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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


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