bio fetch: get data

bio can fetch data from GenBank or from Ensembl.

Fetch data from GenBank

You may use multiple accession numbers:

bio fetch NC_045512 MN996532 > genomes.gb

You may pipe accession numbers into the tool

echo NC_045512 | bio fetch > genomes.gb

the fetch task is not a replacement for other means of accessing NCBI, notably entrez-direct. Instead, think of it as a convenience function that simplifies a few common use cases.

For more advance command line data access options see Entrez Direct:

Fetch data from Ensembl

bio fetch recognzies Ensemble gene and transcript names (ENSG, ENST) and will automatically connect to the Ensembl REST API:

bio fetch ENSG00000157764 | head

# Transcript data un genomic context
bio fetch ENST00000288602  | head

# Transcript data as CDNA
bio fetch ENST00000288602 --type cdna | head

# Transcript data as CDS
bio fetch ENST00000288602 --type cds | head

# Transcript data as protein
bio fetch ENST00000288602 --type cds | head

For more information see the Ensembl REST API: