nnfasta 0.1.7

Neural Net efficient Fasta

nnfasta

Neural Net efficient fasta Dataset for Training.

Should be memory efficient across process boundaries. So useful as input to torch/tensorflow dataloaders etc.

Presents a list of fasta files as a simple abc.Sequence so you can inquire about len(dataset) and retrieve Records with dataset[i]

Install

Install:

pip install nnfasta

There are no dependencies.

Usage

from nnfasta import nnfastas 

dataset = nnfastas(['athaliana.fasta','triticum.fasta','zmays.fasta'])

# display the number of sequences
print(len(dataset))

# get a particular record
rec = dataset[20]
print('sequence', rec.id, rec.description, rec.seq)

Warning: No checks are made for the existence of the fasta files. Also files of zero length will be rejected by mmap.

A Record mimics biopython's Record and is simply:

@dataclass
class Record:
    id: str
    """Sequence ID"""
    description: str
    """Line prefixed by '>'"""
    seq: str
    """Sequence stripped of whitespace and uppercased"""

    @property
    def name(self) -> str:
        return self.id