Hypothesis-Bio

fasta

Strategies for generating FASTA formatted sequences.

fasta_entry()

@composite
def fasta_entry(draw, comment_source: SearchStrategy = None, sequence_source: SearchStrategy = None, wrap_length: Optional[int] = None, allow_windows_line_endings=True) -> str

Generates individual FASTA entries.

Warning

Unless you specifically want to generate single FASTA-formatted entries, use fasta instead when testing code that expects FASTA strings.

Arguments

  • comment_source: The source of the comments. Defaults to text(alphabet=characters(min_codepoint=32, max_codepoint=126)))
  • sequence_source: The source of the sequence. Defaults to dna.
  • wrap_length: The width to wrap the sequence on. If None, mixed sizes are used.
  • allow_windows_line_endings: Whether to allow \\r\\n in the linebreaks.

fasta()

@composite
def fasta(draw, entry_source: Optional[SearchStrategy] = None, min_reads: int = 1, max_reads: int = 100) -> str

Generates string representations of FASTA files.

Arguments

  • entry_source: The search strategy to use for generating FASTA entries. The default (None) will use fasta_entry with default settings.
  • min_reads: Minimum number of FASTA entries to generate.
  • max_reads: Maximum number of FASTA entries to generate.

← fastq →