INNER CODE UNIT · Python

set_gene_data

BortonWrightonLabs/DRAM · bin/combine_annotations.py:97

def set_gene_data(gene_faa, genes_faa_dict=None):
    if genes_faa_dict is None:
        genes_faa_dict = dict()
    for seq in read_sequence(gene_faa, format="fasta"):
        if seq.metadata["id"] not in genes_faa_dict:
            genes_faa_dict[seq.metadata["id"]] = {}

        split_label = seq.metadata["id"].split("_")
        gene_position = split_label[-1]
        start_position, end_position, strandedness = seq.metadata["description"].split(
            "#"
        )[1:4]

        input_fasta_name = Path(gene_faa).stem.split("_called_genes")[0]
        genes_faa_dict[seq.metadata["id"]][FASTA_COLUMN] = input_fasta_name
        genes_faa_dict[seq.metadata["id"]]["scaffold"] = (
            seq.metadata["id"]
            .removeprefix(genes_faa_dict[seq.metadata["id"]][FASTA_COLUMN])

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