Package Bio :: Module utils
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Module utils

source code

Miscellaneous functions for dealing with sequences (obsolete?).

Functions [hide private]
 
ungap(seq)
given a sequence with gap encoding, return the ungapped sequence
source code
 
verify_alphabet(seq) 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'
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