You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
(This was already mentioned in #13 (comment), but I think it is better to have a separate issue.)
ncbi-acc-download --format fasta --recursive --verbose AAXATB000000000.1 creates an empty fasta file, while ncbi-acc-download --format genbank --recursive --verbose AAXATB000000000.1 creates a genbank file as expected.
The same thing happened when I tried on ACIN00000000.3.
The text was updated successfully, but these errors were encountered:
IIUC, an easy fix is to implement --format fasta by using --format genbank (the default) and then using SeqIO.convert (from Biopython), e.g.: SeqIO.convert('AAXATB000000000.1.gbk', 'genbank', 'AAXATB000000000.1.gbk.fasta', 'fasta')
The NCBI Entrez API does deliver FASTA files, just not if you query for WGS master entries.
I don't really want to depend on Biopython for all of ncbi-genome-download, but arguably we could go that path if --recursive is specified, as we depend on Biopython for --recursive anyway.
(This was already mentioned in #13 (comment), but I think it is better to have a separate issue.)
ncbi-acc-download --format fasta --recursive --verbose AAXATB000000000.1
creates an empty fasta file, whilencbi-acc-download --format genbank --recursive --verbose AAXATB000000000.1
creates a genbank file as expected.The same thing happened when I tried on
ACIN00000000.3
.The text was updated successfully, but these errors were encountered: