Command Line Interface

To use command line interface, first install the package using pip3. You can then access Fetcher functions using ref-seq-fetcher

ref-seq-fetcher --help

ref-seq-fetcher [OPTIONS] COMMAND [ARGS]...

Options:
--help  Show this message and exit.

Commands:
metadata  retrieve metadata using base_url and checksum
sequence  retrieve sequence using base_url and checksum

To retrieve service-info

ref-seq-fetcher info --help

info [OPTIONS] BASE_URL

retrieve service info using base_url

Options:
--help  Show this message and exit.

Examples

ref-seq-fetcher info https://www.ebi.ac.uk/ena/cram/

{"service": {"circular_supported": "true", "subsequence_limit": 4000000, "algorithms": ["md5", "trunc512"], "supported_api_versions": ["1.0"]}}

To retrieve a sequence

ref-seq-fetcher sequence --help

sequence [OPTIONS] BASE_URL CHECKSUM

retrieve sequence using base_url and checksum

Options:
 -s, --start INTEGER   first byte of the checksum. 0-start inclusive
 -e, --end INTEGER     last byte of the checksum. 0-start exclusive
 --help                Show this message and exit.

server_base_url and checksum are required arguments while rest are optional. It internally invokes classmethod sequence of Fetcher.

Examples

ref-seq-fetcher sequence https://www.ebi.ac.uk/ena/cram/ 6681ac2f62509cfc220d78751b8dc524
CCACA........GTGGG

ref-seq-fetcher sequence https://www.ebi.ac.uk/ena/cram/ 6681ac2f62509cfc220d78751b8dc524 --start 10 --end 20
CCCACACACC

ref-seq-fetcher sequence https://www.ebi.ac.uk/ena/cram/ 3332ed720ac7eaa9b3655c06f6b9e196 -s 5374 -e 5
ATCCAACCTGCAGAGTT

To retrieve a metadata

ref-seq-fetcher metadata --help

retrieve metadata using base_url and checksum

Options:
  --help                Show this message and exit.

server_base_url and checksum are required arguments while rest are optional. It internally invokes classmethod metadata of Fetcher.

Examples

ref-seq-fetcher metadata https://www.ebi.ac.uk/ena/cram/ 3332ed720ac7eaa9b3655c06f6b9e196 > metadata.json