bioutils.digests module

bioutils.digests.seq_md5(seq, normalize=True)[source]

Converts sequence to unicode md5 hex digest.

Parameters

  • seq (str) – A sequence.

  • normalize (bool, optional) – Whether to normalize the sequence before conversion, i.e. to ensure representation as uppercase letters without whitespace or asterisks. Defaults to True.

Returns

Unicode md5 hex digest representation of sequence.

Return type

str

Examples

>>> seq_md5('')
'd41d8cd98f00b204e9800998ecf8427e'

>>> seq_md5('ACGT')
'f1f8f4bf413b16ad135722aa4591043e'

>>> seq_md5('ACGT*')
'f1f8f4bf413b16ad135722aa4591043e'

>>> seq_md5(' A C G T ')
'f1f8f4bf413b16ad135722aa4591043e'

>>> seq_md5('acgt')
'f1f8f4bf413b16ad135722aa4591043e'

>>> seq_md5('acgt', normalize=False)
'db516c3913e179338b162b2476d1c23f'
bioutils.digests.seq_seguid(seq, normalize=True)[source]

Converts sequence to seguid.

This seguid is compatible with BioPython’s seguid.

Parameters

  • seq (str) – A sequence.

  • normalize (bool, optional) – Whether to normalize the sequence before conversion, i.e. to ensure representation as uppercase letters without whitespace or asterisks. Defaults to True.

Returns

seguid representation of sequence.

Return type

str

Examples

>>> seq_seguid('')
'2jmj7l5rSw0yVb/vlWAYkK/YBwk'

>>> seq_seguid('ACGT')
'IQiZThf2zKn/I1KtqStlEdsHYDQ'

>>> seq_seguid('acgt')
'IQiZThf2zKn/I1KtqStlEdsHYDQ'

>>> seq_seguid('acgt', normalize=False)
'lII0AoG1/I8qKY271rgv5CFZtsU'
bioutils.digests.seq_seqhash(seq, normalize=True)[source]

Converts sequence to 24-byte Truncated Digest.

Parameters

  • seq (str) – A sequence.

  • normalize (bool, optional) – Whether to normalize the sequence before conversion, i.e. to ensure representation as uppercase letters without whitespace or asterisks. Defaults to True.

Returns

24-byte Truncated Digest representation of sequence.

Return type

str

Examples

>>> seq_seqhash("")
'z4PhNX7vuL3xVChQ1m2AB9Yg5AULVxXc'

>>> seq_seqhash("ACGT")
'aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'

>>> seq_seqhash("acgt")
'aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'

>>> seq_seqhash("acgt", normalize=False)
'eFwawHHdibaZBDcs9kW3gm31h1NNJcQe'
bioutils.digests.seq_sha1(seq, normalize=True)[source]

Converts sequence to unicode sha1 hexdigest.

Parameters

  • seq (str) – A sequence.

  • normalize (bool, optional) – Whether to normalize the sequence before conversion, i.e. to ensure representation as uppercase letters without whitespace or asterisks before encoding. Defaults to True.

Returns

Unicode sha1 hexdigest representation of sequence.

Return type

str

Examples

>>> seq_sha1('')
'da39a3ee5e6b4b0d3255bfef95601890afd80709'

>>> seq_sha1('ACGT')
'2108994e17f6cca9ff2352ada92b6511db076034'

>>> seq_sha1('acgt')
'2108994e17f6cca9ff2352ada92b6511db076034'

>>> seq_sha1('acgt', normalize=False)
'9482340281b5fc8f2a298dbbd6b82fe42159b6c5'
bioutils.digests.seq_sha512(seq, normalize=True)[source]

Converts sequence to unicode sha512 hexdigest.

Parameters

  • seq (str) – A sequence.

  • normalize (bool, optional) – Whether to normalize the sequence before conversion, i.e. to ensure representation as uppercase letters without whitespace or asterisks. Defaults to True.

Returns

Unicode sha512 hexdigest representation of sequence.

Return type

str

Examples

>>> seq_sha512('')
'cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e'

>>> seq_sha512('ACGT')
'68a178f7c740c5c240aa67ba41843b119d3bf9f8b0f0ac36cf701d26672964efbd536d197f51ce634fc70634d1eefe575bec34c83247abc52010f6e2bbdb8253'

>>> seq_sha512('acgt')
'68a178f7c740c5c240aa67ba41843b119d3bf9f8b0f0ac36cf701d26672964efbd536d197f51ce634fc70634d1eefe575bec34c83247abc52010f6e2bbdb8253'

>>> seq_sha512('acgt', normalize=False)
'785c1ac071dd89b69904372cf645b7826df587534d25c41edb2862e54fb2940d697218f2883d2bf1a11cdaee658c7f7ab945a1cfd08eb26cbce57ee88790250a'
bioutils.digests.seq_vmc_id(seq, normalize=True)[source]

Converts sequence to VMC id.

See https://github.com/ga4gh/vmc

Parameters

  • seq (str) – A sequence.

  • normalize (bool, optional) – Whether to normalize the sequence before conversion, i.e. to ensure representation as uppercase letters without whitespace or asterisks. Defaults to True.

Returns

VMC id representation of sequence.

Return type

str

Examples

>>> seq_vmc_id("")
'VMC:GS_z4PhNX7vuL3xVChQ1m2AB9Yg5AULVxXc'

>>> seq_vmc_id("ACGT")
'VMC:GS_aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'

>>> seq_vmc_id("acgt")
'VMC:GS_aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'

>>> seq_vmc_id("acgt", normalize=False)
'VMC:GS_eFwawHHdibaZBDcs9kW3gm31h1NNJcQe'
bioutils.digests.seq_vmc_identifier(seq, normalize=True)[source]

Converts sequence to VMC identifier (record).

See https://github.com/ga4gh/vmc

Parameters

  • seq (str) – A sequence.

  • normalize (bool, optional) – Whether to normalize the sequence before conversion, i.e. to ensure representation as uppercase letters without whitespace or asterisks. Defaults to True.

Returns

VMC identifier (record) representation of sequnce.

Return type

str

Examples

>>> seq_vmc_identifier("") == {'namespace': 'VMC', 'accession': 'GS_z4PhNX7vuL3xVChQ1m2AB9Yg5AULVxXc'}
True

>>> seq_vmc_identifier("ACGT") == {'namespace': 'VMC', 'accession': 'GS_aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'}
True

>>> seq_vmc_identifier("acgt") == {'namespace': 'VMC', 'accession': 'GS_aKF498dAxcJAqme6QYQ7EZ07-fiw8Kw2'}
True

>>> seq_vmc_identifier("acgt", normalize=False) == {'namespace': 'VMC', 'accession': 'GS_eFwawHHdibaZBDcs9kW3gm31h1NNJcQe'}
True