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
|
.. _dna-rna-seqs:
Sequences
---------
The ``Sequence`` object provides generic biological sequence manipulation functions, plus functions that are critical for the ``evolve`` module calculations.
Generic molecular types
^^^^^^^^^^^^^^^^^^^^^^^
Sequence properties are affected by the moltype you specify. The default type for a sequence is ``"text"``.
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("AGTACACTGGT")
my_seq.moltype.label
.. jupyter-execute::
my_seq
In some circumstances you can also have a ``"bytes"`` moltype, which I'll explicitly construct here.
.. jupyter-execute::
my_seq = make_seq("AGTACACTGGT", moltype="bytes")
my_seq.moltype.label
.. jupyter-execute::
my_seq
DNA and RNA sequences
^^^^^^^^^^^^^^^^^^^^^
.. authors, Gavin Huttley, Kristian Rother, Patrick Yannul, Tom Elliott, Tony Walters, Meg Pirrung
Creating a DNA sequence from a string
"""""""""""""""""""""""""""""""""""""
Sequence properties are affected by the moltype you specify. Here we specify the ``DNA`` ``MolType``.
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("AGTACACTGGT", moltype="dna")
my_seq
Creating a RNA sequence from a string
"""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna")
Converting to FASTA format
""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("AGTACACTGGT", moltype="dna")
my_seq
Convert a RNA sequence to FASTA format
""""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna")
rnaseq
Creating a named sequence
"""""""""""""""""""""""""
You can also use a convenience ``make_seq()`` function, providing the moltype as a string.
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("AGTACACTGGT", "my_gene", moltype="dna")
my_seq
type(my_seq)
Setting or changing the name of a sequence
""""""""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("AGTACACTGGT", moltype="dna")
my_seq.name = "my_gene"
my_seq
Complementing a DNA sequence
""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("AGTACACTGGT", moltype="dna")
my_seq.complement()
Reverse complementing a DNA sequence
""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
my_seq.rc()
.. _translation:
Translate a ``DnaSequence`` to protein
""""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("GCTTGGGAAAGTCAAATGGAA", name="s1", moltype="dna")
pep = my_seq.get_translation()
type(pep)
.. jupyter-execute::
pep
Converting a DNA sequence to RNA
""""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("ACGTACGTACGTACGT", moltype="dna")
rnaseq = my_seq.to_rna()
rnaseq
Convert an RNA sequence to DNA
""""""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
rnaseq = make_seq("ACGUACGUACGUACGU", moltype="rna")
dnaseq = rnaseq.to_dna()
dnaseq
Testing complementarity
"""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
a = make_seq("AGTACACTGGT", moltype="dna")
a.can_pair(a.complement())
.. jupyter-execute::
a.can_pair(a.rc())
Joining two DNA sequences
"""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
my_seq = make_seq("AGTACACTGGT", moltype="dna")
extra_seq = make_seq("CTGAC", moltype="dna")
long_seq = my_seq + extra_seq
long_seq
Slicing DNA sequences
"""""""""""""""""""""
.. jupyter-execute::
my_seq[1:6]
Getting 3rd positions from codons
"""""""""""""""""""""""""""""""""
The easiest approach is to work off the ``cogent3`` ``ArrayAlignment`` object.
.. jupyter-execute::
from cogent3 import make_seq
seq = make_seq("ATGATGATGATG", moltype="dna")
pos3 = seq[2::3]
assert str(pos3) == "GGGG"
Getting 1st and 2nd positions from codons
"""""""""""""""""""""""""""""""""""""""""
In this instance we can use features.
.. jupyter-execute::
from cogent3 import make_seq
seq = make_seq("ATGATGATGATG", moltype="dna")
indices = [(i, i + 2) for i in range(len(seq))[::3]]
pos12 = seq.add_feature(biotype="pos12", name="pos12", spans=indices)
pos12 = pos12.get_slice()
assert str(pos12) == "ATATATAT"
Return a randomized version of the sequence
"""""""""""""""""""""""""""""""""""""""""""
.. jupyter-execute::
rnaseq.shuffle()
Remove gaps from a sequence
"""""""""""""""""""""""""""
.. jupyter-execute::
from cogent3 import make_seq
s = make_seq("--AUUAUGCUAU-UAu--", moltype="rna")
s.degap()
|
