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)
__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