How to make surpi db for new NCBI accession2taxid files #36
Description
I modified the create_taxonomy shell and python scripts with replacing "gi_taxid_nucl.dmp.gz" into ”nucl_gb.accession2taxid.gz“ and also replacing such filename for protein.
However, when it comes to the step 4 of create_taxonomy shell script, there is always an error:
Starting creation of taxonomy SQLite databases...
Creating names_nodes_scientific.db...
Creating taxid_prot.db...
Traceback (most recent call last):
File "/mnt/upan/share/surpi/create_taxonomy_db.py", line 76, in
c.execute("INSERT INTO gi_taxid VALUES ("+line[0]+","+line[1]+")")
sqlite3.OperationalError: no such column: accession
I found that there is actually "accession" in the header of corresponding files, so, where should I modify to correctly build the surpi protein and nucleotide db?