Package Bio :: Package SeqUtils :: Module CheckSum
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Module CheckSum

source code

Functions to calculate assorted sequence checksums.
Functions [hide private]
 
crc32(seq)
Returns the crc32 checksum for a sequence (string or Seq object).
source code
 
_init_table_h() source code
 
crc64(s)
Returns the crc64 checksum for a sequence (string or Seq object).
source code
 
gcg(seq)
Returns the GCG checksum (int) for a sequence (string or Seq object).
source code
 
seguid(seq)
Returns the SEGUID (string) for a sequence (string or Seq object).
source code
Variables [hide private]
  _table_h = [0, 28311552, 56623104, 47185920, 113246208, 124780...
  __package__ = 'Bio.SeqUtils'
Function Details [hide private]

crc32(seq)

source code 

Returns the crc32 checksum for a sequence (string or Seq object).

Note that the case is important:

>>> crc32("ACGTACGTACGT")
20049947
>>> crc32("acgtACGTacgt")
1688586483

crc64(s)

source code 

Returns the crc64 checksum for a sequence (string or Seq object).

Note that the case is important:

>>> crc64("ACGTACGTACGT")
'CRC-C4FBB762C4A87EBD'
>>> crc64("acgtACGTacgt")
'CRC-DA4509DC64A87EBD'

gcg(seq)

source code 

Returns the GCG checksum (int) for a sequence (string or Seq object).

Given a nucleotide or amino-acid secuence (or any string), returns the GCG checksum (int). Checksum used by GCG program. seq type = str.

Based on BioPerl GCG_checksum. Adapted by Sebastian Bassi with the help of John Lenton, Pablo Ziliani, and Gabriel Genellina.

All sequences are converted to uppercase.

>>> gcg("ACGTACGTACGT")
5688
>>> gcg("acgtACGTacgt")
5688

seguid(seq)

source code 

Returns the SEGUID (string) for a sequence (string or Seq object).

Given a nucleotide or amino-acid secuence (or any string), returns the SEGUID string (A SEquence Globally Unique IDentifier). seq type = str.

Note that the case is not important:

>>> seguid("ACGTACGTACGT")
'If6HIvcnRSQDVNiAoefAzySc6i4'
>>> seguid("acgtACGTacgt")
'If6HIvcnRSQDVNiAoefAzySc6i4'

For more information about SEGUID, see: http://bioinformatics.anl.gov/seguid/ DOI: 10.1002/pmic.200600032


Variables Details [hide private]

_table_h

Value:
[0,
 28311552,
 56623104,
 47185920,
 113246208,
 124780544,
 94371840,
 68157440,
...