Module utils

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Miscellaneous functions for dealing with sequences (obsolete?).

Functions

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ungap(seq)
given a sequence with gap encoding, return the ungapped sequence

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verify_alphabet(seq)

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count_monomers(seq)

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percent_monomers(seq)

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sum(seq, table, zero=0.0)

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sum_2ple(seq, table, zero=(0.0, 0.0)) source code

total_weight(seq, weight_table=None)

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total_weight_range(seq, weight_table=None)

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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.

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Variables

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__package__ = 'Bio'

Function Details

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reduce_sequence(seq, reduction_table, new_alphabet=None)

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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