Module hgvs::sequences

Utility code for working with sequences.

Partially ported over from bioutils.sequences.

Structs

• AA3_TO_AA1_VEC
• DNA_TO_AA1_LUT_VEC
  NCBI standard translation table.
• DNA_TO_AA1_SEC_VEC
  Translation table for selenocysteine.

Enums

• Error
  Error type for normalization of HGVS expressins.
• TranslationTable
  Allow selection of translation table.

Functions

• aa1_to_aa3
  Converts string of 1-letter amino acids to 3-letter amino acids.
• aa3_to_aa1
  Converts string of 3-letter amino acids to 1-letter amino acids.
• aa_to_aa1
  Coerces string of 1- or 3-letter amino acids to 1-letter representation.
• aa_to_aa3
  Coerces string of 1- or 3-letter amino acids to 3-letter representation.
• normalize_sequence
  Converts sequence to normalized representation for hashing.
• revcomp
  Reverse complementing shortcut.
• seq_md5
  Convert sequence to unicode MD5 hex digest.
• translate_cds
  Translates a DNA or RNA sequence into a single-letter amino acid sequence.
• trim_common_prefixes
• trim_common_suffixes