Request type
Extension of existing module
Request description
The default BLAST database for NCBI web blast is now core_nt; this database doesn't seem to be supported by gget blast currently.
Example command
ec2-user@ip-172-31-36-217:long_reads ❯ gget blast -p blastn -db core_nt -l 10 -o blast-out.txt subsample.fasta main
usage: gget blast [-h] [-p {blastn,blastp,blastx,tblastn,tblastx}] [-db {nt,nr,refseq_rna,refseq_protein,swissprot,pdbaa,pdbnt}] [-l LIMIT]
[-e EXPECT] [-lcf] [-mbo] [-q] [-csv] [-o OUT] [-seq SEQ_DEPRECATED] [-j]
sequence
gget blast: error: argument -db/--database: invalid choice: 'core_nt' (choose from nt, nr, refseq_rna, refseq_protein, swissprot, pdbaa, pdbnt)Example return value
No response
Request type
Extension of existing module
Request description
The default BLAST database for NCBI web blast is now core_nt; this database doesn't seem to be supported by
gget blastcurrently.Example command
ec2-user@ip-172-31-36-217:long_reads ❯ gget blast -p blastn -db core_nt -l 10 -o blast-out.txt subsample.fasta main usage: gget blast [-h] [-p {blastn,blastp,blastx,tblastn,tblastx}] [-db {nt,nr,refseq_rna,refseq_protein,swissprot,pdbaa,pdbnt}] [-l LIMIT] [-e EXPECT] [-lcf] [-mbo] [-q] [-csv] [-o OUT] [-seq SEQ_DEPRECATED] [-j] sequence gget blast: error: argument -db/--database: invalid choice: 'core_nt' (choose from nt, nr, refseq_rna, refseq_protein, swissprot, pdbaa, pdbnt)Example return value
No response