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
|
Annotations
^^^^^^^^^^^
In its simplest usage, annotations provide a way of labeling a particular region or segment of a ``DnaSequence`` or ``Alignment`` object as containing a feature. Different segments of the same type (cds or exon or any new feature you define), can then grouped together for analysis. The Python slice operator ([ ], ``__getitem__``) can be used to access a particular feature.
All the features of a given type can be obtained in a list by using the method ``getAnnotationsMatching()``
.. doctest::
>>> from cogent import DNA
>>> s = DNA.makeSequence('ATGACCCTGTAAAAAATGTGTTAACCC',
... Name='a')
>>> cds1 = s.addFeature('cds','cds1', [(0,12)])
>>> cds2 = s.addFeature('cds','cds2', [(15,24)])
>>> s
DnaSequence(ATGACCC... 27)
>>> cds1
cds "cds1" at [0:12]/27
>>> type(cds1)
<class 'cogent.core.annotation.AnnotatableFeature'>
>>> s[cds2]
DnaSequence(ATGTGTTAA)
>>> all_cds = s.getAnnotationsMatching('cds')
>>> all_cds
[cds "cds1" at [0:12]/27, cds "cds2" at [15:24]/27]
In addition, ``getRegionCoveringAll()`` and ``getShadow()`` can be used to grab all the coding sequences or non-coding sequences in a ``DnaSequence`` object.
>>> coding_seqs = s.getRegionCoveringAll(all_cds)
>>> coding_seqs
region "cds" at [0:12, 15:24]/27
>>> type(coding_seqs)
<class 'cogent.core.annotation._Feature'>
>>> coding_seqs.getSlice()
DnaSequence(ATGACCC... 21)
>>> noncoding_seqs = coding_seqs.getShadow()
>>> noncoding_seqs
region "not cds" at [12:15, 24:27]/27
>>> print noncoding_seqs.getSlice()
AAACCC
For more extensive documentation about annotations see :ref:`seq-annotations`.
Annotations with coordinates
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
*To be written.*
Automated introduction from reading genbank files
"""""""""""""""""""""""""""""""""""""""""""""""""
*To be written.*
Manipulating annotated regions
""""""""""""""""""""""""""""""
*To be written.*
Annotation display
""""""""""""""""""
*To be written.*
Introducing your own
""""""""""""""""""""
*To be written.*
Displaying them
"""""""""""""""
*To be written.*
Generic metadata
^^^^^^^^^^^^^^^^
*To be written.*
Info object
"""""""""""
*To be written.*
|
