Miscellaneous#

class pyhmmer.easel.GeneticCode#

A genetic code table for translation.

Added in version 0.7.2.

__init__(translation_table=1, *, nucleotide_alphabet=None, amino_alphabet=None)#

Create a new genetic code for translating nucleotide sequences.

Parameters:

  • translation_table (int) – The translation table to use. Check the Wikipedia page listing all genetic codes for the available values.

  • nucleotide_alphabet (Alphabet) – The nucleotide alphabet from which to translate the sequence.

  • amino_alphabet (Alphabet) – The target alphabet into which to translate the sequence.

translate(sequence)#

Translate a raw nucleotide sequence into a protein.

Parameters:

sequence (object, buffer-like) – A raw sequence in digital format. Any object implementing the buffer protocol (like bytearray, VectorU8, etc.) may be given.

Returns:

VectorU8 – The translation of the input sequence, as a raw digital sequence.

Raises:

ValueError – When sequence could not be translated properly, because of a codon could not be recognized, or because the sequence has an invalid length.

Note

The translation of a DNA/RNA codon supports ambiguous codons. If the amino acid is unambiguous, despite codon ambiguity, the correct amino acid is still determined: GGR translates as Gly, UUY as Phe, etc. If there is no single unambiguous amino acid translation, the codon is translated as X. Ambiguous amino acids (such as J or B) are never produced.

description#

A description of the translation table currently in use.

Type:

str

translation_table#

The translation table in use.

Can be set manually to a different number to change the translation table for the current GeneticCode object.

Type:

int

class pyhmmer.easel.Randomness#

A portable, thread-safe random number generator.

Methods with an implementation in Easel are named after the equivalent methods of random.Random.

Added in version 0.4.2.

__init__(seed=None, fast=False)#

Create a new random number generator with the given seed.

Parameters:

  • seed (int) – The seed to initialize the generator with. If 0 or None is given, an arbitrary seed will be chosen using the system clock.

  • fast (bool) – If True, use a linear congruential generator (LCG), which is low quality and should only be used for integration with legacy code. With False, use the Mersenne Twister MT19937 algorithm instead.

copy()#

Return a copy of the random number generator in the same exact state.

getstate()#

Get a tuple containing the current state.

normalvariate(mu, sigma)#

Generate a Gaussian-distributed sample.

Parameters:

  • mu (float) – The mean of the Gaussian being sampled.

  • sigma (float) – The standard deviation of the Gaussian being sampled.

random()#

Generate a uniform random deviate on \(\left[ 0, 1 \right)\).

seed(n=None)#

Reinitialize the random number generator with the given seed.

Parameters:

n (int, optional) – The seed to use. If 0 or None, an arbitrary seed will be chosen using the current time.

setstate(state)#

Restores the state of the random number generator.

fast#

True when the linear congruential generator is in use.

Type:

bool

class pyhmmer.easel.SSIReader#

A read-only handler for sequence/subsequence index file.

class Entry(fd, record_offset, data_offset, record_length)#
data_offset#

Alias for field number 2

fd#

Alias for field number 0

record_length#

Alias for field number 3

record_offset#

Alias for field number 1

class FileInfo(name, format)#
format#

Alias for field number 1

name#

Alias for field number 0

__init__(file)#

Create a new SSI file reader for the file at the given location.

Parameters:

file (str, bytes or os.PathLike) – The path to a sequence/subsequence index file to read.

close()#

Close the SSI file reader.

file_info(fd)#

Retrieve the FileInfo of the descriptor.

find_name(key)#

Retrieve the Entry for the given name.

primary_keys#

The primary keys in the index.

Added in version 0.12.0.

Type:

collections.abc.Sequence of str

class pyhmmer.easel.SSIWriter#

A writer for sequence/subsequence index files.

__init__(file, exclusive=False)#

Create a new SSI file write for the file at the given location.

Parameters:

  • file (str, bytes or os.PathLike) – The path to a sequence/subsequence index file to write.

  • exclusive (bool) – Whether or not to create a file if one does not exist.

Raises:
add_alias(alias, key)#

Make alias an alias of key in the index.

add_file(filename, format=0)#

Add a new file to the index.

Parameters:

  • filename (str, bytes or os.PathLike) – The name of the file to register.

  • format (int) – A format code to associate with the file, or 0 by default.

Returns:

int – The filehandle associated with the new indexed file.

add_key(key, fd, record_offset, data_offset=0, record_length=0)#

Add a new entry to the index with the given key.

close()#

Close the SSI file writer.