kedro.contrib.io.bioinformatics.BioSequenceLocalDataSet¶
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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.release
()Release any cached data. 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 tofilepath
.
Return type: None
- filepath (
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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.
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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 forload
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 forsave
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.- name (
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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.
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release
()¶ Release any cached data.
Raises: DataSetError
– when underlying exists method raises error.Return type: bool
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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
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