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
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: