essential_genes_from_tables.py 文件源码

def parse_gene_id_and_name():
    """return a mapping of genes ids to gene names/description as dictionary

    deliberately only looking at protein coding genes
    """

    gene_id_to_name = dict()

    # modelled after http://genome.crg.es/~lpryszcz/scripts/gb2gtf.py
    #allowed_types = set(['gene', 'CDS', 'tRNA', 'tmRNA', 'rRNA', 'ncRNA'])
    allowed_types = set(['CDS'])
    #wanted_qualifiers = set(['product', 'locus_tag'])
    with open(GB_FILE) as fh:
        for gb in SeqIO.parse(fh, 'gb'):
            for f in gb.features:
                if f.type not in allowed_types:
                    continue
                qualifiers = dict(f.qualifiers)
                assert len(qualifiers['locus_tag'])==1 and len(qualifiers['product'])==1
                gene_id = qualifiers['locus_tag'][0]
                gene_name = qualifiers['product'][0]
                assert len(qualifiers['locus_tag']) == 1, (qualifiers['locus_tag'])
                gene_id_to_name[gene_id] = gene_name
    return gene_id_to_name