API Documentation

htsget.get(url, output, reference_name=None, reference_md5=None, start=None, end=None, fields=None, tags=None, notags=None, data_format=None, max_retries=5, retry_wait=5, timeout=120, bearer_token=None, headers=None)[source]

Runs a request to the specified URL and write the resulting data to the specified file-like object.

  • url (str) – The URL of the data to retrieve. This may be composed of a prefix such as http://example.com/reads/ and an ID suffix such as NA12878. The full URL must be supplied here, i.e., in this example http://example.com/reads/NA12878.
  • output (file) – A file-like object to write the downloaded data to. To support retrying of failed transfers, this file must be seekable. For this reason, retry will fail if stdout is provided.
  • reference_name (str) – The reference sequence name, for example “chr1”, “1”, or “chrX”. If unspecified, all data is returned.
  • reference_md5 (str) – The MD5 checksum uniquely representing the reference sequence as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (this is equivalent to SQ:M5 in SAM).
  • start (int) – The start position of the range on the reference, 0-based, inclusive. If specified, reference_name or reference_md5 must also be specified.
  • end (int) – The end position of the range on the reference, 0-based exclusive. If specified, reference_name or reference_md5 must also be specified.
  • data_format (str) – The requested format of the returned data.
  • max_retries (int) – The maximum number of times that an individual transfer will be retried.
  • retry_wait (float) – The amount of time in seconds to wait before retrying a failed transfer.
  • timeout (float) – The socket timeout for I/O operations.
  • bearer_token – The OAuth2 Bearer token to present to the htsget ticket server. If this value is specified, the token is provided to the ticket server using the Authorization: Bearer [token] header. If bearer_token is None or not specified, no Authorization header is sent to the server. Obtaining the bearer token is beyond the scope of htsget; consult the documentation for your server for information on authentication and how to obtain a valid token.
  • headers – Additional headers needed for the requests to the htsget service.