Skip to main content

FASTA file reader

Project description

fasta-reader-py

FASTA file reader/writer.

Examples

Open a file and loop over its contents.

from fasta_reader import read_fasta

for item in read_fasta("fasta_reader/test/correct1.faa"):
  print(item)
# FASTAItem(defline='ID1', sequence='GAGUUA')
# FASTAItem(defline='ID2', sequence='CAUAACAAATT')
# FASTAItem(defline='ID3', sequence='AAGAA')
# FASTAItem(defline='ID4', sequence='AAGAA')

Open a compressed file and show the first item.

from fasta_reader import read_fasta

with read_fasta("fasta_reader/test/protein.faa.gz") as file:
    item = file.read_item()
    print(item.defline, item.sequence[:10] + "...")
# P01013 GENE X PROTEIN (OVALBUMIN-RELATED) QIKDLLVSSS...

Write to output.faa.gz.

from fasta_reader import write_fasta

with write_fasta("output.faa.gz") as file:
    file.write_item("id1 gene x protein", "AGUTAGA")
    file.write_item("id2 gene x protein", "TUUA")

Install

pip install fasta-reader

Author

License

This project is licensed under the MIT License.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

fasta-reader-1.0.0.tar.gz (8.7 kB view hashes)

Uploaded Source

Built Distribution

fasta_reader-1.0.0-py3-none-any.whl (10.7 kB view hashes)

Uploaded Python 3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page