Fill in taxonomic ranks from relatives

[dcdanko]

Add a script that fills in taxonomic ranks from their relatives.

e.g.

• If a genus has n/a for spore forming check all its children and set the value to always/sometimes/never/na.
• If a species has n/a for gram-stain check if gram-stain is defined by one of its parents

[Chandrima-04]

Updated code in cli.py

New output have integrated results

[dcdanko]

Most (all?) rows for taxonomic ranks higher than genus are still completely unfilled

[Chandrima-04]

Most (all?) rows for taxonomic ranks higher than genus are still completely unfilled

That is because the information concerning the rows were not present.

• In cases for which we do not know for certain that the Genus is spore forming or not at all, species could not be filled.

• If either the species or genus did not have prior information about gram-stain, it is not possible to fill it until and unless it is manually annotated for either Genus or Species... The code just checks whether any level below Genus have gram-stain info, and fills it up for all species in the genus......

[Chandrima-04]