Basic usage¶

Here we introduce the three basic operations on a coding space: counting, sampling and enumeration.

Counting¶

To create a coding space and count sequences:

from codeine import CodingSpace

space = CodingSpace('SEQVENCE')

print(f"{space.n_valid_sequences} valid coding sequences")

Output:

1536 valid coding sequences

Coding sequences for the chosen amino acid sequence can be obtained by randomly sampling the space. For example:

from codeine import CodingSpace

space = CodingSpace('SEQVENCE', seed=42)

print(space.sample())

Output:

TCGGAACAAGTTGAGAACTGCGAA

You can also sample batches of sequences:

for seq in space.sample(5):
    print(seq)

Output:

TCGGAACAAGTTGAGAACTGCGAA
TCAGAACAAGTAGAAAATTGCGAG
TCCGAGCAGGTTGAGAACTGTGAA
AGCGAACAAGTTGAGAACTGCGAG
TCGGAGCAAGTAGAGAACTGCGAG

Coding spaces can be iterated over or enumerated. Full enumeration is only practical for relatively small spaces. You can do:

from codeine import CodingSpace

space = CodingSpace('MILK')

for seq in space.enumerate():
    print(seq)

Or simply:

for seq in space:
   print(seq)

Output:

 ATGATTTTAAAA
 ATGATTTTAAAG
 ATGATTTTGAAA
 ATGATTTTGAAG
 ATGATTCTTAAA
 ATGATTCTTAAG
...

You can also just grab the first few sequences:

from codeine import CodingSpace

space = CodingSpace('SEQVENCE')

for seq in space[:3]:
   print(seq)

Output:

ATGATTTTAAAA
ATGATTTTAAAG
ATGATTTTGAAA