Computing digests locally¶

Introduction¶

This tutorial shows you how to compute GA4GH content-addressable identifiers for sequences and FASTA files using the refget package.

New to GA4GH digests?

See What are GA4GH digests? for background on why content-addressable identifiers matter.

Learning objectives

• Compute a refget sequence digest for a sequence
• Compute a refget sequence collection digest from a FASTA file
• Understand level 1 and level 2 representations

Computing a sequence digest¶

Use sha512t24u_digest() to compute the GA4GH digest for any string:

In [1]:

from refget.digests import sha512t24u_digest
from refget.store import digest_fasta
from refget.utils import fasta_to_seqcol_dict

from refget.digests import sha512t24u_digest from refget.store import digest_fasta from refget.utils import fasta_to_seqcol_dict

In [2]:

sha512t24u_digest('GGAA')

sha512t24u_digest('GGAA')

Out[2]:

'YBbVX0dLKG1ieEDCiMmkrTZFt_Z5Vdaj'

Computing a collection digest from FASTA¶

For a FASTA file containing multiple sequences, compute the top-level collection digest:

In [3]:

digest_fasta('../../../test_fasta/base.fa').digest

digest_fasta('../../../test_fasta/base.fa').digest

Out[3]:

'XZlrcEGi6mlopZ2uD8ObHkQB1d0oDwKk'

Getting the full sequence collection (level 2)¶

To see the complete sequence collection representation with all attributes (names, lengths, sequences, and derived attributes), use fasta_to_seqcol_dict():

Note: sequences contains SQ.-prefixed digests for each sequence. The sorted_* attributes enable order-independent comparison.

In [4]:

fasta_to_seqcol_dict('../../../test_fasta/base.fa')

fasta_to_seqcol_dict('../../../test_fasta/base.fa')

Out[4]:

{'lengths': [8, 4, 4],
 'names': ['chrX', 'chr1', 'chr2'],
 'sequences': ['SQ.iYtREV555dUFKg2_agSJW6suquUyPpMw',
  'SQ.YBbVX0dLKG1ieEDCiMmkrTZFt_Z5Vdaj',
  'SQ.AcLxtBuKEPk_7PGE_H4dGElwZHCujwH6'],
 'sorted_name_length_pairs': ['IWFt7HQ4XoMk34U27BKO-4szSRifP6H5',
  'chDD8A4S8YZKNNctCimHasAA2Dn596SZ',
  'enZNOGccwFbN9yJ3YZVifFTFCVA9hIpH'],
 'sorted_sequences': ['SQ.iYtREV555dUFKg2_agSJW6suquUyPpMw',
  'SQ.YBbVX0dLKG1ieEDCiMmkrTZFt_Z5Vdaj',
  'SQ.AcLxtBuKEPk_7PGE_H4dGElwZHCujwH6']}

Iterating over sequences¶

For lower-level access to individual sequence metadata (name, length, digests), use the digest_fasta function. This returns an iterator over each sequence:

Summary

• sha512t24u_digest() computes GA4GH digests for sequences
• digest_fasta() computes collection digests from FASTA files
• fasta_to_seqcol_dict() returns full level 2 sequence collection data