extract raises an error if optional sites vcf input is not passed

[jethror1]

• biometrics version: 0.2.13
• Python version: 3.8
• Operating System: Ubuntu 20

Description

When running biometrics extract without --vcf specified, it results in the following error being raised:

This looks to stem from the fact that the vcf input is optional, and if not given the self.sites attribute remains an empty list from here:

biometrics/biometrics/extract.py

Line 34 in 1e87bd5

def _parse_vcf(self):

If the self.sites is then an empty list, the self.pileup attribute is left as None instead of being a DataFrame from here:

biometrics/biometrics/extract.py

Line 260 in 1e87bd5

def _extract_sites(self, sample):

When extract is then run, and save_to_file() is called, the above error is raised as self.pileup is None and not a dataframe:

biometrics/biometrics/sample.py

Line 38 in 1e87bd5

pileup_data = self.pileup.to_dict("records")