modos.genomics.refget

refget loader implementation

In the refget specifications each sequence object is associated by a metadata object. Metadata provide a json encoded list of all known identifiers and aliases (see [1]).

Sequence and metadata objects must have content-type header to fulfill the refget specification.

In S3 redirection can be used to enable sequence access via different ids. This can be achieved by an empty object with the alternative id as filename and a Website-Redirect-Location header mapping to the sequence location (see [2]).

References

[1]

http://samtools.github.io/hts-specs/refget.html

[2]

ga4gh/refget-cloud

Classes

RefgetStorage

Functions

calculate_checksums(seq)
upload_to_s3(fs, bucket, key[, data, headers])

Module Contents

class modos.genomics.refget.RefgetStorage

fs: s3fs.S3FileSystem

bucket: str

upload_seq(seq, primary='md5', checksums=None)

Parameters:

• seq (str)

• primary (str)

• checksums (Optional[Dict[str, str]])

upload_fasta(fasta_file)

Parameters:

fasta_file (str)

modos.genomics.refget.calculate_checksums(seq)

Parameters:

seq (str)

Return type:

Dict

modos.genomics.refget.upload_to_s3(fs, bucket, key, data='', headers=None)

Parameters:

• fs (s3fs.S3FileSystem)

• bucket (str)

• key (str)

• data (str)

• headers (Optional[Dict[str, str]])