The bioBakery help forum

Error:customizing the database

I want to use this function of metaphlan3.0, customizing the database. It seems that there is no fungus I need in the database. I added the marker sequence stored in a file new_marker.fasta to the marker. And the new marker was extracted from Microsporidia genome. I executed the following command, but got an error:

import pickle
import bz2

db = pickle.load(bz2.open(‘metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.pkl’, ‘r’))

db[‘taxonomy’][‘k__Fungi|p__Fungi_incertae_sedis|c__Microsporidia|o__Apansporoblastina|f__Unikaryonidae|g__Encephalitozoon|s__Encephalitozoon_intestinalis’]=(||||||2591,2216898)
File “”, line 1
db[‘taxonomy’][‘k__Fungi|p__Fungi_incertae_sedis|c__Microsporidia|o__Apansporoblastina|f__Unikaryonidae|g__Encephalitozoon|s__Encephalitozoon_intestinalis|t__GCA_000146465.1’]=(’||||||2591’,2216898)
^
SyntaxError: invalid syntax

Make sure that you are using single quotes instead of backquotes, probably this happened if you copy-pasted the code from the wiki