skbio.sequence.Sequence

class skbio.sequence.Sequence(sequence, metadata=None, positional_metadata=None, interval_metadata=None, lowercase=False)

Store generic sequence data and optional associated metadata.

Sequence objects do not enforce an alphabet or grammar and are thus the most generic objects for storing sequence data. Sequence objects do not necessarily represent biological sequences. For example, Sequence can be used to represent a position in a multiple sequence alignment. Subclasses DNA, RNA, and Protein enforce the IUPAC character set [1] for, and provide operations specific to, each respective molecule type.

Sequence objects consist of the underlying sequence data, as well as optional metadata and positional metadata. The underlying sequence is immutable, while the metdata and positional metadata are mutable.

Parameters:

sequencestr, Sequence, or 1D np.ndarray (np.uint8 or ‘|S1’)

Characters representing the sequence itself.

metadatadict, optional

Arbitrary metadata which applies to the entire sequence. A shallow copy of the dict will be made (see Examples section below for details).

positional_metadatapd.DataFrame consumable, optional

Arbitrary per-character metadata (e.g., sequence read quality scores). Must be able to be passed directly to pd.DataFrame constructor. Each column of metadata must be the same length as sequence. A shallow copy of the positional metadata will be made if necessary (see Examples section below for details).

interval_metadataIntervalMetadata

Arbitrary metadata which applies to intervals within a sequence to store interval features (such as genes, ncRNA on the sequence).

lowercasebool or str, optional

If True, lowercase sequence characters will be converted to uppercase characters. If False, no characters will be converted. If a str, it will be treated as a key into the positional metadata of the object. All lowercase characters will be converted to uppercase, and a True value will be stored in a boolean array in the positional metadata under the key.

See also

DNA

RNA

Protein

References

[1]

Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res. May 10, 1985; 13(9): 3021-3030. A Cornish-Bowden

Examples

>>> from skbio import Sequence
>>> from skbio.metadata import IntervalMetadata

Creating sequences:

Create a sequence without any metadata:

>>> seq = Sequence('GGUCGUGAAGGA')
>>> seq
Sequence
---------------
Stats:
    length: 12
---------------
0 GGUCGUGAAG GA

Create a sequence with metadata and positional metadata:

>>> metadata = {'authors': ['Alice'], 'desc':'seq desc', 'id':'seq-id'}
>>> positional_metadata = {'exons': [True, True, False, True],
...                        'quality': [3, 3, 4, 10]}
>>> interval_metadata = IntervalMetadata(4)
>>> interval = interval_metadata.add([(1, 3)], metadata={'gene': 'sagA'})
>>> seq = Sequence('ACGT', metadata=metadata,
...                positional_metadata=positional_metadata,
...                interval_metadata=interval_metadata)
>>> seq
Sequence
-----------------------------
Metadata:
    'authors': <class 'list'>
    'desc': 'seq desc'
    'id': 'seq-id'
Positional metadata:
    'exons': <dtype: bool>
    'quality': <dtype: int64>
Interval metadata:
    1 interval feature
Stats:
    length: 4
-----------------------------
0 ACGT

Retrieving underlying sequence data:

Retrieve underlying sequence:

>>> seq.values 
array([b'A', b'C', b'G', b'T'],
      dtype='|S1')

Underlying sequence immutable:

>>> values = np.array([b'T', b'C', b'G', b'A'], dtype='|S1')
>>> seq.values = values 
Traceback (most recent call last):
    ...
AttributeError: can't set attribute

>>> seq.values[0] = b'T'
Traceback (most recent call last):
    ...
ValueError: assignment destination is read-only

Retrieving sequence metadata:

Retrieve metadata:

>>> seq.metadata
{'authors': ['Alice'], 'desc': 'seq desc', 'id': 'seq-id'}

Retrieve positional metadata:

>>> seq.positional_metadata
   exons  quality
0   True        3
1   True        3
2  False        4
3   True       10

Retrieve interval metadata:

>>> seq.interval_metadata   
1 interval feature
------------------
Interval(interval_metadata=<...>, bounds=[(1, 3)], fuzzy=[(False, False)], metadata={'gene': 'sagA'})

Updating sequence metadata:

Warning

Be aware that a shallow copy of metadata and positional_metadata is made for performance. Since a deep copy is not made, changes made to mutable Python objects stored as metadata may affect the metadata of other Sequence objects or anything else that shares a reference to the object. The following examples illustrate this behavior.

First, let’s create a sequence and update its metadata:

>>> metadata = {'id': 'seq-id', 'desc': 'seq desc', 'authors': ['Alice']}
>>> seq = Sequence('ACGT', metadata=metadata)
>>> seq.metadata['id'] = 'new-id'
>>> seq.metadata['pubmed'] = 12345
>>> seq.metadata
{'id': 'new-id', 'desc': 'seq desc', 'authors': ['Alice'], 'pubmed': 12345}

Note that the original metadata dictionary (stored in variable metadata) hasn’t changed because a shallow copy was made:

>>> metadata
{'id': 'seq-id', 'desc': 'seq desc', 'authors': ['Alice']}
>>> seq.metadata == metadata
False

Note however that since only a shallow copy was made, updates to mutable objects will also change the original metadata dictionary:

>>> seq.metadata['authors'].append('Bob')
>>> seq.metadata['authors']
['Alice', 'Bob']
>>> metadata['authors']
['Alice', 'Bob']

This behavior can also occur when manipulating a sequence that has been derived from another sequence:

>>> subseq = seq[1:3]
>>> subseq
Sequence
-----------------------------
Metadata:
    'authors': <class 'list'>
    'desc': 'seq desc'
    'id': 'new-id'
    'pubmed': 12345
Stats:
    length: 2
-----------------------------
0 CG
>>> subseq.metadata
{'id': 'new-id', 'desc': 'seq desc', 'authors': ['Alice', 'Bob'], 'pubmed': 12345}

The subsequence has inherited the metadata of its parent sequence. If we update the subsequence’s author list, we see the changes propagated in the parent sequence and original metadata dictionary:

>>> subseq.metadata['authors'].append('Carol')
>>> subseq.metadata['authors']
['Alice', 'Bob', 'Carol']
>>> seq.metadata['authors']
['Alice', 'Bob', 'Carol']
>>> metadata['authors']
['Alice', 'Bob', 'Carol']

The behavior for updating positional metadata is similar. Let’s create a new sequence with positional metadata that is already stored in a pd.DataFrame:

>>> positional_metadata = pd.DataFrame(
...     {'list': [[], [], [], []], 'quality': [3, 3, 4, 10]})
>>> seq = Sequence('ACGT', positional_metadata=positional_metadata)
>>> seq
Sequence
-----------------------------
Positional metadata:
    'list': <dtype: object>
    'quality': <dtype: int64>
Stats:
    length: 4
-----------------------------
0 ACGT
>>> seq.positional_metadata
  list  quality
0   []        3
1   []        3
2   []        4
3   []       10

Now let’s update the sequence’s positional metadata by adding a new column and changing a value in another column:

>>> seq.positional_metadata['gaps'] = [False, False, False, False]
>>> seq.positional_metadata.loc[0, 'quality'] = 999
>>> seq.positional_metadata
  list  quality   gaps
0   []      999  False
1   []        3  False
2   []        4  False
3   []       10  False

Note that the original positional metadata (stored in variable positional_metadata) hasn’t changed because a shallow copy was made:

>>> positional_metadata
  list  quality
0   []        3
1   []        3
2   []        4
3   []       10
>>> seq.positional_metadata.equals(positional_metadata)
False

Next let’s create a sequence that has been derived from another sequence:

>>> subseq = seq[1:3]
>>> subseq
Sequence
-----------------------------
Positional metadata:
    'list': <dtype: object>
    'quality': <dtype: int64>
    'gaps': <dtype: bool>
Stats:
    length: 2
-----------------------------
0 CG
>>> subseq.positional_metadata
  list  quality   gaps
0   []        3  False
1   []        4  False

As described above for metadata, since only a shallow copy was made of the positional metadata, updates to mutable objects will also change the parent sequence’s positional metadata and the original positional metadata pd.DataFrame:

>>> subseq.positional_metadata.loc[0, 'list'].append('item')
>>> subseq.positional_metadata
     list  quality   gaps
0  [item]        3  False
1      []        4  False
>>> seq.positional_metadata
     list  quality   gaps
0      []      999  False
1  [item]        3  False
2      []        4  False
3      []       10  False
>>> positional_metadata
     list  quality
0      []        3
1  [item]        3
2      []        4
3      []       10

You can also update the interval metadata. Let’s re-create a Sequence object with interval metadata at first:

>>> seq = Sequence('ACGT')
>>> interval = seq.interval_metadata.add(
...     [(1, 3)], metadata={'gene': 'foo'})

You can update directly on the Interval object:

>>> interval  
Interval(interval_metadata=<...>, bounds=[(1, 3)], fuzzy=[(False, False)], metadata={'gene': 'foo'})
>>> interval.bounds = [(0, 2)]
>>> interval  
Interval(interval_metadata=<...>, bounds=[(0, 2)], fuzzy=[(False, False)], metadata={'gene': 'foo'})

You can also query and obtain the interval features you are interested and then modify them:

>>> intervals = list(seq.interval_metadata.query(metadata={'gene': 'foo'}))
>>> intervals[0].fuzzy = [(True, False)]
>>> print(intervals[0])  
Interval(interval_metadata=<...>, bounds=[(0, 2)], fuzzy=[(True, False)], metadata={'gene': 'foo'})

Attributes

default_write_format
interval_metadata	IntervalMetadata object containing info about interval features.
metadata	dict containing metadata which applies to the entire object.
observed_chars	Set of observed characters in the sequence.
positional_metadata	pd.DataFrame containing metadata along an axis.
values	Array containing underlying sequence characters.

Built-ins

__bool__()	Return truth value (truthiness) of sequence.
__contains__(subsequence)	Determine if a subsequence is contained in this sequence.
__copy__()	Return a shallow copy of this sequence.
__deepcopy__(memo)	Return a deep copy of this sequence.
__eq__(other)	Determine if this sequence is equal to another.
__ge__(value, /)	Return self>=value.
__getitem__(indexable)	Slice this sequence.
__getstate__(/)	Helper for pickle.
__gt__(value, /)	Return self>value.
__iter__()	Iterate over positions in this sequence.
__le__(value, /)	Return self<=value.
__len__()	Return the number of characters in this sequence.
__lt__(value, /)	Return self<value.
__ne__(other)	Determine if this sequence is not equal to another.
__reversed__()	Iterate over positions in this sequence in reverse order.
__str__()	Return sequence characters as a string.

Methods

concat(sequences[, how])	Concatenate an iterable of Sequence objects.
count(subsequence[, start, end])	Count occurrences of a subsequence in this sequence.
distance(other[, metric])	Compute the distance to another sequence.
find_with_regex(regex[, ignore])	Generate slices for patterns matched by a regular expression.
frequencies([chars, relative])	Compute frequencies of characters in the sequence.
has_interval_metadata()	Determine if the object has interval metadata.
has_metadata()	Determine if the object has metadata.
has_positional_metadata()	Determine if the object has positional metadata.
index(subsequence[, start, end])	Find position where subsequence first occurs in the sequence.
iter_contiguous(included[, min_length, invert])	Yield contiguous subsequences based on included.
iter_kmers(k[, overlap])	Generate kmers of length k from this sequence.
kmer_frequencies(k[, overlap, relative])	Return counts of words of length k from this sequence.
lowercase(lowercase)	Return a case-sensitive string representation of the sequence.
match_frequency(other[, relative])	Return count of positions that are the same between two sequences.
matches(other)	Find positions that match with another sequence.
mismatch_frequency(other[, relative])	Return count of positions that differ between two sequences.
mismatches(other)	Find positions that do not match with another sequence.
read(file[, format])	Create a new Sequence instance from a file.
replace(where, character)	Replace values in this sequence with a different character.
to_indices([alphabet, mask_gaps, wildcard, ...])	Convert the sequence into indices of characters.
write(file[, format])	Write an instance of Sequence to a file.