Examples

The following examples are derived directly from IPython notebooks in the hgvs source code examples directory.

• Creating a SequenceVariant from scratch
  • 0. Overview
  • 1. Make an Interval to define a position of the edit
  • 2. Make an edit object
  • 3. Make the variant
  • 4. Update your variant
• Manuscript Example
  • Parse an HGVS string into a Python structure
  • Open the UTA public data source for mapping and validation
  • Project transcript variant NM_182763.2:c.688+403C>T to GRCh37 primary assembly using splign alignments
  • Project genomic variant to a new transcript
  • Infer protein changes for these transcript variants
  • Format the results by “stringification”
  • Validate a variant
• Automated liftover of NM_001261456.1:c.1762A>G (rs509749) to NM_001261457.1 via GRCh37
• Manual liftover of NM_001261456.1:c.1762A>G (rs509749) to NM_001261457.1 via GRCh37
• Using hgvs
  • Variant I/O
    • Initialize the parser
    • Parse a simple variant
    • Parsing complex variants
    • Formatting variants
  • Projecting variants between sequences
    • Set up a dataprovider
    • Initialize mapper classes
    • c_to_g
    • g_to_c
    • c_to_p
    • Projecting in the presence of a genome-transcript gap
  • Normalizing variants
  • A more complex normalization example
  • Validating variants