FR: get mitochondrial genes from genomepy for SCTK

[siebrenf]

import genomepy

def mito_genes(annotation_path):
    ann = genomepy.annotation(annotation_path)
    gtf = ann.named_gtf
    
    # very quick, very dirty way to find the name for the mitochondrion.
    # could also try to read this from the assembly report, but that's also not perfect. 
    mt = gtf[gtf["seqname"].str.contains("chrM", case=False, regex=False)]["seqname"].unique()
    if len(mt) != 1:
        mt = gtf[gtf["seqname"].str.contains("MT", case=False, regex=False)]["seqname"].unique()
    if len(mt) != 1:
        mt = gtf[gtf["seqname"].str.contains("mito", case=False, regex=False)]["seqname"].unique()
    if len(mt) != 1:
        mt = gtf[gtf["seqname"].str.contains("m", case=False, regex=False)]["seqname"].unique()
    if len(mt) != 1:
        print("we tried...")
        return {}
    
    genes = set(gtf[gtf["seqname"] == mt[0]].index)
    return genes

[Maarten-vd-Sande]

Could be a regex? Only the "m" one is tricky 😄

[stale]

Is this still relevant? If so, what is blocking it? Is there anything you can do to help move it forward?