biotite.application.sra.FastqDumpApp¶

class biotite.application.sra.FastqDumpApp(uid, output_path_prefix=None, bin_path='fasterq-dump', offset='Sanger')[source]¶

Bases: biotite.application.localapp.LocalApp

Fetch sequencing data as FASTQ 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.
bin_pathstr, optional: Path to the fasterq-dump binary.
offsetint or {‘Sanger’, ‘Solexa’, ‘Illumina-1.3’, ‘Illumina-1.5’, ‘Illumina-1.8’}, optional: This value is subtracted from the FASTQ ASCII code to obtain the quality score. Can either be directly the value, or a string that indicates the score format.

add_additional_options(options)¶

Add additional options for the command line program. These options are put before the arguments automatically determined by the respective LocalApp subclass.

This method is focused on advanced users, who have knowledge on the available options of the command line program and the options already used by the LocalApp subclasses. Ignoring the already used options may result in conflicting CLI arguments and potential unexpected results. It is recommended to use this method only, when the respective LocalApp subclass does not provide a method to set the desired option.

Parameters

optionslist of str: A list of strings representing the command line options.

Notes

In order to see which options the command line execution used, try the get_command() method.

Examples

>>> seq1 = ProteinSequence("BIQTITE")
>>> seq2 = ProteinSequence("TITANITE")
>>> seq3 = ProteinSequence("BISMITE")
>>> seq4 = ProteinSequence("IQLITE")
>>> # Run application without additional arguments
>>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4])
>>> app.start()
>>> app.join()
>>> print(app.get_command())
clustalo --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree
>>> # Run application with additional argument
>>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4])
>>> app.add_additional_options(["--full"])
>>> app.start()
>>> app.join()
>>> print(app.get_command())
clustalo --full --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree

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.

static fetch(uid, output_path_prefix=None, bin_path='fasterq-dump', offset='Sanger')¶

Get the sequences and score values 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.
bin_pathstr, optional: Path to the fasterq-dump binary.
offsetint or {‘Sanger’, ‘Solexa’, ‘Illumina-1.3’, ‘Illumina-1.5’, ‘Illumina-1.8’}, optional: This value is subtracted from the FASTQ ASCII code to obtain the quality score. Can either be directly the value, or a string that indicates the score format.

Returns

sequences_and_scoreslist of dict (str -> (NucleotideSequence, ndarray)): 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 and score values.

get_app_state()¶

Get the current app state.

Returns

app_stateAppState: The current app state.

get_command()¶

Get the executed command.

Cannot be called until the application has been started.

Returns

commandstr: The executed command.

Examples

>>> seq1 = ProteinSequence("BIQTITE")
>>> seq2 = ProteinSequence("TITANITE")
>>> seq3 = ProteinSequence("BISMITE")
>>> seq4 = ProteinSequence("IQLITE")
>>> app = ClustalOmegaApp([seq1, seq2, seq3, seq4])
>>> app.start()
>>> print(app.get_command())
clustalo --in ...fa --out ...fa --force --output-order=tree-order --seqtype Protein --guidetree-out ...tree

get_exit_code()¶

Get the exit code of the process.

PROTECTED: Do not call from outside.

Returns

codeint: The exit code.

get_fastq()¶

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

Returns

fastq_fileslist of FastqFile: 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_file_paths()¶

Get the file paths to the downloaded FASTQ files.

Returns

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

get_process()¶

Get the Popen instance.

PROTECTED: Do not call from outside.

Returns

processPopen: The Popen instance

get_sequences()¶

Get the sequences and score values from the downloaded file(s).

Returns

sequences_and_scoreslist of dict (str -> (NucleotideSequence, ndarray)): 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 and score values.

get_stderr()¶

Get the STDERR pipe content of the process.

PROTECTED: Do not call from outside.

Returns

stdoutstr: The standard error.

get_stdout()¶

Get the STDOUT pipe content of the process.

PROTECTED: Do not call from outside.

Returns

stdoutstr: The standard outpout.

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.

set_arguments(arguments)¶

Set command line arguments for the application run.

PROTECTED: Do not call from outside.

Parameters

argumentslist of str: A list of strings representing the command line options.

set_exec_dir(exec_dir)¶

Set the directory where the application should be executed. If not set, it will be executed in the working directory at the time the application was created.

PROTECTED: Do not call from outside.

Parameters

exec_dirstr: The execution directory.

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()

Gallery¶