dynast.ref

Module Contents

Functions

STAR_genomeGenerate(fasta_path: str, gtf_path: str, index_dir: str, n_threads: int = 8, memory: int = 16 * 1024**3, temp_dir: Optional[str] = None) → Dict[str, str]	Generate a STAR index from a reference.
ref(fasta_path: str, gtf_path: str, index_dir: str, n_threads: int = 8, memory: int = 16 * 1024**3, temp_dir: Optional[str] = None)	Main interface for the `ref command.

dynast.ref.STAR_genomeGenerate(fasta_path: str, gtf_path: str, index_dir: str, n_threads: int = 8, memory: int = 16 * 1024 ** 3, temp_dir: Optional[str] = None) → Dict[str, str]

Generate a STAR index from a reference.

Parameters

fasta_path

Path to genome fasta

gtf_path

Path to GTF annotation

index_dir

Path to output STAR index

n_threads

Number of threads, defaults to 8

memory

Suggested memory to use (this is not guaranteed), in bytes

temp_dir

Temporary directory

Retuurns:

Dictionary of generated index

dynast.ref.ref(fasta_path: str, gtf_path: str, index_dir: str, n_threads: int = 8, memory: int = 16 * 1024 ** 3, temp_dir: Optional[str] = None)

Main interface for the `ref command.

Parameters

fasta_path

Path to genome fasta

gtf_path

Path to GTF annotation

index_dir

Path to output STAR index

n_threads

Number of threads, defaults to 8

memory

Suggested memory to use (this is not guaranteed), in bytes

temp_dir

Temporary directory