Package Bio :: Module utils
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Module utils

source code

Miscellaneous functions for dealing with sequences (DEPRECATED).

This module is deprecated, and is expected to be removed in the next release. If you use this module, please contact the Biopython developers via the mailing lists.

Functions [hide private]
 
ungap(seq)
given a sequence with gap encoding, return the ungapped sequence
source code
 
count_monomers(seq) source code
 
percent_monomers(seq) source code
 
sum(seq, table, zero=0.0) source code
 
sum_2ple(seq, table, zero=(0.0, 0.0)) source code
 
total_weight(seq, weight_table=None) source code
 
total_weight_range(seq, weight_table=None) source code
 
reduce_sequence(seq, reduction_table, new_alphabet=None)
given an amino-acid sequence, return it in reduced alphabet form based on the letter-translation table passed.
source code
Variables [hide private]
  __package__ = 'Bio'
  __warningregistry__ = {('Bio.utils has been deprecated, and we...
Function Details [hide private]

reduce_sequence(seq, reduction_table, new_alphabet=None)

source code 

given an amino-acid sequence, return it in reduced alphabet form based on the letter-translation table passed. Some "standard" tables are in Alphabet.Reduced. seq: a Seq.Seq type sequence reduction_table: a dictionary whose keys are the "from" alphabet, and values are the "to" alphabet


Variables Details [hide private]

__warningregistry__

Value:
{('Bio.utils has been deprecated, and we intend to remove it in the ne\
xt release of Biopython.',
  <class 'Bio.BiopythonDeprecationWarning'>,
  17): True}