kedro.contrib.io.bioinformatics package¶
AbstractDataSet
implementation for reading/writing from/to a sequence
file.
Submodules¶
kedro.contrib.io.bioinformatics.sequence_dataset module¶
BioSequenceLocalDataSet loads and saves data to/from bio-sequence objects to file.
-
class
kedro.contrib.io.bioinformatics.sequence_dataset.
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)
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__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 (
-