:
return self.charlabels
return newcharlabels
def invert(self, charlist):
"""Return all character indices that are not in charlist."""
return [c for c in range(self.nchar) if c not in charlist]
def gaponly(self, include_missing=False):
"""Return gap-only sites."""
gap = set(self.gap)
if include_missing:
gap.add(self.missing)
sitesm = zip(*(str(self.matrix[t]) for t in self.taxlabels))
return [i for i, site in enumerate(sitesm) if set(site).issubset(gap)]
def terminal_gap_to_missing(self, missing=None, skip_n=True):
"""Replace all terminal gaps with missing character.
Mixtures like ???------??------- are properly resolved.
"""
if not missing:
missing = self.missing
replace = [self.missing, self.gap]
if not skip_n:
replace.extend(["n", "N"])
for taxon in self.taxlabels:
sequence = str(self.matrix[taxon])
length = len(sequence)
start, end = get_start_end(sequence, skiplist=replace)
if start == -1 and end == -1:
sequence = missing * length
else:
sequence = sequence[: end + 1] + missing * (length - end - 1)
sequence = start * missing + sequence[start:]
if length != len(sequence):
raise RuntimeError(
"Illegal sequence manipulation in "
"Nexus.terminal_gap_to_missing in taxon %s" % taxon
)
self.matrix[taxon] = Seq(sequence)
try:
import cnexus
except ImportError:
def _get_command_lines(file_contents):
lines = _kill_comments_and_break_lines(file_contents)
commandlines = _adjust_lines(lines)
return commandlines
else:
def _get_command_lines(file_contents):
decommented = cnexus.scanfile(file_contents)
# check for unmatched parentheses
if decommented == "[" or decommented == "]":
raise NexusError(f"Unmatched {decommented}")
# cnexus can't return lists, so in analogy we separate
# commandlines with chr(7) (a character that shouldn't be part of a
# nexus file under normal circumstances)
commandlines = _adjust_lines(decommented.split(chr(7)))
return commandlines
if __name__ == "__main__":
from Bio._utils import run_doctest
run_doctest()
|