Feat: Filter adVNTR results to exclude false positives like D23_2

[berntpopp]

adVNTr outputs some false positive calls like D23_2.
This shoudl be filtered

We need a logic.

Is this available in version 1.3?

[hassansaei]

The logic was implemented in version 1.3 with functions: advntr_processing_del and advntr_processing_ins

def advntr_processing_del(df):

df1 = df.copy()
df1.rename(columns={'State': 'Variant', 'Pvalue\n':'Pvalue'}, inplace = True)
df1['Deletion_length'] = df1['Variant'].str.count('D').add(0).fillna(0)
df1['Insertion'] = df1['Variant'].str.count('I').add(0).fillna(0)
df1['Insertion_len'] = df1['Variant'].str.extract('(LEN.*)')
df1.Insertion_len = df1.Insertion_len.fillna('LEN')
df1[['I', 'Insertion_len']]= df1['Insertion_len'].str.split('LEN', expand=True)
df1.Insertion_len = df1.Insertion_len.replace('', 0)
df1.Deletion_length = df1.Deletion_length.fillna('0')
df1.Deletion_length = df1.Deletion_length.astype(int)
df1.Insertion_len = df1.Insertion_len.astype(int)
df1['frame'] = abs(df1.Insertion_len - df1.Deletion_length)
df1.frame = df1['frame'].astype(str)
df1 = df1.loc[(df1['Deletion_length'] >= 1)]
df1 = df1[df1['frame'].isin(del_frame)]

return df1

def advntr_processing_ins(df):

dff = df.copy()
dff.rename(columns={'State': 'Variant', 'Pvalue\n':'Pvalue'}, inplace = True)
dff['Deletion_length'] = dff['Variant'].str.count('D').add(0).fillna(0)
dff['Insertion'] = dff['Variant'].str.count('I').add(0).fillna(0)
dff['Insertion_len'] = dff['Variant'].str.extract('(LEN.*)')
dff.Insertion_len = dff.Insertion_len.fillna('LEN')
dff[['I', 'Insertion_len']]= dff['Insertion_len'].str.split('LEN', expand=True)
dff.Insertion_len = dff.Insertion_len.replace('', 0)
dff.Deletion_length = dff.Deletion_length.fillna('0')
dff.Deletion_length = dff.Deletion_length.astype(int)
dff.Insertion_len = dff.Insertion_len.astype(int)
dff['frame'] = abs(dff.Insertion_len - dff.Deletion_length)
dff.frame = dff['frame'].astype(str)
dff = dff.loc[(dff['Insertion_len'] >= 1)]
dff = dff[dff['frame'].isin(ins_frame)]
     
return dff

[berntpopp]

ok, I will reimplement this.