extract_features_from_genbank uses isolate as strain id, if strain is…

[vinuesa]

extract_features_from_genbank in phyTools.pm now uses isolate as a strain ID if the strain attribute is undefined.

[eead-csic-compbio]

Thanks @vinuesa , I guess

elsif($f->has_tag('isolate') and !$f->has_tag('strain'))

should be simply

elsif($f->has_tag('isolate'))

Can you please propagate this change to all extract_*_from_genbank subs?

[vinuesa]

Hi @eead-csic-compbio, the proposed code snippet avoids overwriting the strain qualifier in the few cases when both strain and isolate are defined in the GenBank file, which can differ, resulting in the isolate tag being assigned to strain. What do you think?

[eead-csic-compbio]

Hola @vinuesa , then I guess it should be something like this?

elsif($strain eq ''  && $f->has_tag('isolate'))