skbio.sequence.Protein

class skbio.sequence.Protein(sequence, metadata=None, positional_metadata=None, interval_metadata=None, lowercase=False, validate=True)[source]

Store protein sequence data and optional associated metadata.

Only characters in the IUPAC protein character set 1 are supported.

Parameters
  • sequence (str, Sequence, or 1D np.ndarray (np.uint8 or '|S1')) – Characters representing the protein sequence itself.

  • metadata (dict, optional) – Arbitrary metadata which applies to the entire sequence.

  • positional_metadata (Pandas DataFrame consumable, optional) – Arbitrary per-character metadata. For example, quality data from sequencing reads. Must be able to be passed directly to the Pandas DataFrame constructor.

  • interval_metadata (IntervalMetadata) – Arbitrary interval metadata which applies to intervals within a sequence to store interval features (such as protein domains).

  • lowercase (bool or str, optional) – If True, lowercase sequence characters will be converted to uppercase characters in order to be valid IUPAC Protein 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.

  • validate (bool, optional) – If True, validation will be performed to ensure that all sequence characters are in the IUPAC protein character set. If False, validation will not be performed. Turning off validation will improve runtime performance. If invalid characters are present, however, there is no guarantee that operations performed on the resulting object will work or behave as expected. Only turn off validation if you are certain that the sequence characters are valid. To store sequence data that is not IUPAC-compliant, use Sequence.

Notes

Subclassing is disabled for Protein, because subclassing makes it possible to change the alphabet, and certain methods rely on the IUPAC alphabet. If a custom sequence alphabet is needed, inherit directly from GrammaredSequence.

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 Protein
>>> Protein('PAW')
Protein
--------------------------
Stats:
    length: 3
    has gaps: False
    has degenerates: False
    has definites: True
    has stops: False
--------------------------
0 PAW

Convert lowercase characters to uppercase:

>>> Protein('paW', lowercase=True)
Protein
--------------------------
Stats:
    length: 3
    has gaps: False
    has degenerates: False
    has definites: True
    has stops: False
--------------------------
0 PAW

Attributes

alphabet

Return valid characters.

default_gap_char

Gap character to use when constructing a new gapped sequence.

default_write_format

definite_chars

Return definite characters.

degenerate_chars

Return degenerate characters.

degenerate_map

Return mapping of degenerate to definite characters.

gap_chars

Return characters defined as gaps.

interval_metadata

IntervalMetadata object containing info about interval features.

metadata

dict containing metadata which applies to the entire object.

nondegenerate_chars

Return non-degenerate characters.

observed_chars

Set of observed characters in the sequence.

positional_metadata

pd.DataFrame containing metadata along an axis.

stop_chars

Return characters representing translation stop codons.

values

Array containing underlying sequence characters.

Built-ins

bool(protein)

Returns truth value (truthiness) of sequence.

x in protein

Determine if a subsequence is contained in this sequence.

copy.copy(protein)

Return a shallow copy of this sequence.

copy.deepcopy(protein)

Return a deep copy of this sequence.

protein1 == protein2

Determine if this sequence is equal to another.

protein[x]

Slice this sequence.

iter(protein)

Iterate over positions in this sequence.

len(protein)

Return the number of characters in this sequence.

protein1 != protein2

Determine if this sequence is not equal to another.

reversed(protein)

Iterate over positions in this sequence in reverse order.

str(protein)

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.

definites()

Find positions containing definite characters in the sequence.

degap()

Return a new sequence with gap characters removed.

degenerates()

Find positions containing degenerate characters in the sequence.

distance(other[, metric])

Compute the distance to another sequence.

expand_degenerates()

Yield all possible definite versions of the sequence.

find_motifs(motif_type[, min_length, ignore])

Search the biological sequence for motifs.

find_with_regex(regex[, ignore])

Generate slices for patterns matched by a regular expression.

frequencies([chars, relative])

Compute frequencies of characters in the sequence.

gaps()

Find positions containing gaps in the biological sequence.

has_definites()

Determine if sequence contains one or more definite characters

has_degenerates()

Determine if sequence contains one or more degenerate characters.

has_gaps()

Determine if the sequence contains one or more gap characters.

has_interval_metadata()

Determine if the object has interval metadata.

has_metadata()

Determine if the object has metadata.

has_nondegenerates()

Determine if sequence contains one or more non-degenerate characters

has_positional_metadata()

Determine if the object has positional metadata.

has_stops()

Determine if the sequence contains one or more stop characters.

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.

nondegenerates()

Find positions containing non-degenerate characters in the sequence.

read(file[, format])

Create a new Protein instance from a file.

replace(where, character)

Replace values in this sequence with a different character.

stops()

Find positions containing stop characters in the protein sequence.

to_regex([within_capture])

Return regular expression object that accounts for degenerate chars.

write(file[, format])

Write an instance of Protein to a file.