`FastaDumpApp`#

class biotite.application.sra.FastaDumpApp(uid, output_path_prefix=None, prefetch_path='prefetch', fasterq_dump_path='fasterq-dump')[source]#

Bases: _DumpApp

Fetch sequencing data from the NCBI sequence read archive (SRA) using sra-tools.

Parameters:

uidstr: A unique identifier (UID) of the file to be downloaded.
output_path_prefixstr, optional: The prefix of the path to store the downloaded FASTQ file. .fastq is appended to this prefix if the run contains a single read per spot. _1.fastq, _2.fastq, etc. is appended if it contains multiple reads per spot. By default, the files are created in a temporary directory and deleted after the files have been read.
prefetch_path, fasterq_dump_pathstr, optional: Path to the prefetch_path and fasterq-dump binary, respectively.

cancel()#: Cancel the application when in RUNNING or FINISHED state.

clean_up()#

Do clean up work after the application terminates.

PROTECTED: Optionally override when inheriting.

evaluate()#

Evaluate application results. Called in join().

PROTECTED: Override when inheriting.

classmethod fetch(uid, output_path_prefix=None, prefetch_path='prefetch', fasterq_dump_path='fasterq-dump')#

Get the sequences belonging to the UID from the NCBI sequence read archive (SRA).

Parameters:

uidstr: A unique identifier (UID) of the file to be downloaded.
output_path_prefixstr, optional: The prefix of the path to store the downloaded FASTQ file. .fastq is appended to this prefix if the run contains a single read per spot. _1.fastq, _2.fastq, etc. is appended if it contains multiple reads per spot. By default, the files are created in a temporary directory and deleted after the files have been read.
prefetch_path, fasterq_dump_pathstr, optional: Path to the prefetch_path and fasterq-dump binary, respectively.

Returns:

sequenceslist of dict (str -> NucleotideSequence): This list contains the reads for each spot: The first item contains the first read for each spot, the second item contains the second read for each spot (if existing), etc. Each item in the list is a dictionary mapping identifiers to its corresponding sequence.

get_app_state()#

Get the current app state.

Returns:

app_stateAppState: The current app state.

get_fasta()#

Get the FastaFile objects from the downloaded file(s).

Returns:

fasta_fileslist of FastaFile: This list contains the reads for each spot: The first item contains the first read for each spot, the second item contains the second read for each spot (if existing), etc.

get_fastq_dump_options()#

Get additional options for the fasterq-dump call.

PROTECTED: Override when inheriting.

Returns:

options: str: The additional options.

get_file_paths()#

Get the file paths to the downloaded files.

Returns:

pathslist of str: The file paths to the downloaded files.

get_prefetch_options()#

Get additional options for the prefetch call.

PROTECTED: Override when inheriting.

Returns:

options: str: The additional options.

get_sequences()#

Get the sequences from the downloaded file(s).

Returns:

sequenceslist of dict (str -> NucleotideSequence): This list contains the reads for each spot: The first item contains the first read for each spot, the second item contains the second read for each spot (if existing), etc. Each item in the list is a dictionary mapping identifiers to its corresponding sequence.

is_finished()#

Check if the application has finished.

PROTECTED: Override when inheriting.

Returns:

finishedbool: True of the application has finished, false otherwise.

join(timeout=None)#

Conclude the application run and set its state to JOINED. This can only be done from the RUNNING or FINISHED state.

If the application is FINISHED the joining process happens immediately, if otherwise the application is RUNNING, this method waits until the application is FINISHED.

Parameters:

timeoutfloat, optional: If this parameter is specified, the Application only waits for finishing until this value (in seconds) runs out. After this time is exceeded a TimeoutError is raised and the application is cancelled.

Raises:

TimeoutError: If the joining process exceeds the timeout value.

run()#

Commence the application run. Called in start().

PROTECTED: Override when inheriting.

start()#: Start the application run and set its state to RUNNING. This can only be done from the CREATED state.

wait_interval()#

The time interval of is_finished() calls in the joining process.

PROTECTED: Override when inheriting.

Returns:

intervalfloat: Time (in seconds) between calls of is_finished() in join().

FastaDumpApp#

`FastaDumpApp`#