Building blast+ databases with taxonomy ID (taxid_map)

Building NCBI BLAST+ databases with linked taxonomy is far more difficult than it should be.
For example, in taxonomy-based tools such as Kraken, mapping
1) taxonomy id to sequence id (gi or accession) and
2) taxonomy id to a human-readable taxonomy tree,
are built-in and transparent to the user.
Unfortunately, with BLAST+ these steps must be completed manually and are included in two separate programs, makeblastdb for (1) and blastn/blastp/blastx for (2).

(1) Taxonomy id <–> sequence id

In BLAST+, a taxid_map file file must be created and passed to makeblastdb

makeblastdb -in <FASTA file> -dbtype nucl -parse_seqids -taxid_map taxid_map.txt 

where taxid_map.txt is a space or tab separated list of sequence ids (either gi or accession) and taxonomy ids.
For example, with gi:

taxid_map.txt

556927176 4570
556926995 4573
501594995 3914

Alternatively with accession:

taxid_map.txt

NC_022714.1 4570
NC_022666.1 4573
NC_021092.1 3914

There is no turn-key way to generate this mapping taxid to sequence_id for a moderately large set of sequencing.

• Creating a look-up dictionary from the complete NCBI taxonomy database is memory prohibitive.
• Entrez API calls are capped at 3 per second.

Fortunately, there is always a hack work-around. NCBI allows export of both the FASTA and GenBank files. The former are used as the default input for makeblastdb, and the latter contain both the sequence_id and taxid. They can both be obtained from the NCBI, searching and exporting with Send to:

This simple Python code snippet will do the trick for small and moderately large datasets.

from Bio import SeqIO
genbankfile = "DNA.gb"
f = open('taxid_map.txt','w')
for gb in SeqIO.parse(genbankfile,"gb"):
    try:
        annotations = gb.annotations['gi']
        taxid = gb.features[0].qualifiers['db_xref'][0].split(':')[1]
        f.write("{} {}\n".format(annotations, taxid))
    except:
        pass
f.close()

For large datasets, the bandwidth cost of of downloading the GenBank from NCBI becomes prohibitive, and the dictionary approach would probably be warranted.
Download both the FASTA and GenBank, alternatively extract the FASTA from GenBank, e.g. with BioPython.

(2) Taxonomy id <–> Taxonomy tree

Simply include this NCBI database in the same directory as your database for the look-up to work with blastn/blastp/blastx: ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz

Eating your cake

blastn -db <DATABASE> -query <QUERY> -outfmt "10 qseqid sseqid pident staxids sscinames scomnames sblastnames sskingdoms"

1,gi|312233363|ref|NC_014692.1|,86.26,310261,Sus scrofa taiwanensis,Sus scrofa taiwanensis,even-toed ungulates,Eukaryota
1,gi|223976078|ref|NC_012095.1|,86.26,9825,Sus scrofa domesticus,domestic pig,even-toed ungulates,Eukaryota
1,gi|5835862|ref|NC_000845.1|,86.26,9823,Sus scrofa,pig,even-toed ungulates,Eukaryota

Your comma separated file (-outfmt) showing human-readable taxonomy info.