biofiles

Pure-Python, zero-dependency collection of bioinformatics-related file readers and writers.

Installation

python -m pip install biofiles

Usage

Reading FASTA files:

from biofiles.fasta import FASTAReader

with FASTAReader("sequences.fasta") as r:
    for seq in r:
        print(seq.id, len(seq.sequence))

# or

with open("sequences.fasta") as f:
    r = FASTAReader(f)
    for seq in r:
        print(seq.id, len(seq.sequence))

Writing FASTA files:

from biofiles.fasta import FASTAWriter
from biofiles.types.sequence import Sequence

seq = Sequence(id="SEQ", description="Important sequence", sequence="GAGAGA")

with FASTAWriter("output.fasta") as w:
    w.write(seq)

Reading GFF genome annotations:

from biofiles.gff import GFFReader
from biofiles.dialects.gencode import GENCODE_DIALECT
from biofiles.dialects.genomic_base import Gene

with GFFReader("GCF_009914755.1_T2T-CHM13v2.0_genomic.gff", dialect=GENCODE_DIALECT) as r:
    for feature in r:
        if isinstance(feature, Gene):
            print(feature.name, len(feature.exons))

Currently three dialects are supported:

biofiles.dialects.gencode.GENCODE_DIALECT for GENCODE genome annotation;
biofiles.dialects.refseq.REFSEQ_DIALECT for RefSeq genome annotation;
biofiles.dialects.stringtie.STRINGTIE_DIALECT for StringTie output files.

License

MIT license, see License.

Metadata

Release files for biofiles 0.1.10

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for biofiles 0.1.10
File	Size	Uploaded
biofiles-0.1.10.tar.gz	20.9 kB	Apr 12, 2026	Details

Built distribution (wheel)

Table of built distributions (wheels) for biofiles 0.1.10
File	Interpreter	ABI	Platform	Reset
biofiles-0.1.10-py3-none-any.whl 27.0 kB Apr 12, 2026	Python 3	none	any	Details

Total release size: 47.9 kB

Release files / biofiles-0.1.10.tar.gz

Download URL	biofiles-0.1.10.tar.gz
Size	20.9 kB
Tags	Source
SHA-256 checksum How to use checksums	`43fdc004ba350ad4089fa76f814921c6be37db82deb6bed210ecf550e7819eb4`
BLAKE2b-256 checksum How to use checksums	`d055cfe634979c7aa5271af05045a4c7c19207873dd4aec3f6e44bf4ebcc30ed`
Upload date	Apr 12, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.0.1 CPython/3.11.9`

Release files / biofiles-0.1.10-py3-none-any.whl

Download URL	biofiles-0.1.10-py3-none-any.whl
Size	27.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`5f72a9012b30757a616045df20503584f9423066751d244ab41bb6a021d20c8c`
BLAKE2b-256 checksum How to use checksums	`5bb91fb9aaad6c401ae8e7d8fa47784776c3f8a9a24059c0a2b64b1ea75d2303`
Upload date	Apr 12, 2026
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/6.0.1 CPython/3.11.9`