***** Exome

def readPanel(root):
    d = pd.read_csv(root /
                    "MiSeq coverage_2022-02-02_12-31-54.tsv",
                    sep= "\t")
    # Clean up data first
    return d[['patientID', 'specimenID', 'target']]

def readReports(root):
    d = pd.read_csv(root    /
                    "Compte-rendus_2022-02-02_12-37-37.tsv",
                    sep= "\t")
    # Clean up data first
    return d[['patientID', 'sampleID',
              'examen', 'resultat',  'interpretation', 'signataire', 'date_rendu']]
def cleanPanel(d):
    cols = ['nom', 'prenom', 'date_de_naissance',
        'sexe', 'parente', 'statut',
        'clinicien_referent', 'clinicien_referentinstitution', 'pathologie',
        'gene',
        'sampleIDdate_de_reception', 'sampleIDorigine_de_l_echantillon',
        'target',
        'examen', 'resultat', 'signataire', 'date_rendu',
        'commentaires', 'commentairespatient']
    d = d[cols].rename(columns = {"gene": "gene_responsable"})
    # Remove none
    d['gene_responsable'].replace("None", "", inplace=True)
    return d

    # Merge exome and sample
    e = readExome(root)
    d = dna.set_index("sampleID").join(e.set_index("specimenID"),

    # Merge panel and sample
    r = readPanel(root)
    d = dna.set_index("sampleID").join(r.set_index("specimenID"),

                                    lsuffix="dna", rsuffix="exome")

                                    lsuffix="dna", rsuffix="panel")

                                        how="inner")

                                        how="inner", lsuffix="patient")
    rep = readReports(root)
    d3 = d2.join(rep.set_index("patientID"), how="inner", lsuffix="cr")

    d2 = cleanExome(d2)
    d2.to_excel(root / "exome dijons.xlsx")

    d3 = cleanPanel(d3)
    d3.to_excel(root / "panel dijon.xlsx")

root = Path("/mnt/c/Users/apraga/Documents/mustard")

root = Path("/mnt/c/Users/alexi/Documents/mustard")

# panel = pd.read_csv(root / "MiSeq coverage_2022-02-02_12-31-54.tsv",
#                     sep = "\t")
# panel = panel[[]]
# print(panel.columns)

#+end_src

#+RESULTS:

#+end_src
***** Panel