Add script to convert genome to gene multiple fasta file

scripts/split-genome-to-gene.py

+#!/usr/bin/env python3
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+from pathlib import Path
+import click
+from itertools import chain
+import re
+
+
+@click.command()
+@click.option(
+    "-d",
+    "--directory",
+    type=click.Path(exists=True, dir_okay=True, file_okay=True),
+    help="Genome input source",
+)
+@click.option(
+    "-o", "--output-dir", type=click.Path("wb"), help="path to the output dir"
+)
+@click.option("-f", "--output-format", type=str, help="output sequence format")
+@click.option("-t", "--feature-type", type=str, help="")
+def split_genomes(directory, output_dir, output_format, feature_type):
+    genomes = gen_path_with_format(directory)
+    gen_genomes = gen_genomes_with_steam(genomes)
+    for filename, genome in gen_genomes:
+        write_sequence(genome, filename, output_dir, output_format, feature_type)
+
+
+def write_sequence(genome, filename, directory, sequence_format, feature_type):
+    with open(
+        Path(directory) / (filename + "." + sequence_format), "w"
+    ) as output_handle:
+        print("# Write file " + filename)
+        for record in genome:
+            for feat in record.features:
+                if feat.type == feature_type:
+                    feature_seq = feat.extract(record.seq)
+                    seq_record = SeqRecord(feature_seq)
+                    locus_tags = feat.qualifiers.get("locus_tag")
+                    product = feat.qualifiers.get("product")
+                    if locus_tags and len(locus_tags) > 0:
+                        seq_record.id = locus_tags[0]
+                        if product:
+                            p = re.compile(r"^\s+$")
+                            if not p.match(product[0]):
+                                seq_record.description = product[0]
+                        SeqIO.write(seq_record, output_handle, sequence_format)
+                    else:
+                        raise ("No locus tag !!!")
+
+
+def gen_path_with_format(input_str):
+    input_path = Path(input_str)
+    if input_path.is_dir():
+        for genome_path in chain(
+            map(lambda genome: ("embl", genome), input_path.rglob("*.embl")),
+            map(lambda genome: ("genbank", genome), input_path.rglob("*.genbank")),
+        ):
+            yield genome_path
+    else:
+        suffix = input_path.suffix
+        if suffix == ".embl":
+            yield ("embl", input_path)
+        else:
+            yield ("genbank", input_path)
+
+
+def gen_genomes_with_steam(genomes):
+    for genome_format, genome in genomes:
+        yield (str(Path(genome.stem)), SeqIO.parse(genome, genome_format))
+
+
+if __name__ == "__main__":
+    split_genomes()