Bio.utils

Package Bio :: Module utils

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Module Bio.utils

Function Summary
	`back_transcribe(seq)`
	`back_translate(seq, id)`
	`count_monomers(seq)`
	`percent_monomers(seq)`
	`reduce_sequence(seq, reduction_table, new_alphabet)` given an amino-acid sequence, return it in reduced alphabet form based on the letter-translation table passed.
	`sum(seq, table, zero)`
	`sum_2ple(seq, table, zero)`
	`total_weight(seq, weight_table)`
	`total_weight_range(seq, weight_table)`
	`transcribe(seq)`
	`translate(seq, id)`
	`translate_to_stop(seq, id)`
	`ungap(seq)` given a sequence with gap encoding, return the ungapped sequence
	`verify_alphabet(seq)`

Function Details

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. 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

ungap(seq)

given a sequence with gap encoding, return the ungapped sequence

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