NCBITaxa() failing

[Jeff Bowman]

ete3 has been working great for me, but the NCBITaxa() function is suddenly failing at the "Inserting synonyms" step.  Traceback pasted below.  I tried a fresh install of ete3 on a different computer with the same result.

Inserting synonyms:      30000 Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/jsbowman/.local/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 110, in __init__
    self.update_taxonomy_database(taxdump_file)
  File "/home/jsbowman/.local/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 129, in update_taxonomy_database
    update_db(self.dbfile)
  File "/home/jsbowman/.local/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 760, in update_db
    upload_data(dbfile)
  File "/home/jsbowman/.local/lib/python3.6/site-packages/ete3/ncbi_taxonomy/ncbiquery.py", line 802, in upload_data
    db.execute("INSERT INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))
sqlite3.IntegrityError: UNIQUE constraint failed: synonym.spname, synonym.taxid

[fransua]

Hi Jeff,

just bumped into the same error.

A quick and dirty fix for me was to replace the line in ete:

db.execute("INSERT INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))

by:

db.execute("INSERT OR REPLACE INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))

before running your script again delete you ncbi DB (usually in ~/.etetoolkit/taxa.sqlite*)

cheers

francois

[Jeff Bowman]

Excellent, thanks Francois!

Jeff

[linshuc...@gmail.com]

it works!!! thx!!!

[pablo...@gmail.com]

Thank you!

[jan.d...@gmail.com]

Hi all,

I think this happens because of the "COLLATE NOCASE" statement used for creating the synonym table. Consequently taxid/synonym pairs that appear as identical because the case is not considered for comparison .. cause a SQLite insertion error..

So you can either delete this statement, or include the line :

db.execute("INSERT INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))

in a try / except block like this:

         try: db.execute("INSERT INTO synonym (taxid, spname) VALUES (?, ?);", (taxid, spname))

         except: print(i,taxid,spname)

That way you really don't modify the expected ouput of ete3 and get track of the taxid/synonym pairs that were skipped.

Jan

[jan.d...@gmail.com]

Le mercredi 9 septembre 2020 19:40:06 UTC+2, pablo...@gmail.com a écrit :