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
,kedro.io.core.ExistsMixin
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 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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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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