FastaResult

class biotite.application_v2.sra.FastaResult(file_paths: list[Path], _temp_dir: TemporaryDirectory[str] | None = None)

Bases: object

The result of a FASTA extraction with FastqDumpApp.extract_fasta().

The parsed files and sequences are not kept in memory, but are read from file_paths on demand via get_files() and get_sequences().

Attributes:

file_pathslist of Path

The paths to the extracted FASTA files. There is one file per read in a spot.

get_files() → list[FastaFile]

Parse the extracted FASTA files.

Returns:

fileslist of FastaFile

The parsed FASTA files, one per read in a spot.

get_sequences() → list[dict[str, NucleotideSequence]]

Get the reads from the extracted FASTA files.

Returns:

sequenceslist of dict (str -> NucleotideSequence)

The reads for each spot: the first item contains the first read for each spot, the second item the second read, etc. Each item maps identifiers to their sequence.