Function: fickett_score

def fickett_score(sequences, n_jobs= 1) -> np.ndarray:

Description

Compute the probability of each sequence to be a coding sequence. See the About section for more details.

Parameters

Parameter	Type	Default	Description
sequences	any iterable containing str	Required	Sequences to encode, can also be dna-parser SequenceReader, pysam FastxFile or Biopython SeqIO.read objects.
n_jobs	int	1	number of threads used to encode the sequences in parallel. 0 to use all CPUs available.

Returns

Type	Description
list[numpy.ndarray] or numpy.ndarray	Returns a 1D numpy.ndarray. Each entry is the probability of the given sequence to be a coding sequence.

Examples

import dna_parser as dps

sequences= ["agt","acc"]
encoding= dps.fickett_score(sequences)
print(encoding)

# Output:
#[0.3203 0.407 ]


reader= dps.SequenceReader("path/to/file") # file with sequences agt, acc, attagc
encoding= dps.fickett_score(reader)
print(encoding)
print(encoding.shape)

# Output:
#[0.3203     0.407      0.49100003]
#(3,)