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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