Anna Syme

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Biopython

Install

pip install biopython

Make the python file

nano get_genes.py

In the file, add this:

#!/usr/bin/python

from Bio import SeqIO

# define the function
# it needs a certain object as input

def get_genes(seq_record):
    for feature in seq_record.features:
        if feature.type == "gene":
            print(feature.qualifiers.get("gene"))

# the `get` part is used to access the dictionary value (gene name) given the key ("gene")

# make an object by providing the filename and file type
genome_record = SeqIO.read("chloro.gbk", "genbank")

# run the function
get_genes(genome_record)

Run

python get_genes.py