biosustain/gnomic

Issues

• Replace "-" with "^" to signify deletions

  #31 opened 6 years ago by lyschoening
  0

• Ensure presence declarations are handled properly

  #30 opened 7 years ago by lyschoening
  0

• Cannot parse gnomic generated string

  #11 opened 7 years ago by the-code-magician
  0

• Features of type "phene" rendered like normal features in Genotype.format()

  #6 opened 7 years ago by lyschoening
  0

• Fix genotype_to_string() rendering fusions and single markers as featuresets

  #7 opened 7 years ago by lyschoening
  0

• Refactor for version 1.0

  #20 opened 7 years ago by lyschoening
  0

• a>{b c}:a not working in v1

  #29 opened 7 years ago by lyschoening
  0

• Add flake8

  #26 opened 7 years ago by lyschoening
  0

• Ranges not being rendered in Genotype.format()

  #4 opened 7 years ago by lyschoening
  0

• Consider adding "Present" mutation type for plasmids and phenotypes

  #8 opened 7 years ago by lyschoening
  0

• Add flag warning when a substitution is ambiguous

  #10 opened 7 years ago by lyschoening
  0

• Single nucleotide deletion not working

  #27 opened 7 years ago by lyschoening
  2

• Rewrite formatting and other functions for version 1.0

  #21 opened 7 years ago by lyschoening
  0

• Support the entire Sequence Variant Nomenclature range for DNA and protein

  #24 opened 7 years ago by lyschoening
  0

• Support parsing genotype changes with spaces

  #22 opened 7 years ago by lyschoening
  1

• Parsing 'None' gives obscure error

  #23 opened 7 years ago by Melanie-M
  1

• Implement HTML format output

  #18 opened 7 years ago by lyschoening
  0

• change_to_text() on plasmid with marker adds plasmid itself as marker

  #14 opened 8 years ago by lyschoening
  0

• genotype_to_string and genotype_to_text failure

  #12 opened 8 years ago by phantomas1234
  5

• Full documentation of the language and behavior

  #9 opened 8 years ago by lyschoening
  0

• Add helper function to determine if a genotype is a subset of another genotype

  #5 opened 8 years ago by lyschoening
  0

• Phylogenetic tree generation from genotypes

  #1 opened 9 years ago by lyschoening
  0