Thursday, May 10, 2018

Downloading sequences from NCBI:

This downloads the GenBank file and puts it into a file called CP011547.gbk (Just change the accession number in the first line to download any other sequence):
curl -s  "${i}&rettype=gb&retmode=txt">$i.gbk

The sequence as nucleotide fasta:
curl -s  "${i}&rettype=fasta&retmode=txt">$i.fna

The CDS as protein fasta:
curl -s  "${i}&rettype=fasta_cds_aa&retmode=txt">$i.cds.faa

The CDS as nucleotide fasta:
curl -s  "${i}&rettype=fasta_cds_na&retmode=txt">$i.cds.fna