Function: eiip_encoding
def eiip_encoding(sequences, pad_type= "after", pad_length= 0, n_jobs= 1) -> list[np.ndarray] | np.ndarray:
Description
Encodes sequences converting each nucleotide to its electron-ion interaction pseudopotential (EIIP):
- A= 0.1260
- C= 0.1340
- G= 0.0806
- T/U= 0.1335
- Other characters or gaps = 0.0
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. |
pad_type |
str |
after |
Whether to trim/pad at the front or at the back of the sequences. Options are before and after. This paramater is ignored if there is no padding |
pad_length |
int |
0 |
Length for padding/trimming. -2 to pad to the longest sequence, -1 to trim to the shortest sequence, any positive integer for a fixed length. |
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 |
The encoded sequences. Returns a list of 1D numpy arrays if there is no trimming/padding, otherwise returns a 2D numpy array with rows representing sequences. |
Examples
import dna_parser as dps
sequences= ["agt","acc"]
encoding= dps.eiip_encoding(sequences)
print(encoding)
# Output:
#[array([0.126 , 0.0806, 0.1335]), array([0.126, 0.134, 0.134])]
reader= dps.SequenceReader("path/to/file") # file with sequences agt, acc, attagc
encoding= dps.eiip_encoding(reader, pad_type="after", pad_length=-2) #pad after the sequences to the longest one
print(encoding)
print(encoding.shape)
# Output:
#[[0.126 0.0806 0.1335 0. 0. 0. ]
# [0.126 0.134 0.134 0. 0. 0. ]
# [0.126 0.1335 0.1335 0.126 0.0806 0.134 ]]
#
#(3, 6)