In BLAST+ to use remote databases, such as nr, you just add the -remote command along with the -db command. For example:

blastp -query my1000seqs.fasta -db nr -remote

Like Neil says, this is a very common task; indeed, if you just want to run the BLAST you describe (i.e. 10000 fasta sequences all in one file), you don't need to use perl or python, you can just give the one file with all the 100000 sequences in it as a query to blast directly

This should help: ftp://ftp.ncbi.nlm.nih.gov/blast/documents/web_blast.pl

I recommend you to download local blast in your computer and run the following:

• update_blastdb.pl nr
• for file in ls your_fasta_files_directory; do ./blastn -query $file -db nr -out $file.xml -task blastn -dust=yes -penalty=-3 -gapopen=5 -gapextend=2 -evalue 1e-10 -html=yes -besthitoverhang 0.1 -besthitscoreedge 0.1 -outfmt 5 -maxtargetseqs 10 -numthreads 4 -parse_deflines=yes; done

You can change parameter values as you want