NCBIStandalone package is missing

Question

[Valentin]

Hello, I am trying to follow the example pipeline here https://biopython.org/wiki/Phylo (at the end of the page). When I run the first cell:

from Bio.Blast import NCBIStandalone, NCBIXML
query_fname = "AAG35789.fasta"
result_handle, error_handle = NCBIStandalone.blastall(
    "/usr/bin/blastall", "blastp", "/db/fasta/swissprot", query_fname
)
blast_record = NCBIXML.read(result_handle)  

# This takes some time to run

I see that the package NCBIStandalone is not in Bio.Blast. How can I fix it? Thank you!

[Sej Modha]

It seems that the error might be because the NCBIStandalone module has been deprecated, see the blog post below.

Code for calling standalone BLAST and parsing plain text output (DEPRECATED).

Source: https://homolog.us/Biopython/Bio.Blast.NCBIStandalone.html