kedro.contrib.io.bioinformatics.BioSequenceLocalDataSet

class kedro.contrib.io.bioinformatics.BioSequenceLocalDataSet(filepath, load_args=None, save_args=None)[source]

Bases: kedro.io.core.AbstractDataSet

BioSequenceLocalDataSet loads and saves data to a sequence file.

Example:

raw_sequence_list = [
    '>gi|2765658|emb|Z78533.1|CIZ78533'
    'C.irapeanum 5.8S rRNA gene and ITS1 and ITS2 DNA'
    'CGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTGATGAGACCGTGGAATAAA'
    'CGATCGAGTGAATCCGGAGGACCGGTGTACTCAGCTCACCGGGGGCATTGCTCCCGTGGT'
    'GACCCTGATTTGTTGTTGGGCCGCCTCGGGAGCGTCCATGGCGGGTTTGAACCTCTAGCC'
    'CGGCGCAGTTTGGGCGCCAAGCCATATGAAAGCATCACCGGCGAATGGCATTGTCTTCCC'
    'CAAAACCCGGAGCGGCGGCGTGCTGTCGCGTGCCCAATGAATTTTGATGACTCTCGCAAA'
    'CGGGAATCTTGGCTCTTTGCATCGGATGGAAGGACGCAGCGAAATGCGATAAGTGGTGTG'
    'AATTGCAAGATCCCGTGAACCATCGAGTCTTTTGAACGCAAGTTGCGCCCGAGGCCATCA'
    'GGCTAAGGGCACGCCTGCTTGGGCGTCGCGCTTCGTCTCTCTCCTGCCAATGCTTGCCCG'
    'GCATACAGCCAGGCCGGCGTGGTGCGGATGTGAAAGATTGGCCCCTTGTGCCTAGGTGCG'
    'GCGGGTCCAAGAGCTGGTGTTTTGATGGCCCGGAACCCGGCAAGAGGTGGACGGATGCTG'
    'GCAGCAGCTGCCGTGCGAATCCCCCATGTTGTCGTGCTTGTCGGACAGGCAGGAGAACCC'
    'TTCCGAACCCCAATGGAGGGCGGTTGACCGCCATTCGGATGTGACCCCAGGTCAGGCGGG'
    'GGCACCCGCTGAGTTTACGC']
data_set = BioSequenceLocalDataSet(filepath="ls_orchid.fasta",
                                   load_args={"format": "fasta"},
                                   save_args={"format": "fasta"})
data_set.save(raw_sequence_list)
sequence_list = data_set.load()
assert raw_sequence_list.equals(sequence_list)

Methods

BioSequenceLocalDataSet.__init__(filepath[, …]) Creates a new instance of BioSequenceLocalDataSet pointing to a concrete filepath.
BioSequenceLocalDataSet.exists() Checks whether a data set’s output already exists by calling the provided _exists() method.
BioSequenceLocalDataSet.from_config(name, config) Create a data set instance using the configuration provided.
BioSequenceLocalDataSet.load() Loads data by delegation to the provided load method.
BioSequenceLocalDataSet.save(data) Saves data by delegation to the provided save method.
__init__(filepath, load_args=None, save_args=None)[source]

Creates a new instance of BioSequenceLocalDataSet pointing to a concrete filepath.

Parameters:
  • filepath (str) – path to sequence file
  • load_args (Optional[Dict[str, Any]]) – Options for loading sequence files. Here you can find all supported file formats: https://biopython.org/wiki/SeqIO
  • save_args (Optional[Dict[str, Any]]) – args supported by Biopython are ‘handle’ and ‘format’. Handle by default is equal to filepath.
Return type:

None

exists()

Checks whether a data set’s output already exists by calling the provided _exists() method.

Return type:bool
Returns:Flag indicating whether the output already exists.
Raises:DataSetError – when underlying exists method raises error.
classmethod from_config(name, config, load_version=None, save_version=None)

Create a data set instance using the configuration provided.

Parameters:
  • name (str) – Data set name.
  • config (Dict[str, Any]) – Data set config dictionary.
  • load_version (Optional[str]) – Version string to be used for load operation if the data set is versioned. Has no effect on the data set if versioning was not enabled.
  • save_version (Optional[str]) – Version string to be used for save operation if the data set is versioned. Has no effect on the data set if versioning was not enabled.
Return type:

AbstractDataSet

Returns:

An instance of an AbstractDataSet subclass.

Raises:

DataSetError – When the function fails to create the data set from its config.

load()

Loads data by delegation to the provided load method.

Return type:Any
Returns:Data returned by the provided load method.
Raises:DataSetError – When underlying load method raises error.
save(data)

Saves data by delegation to the provided save method.

Parameters:data (Any) – the value to be saved by provided save method.
Raises:DataSetError – when underlying save method raises error.
Return type:None