--- a +++ b/openomics/genomics.py @@ -0,0 +1,106 @@ +from openomics.database.base import Annotatable +from openomics.transcriptomics import Expression +__all__ = ['SomaticMutation', 'DNAMethylation', 'CopyNumberVariation'] + +class SingleNucleotideVariants(Expression, Annotatable): + def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index", + transform_fn=None, dropna=False, npartitions=None, cohort_name=None): + """ + Args: + data: + transpose: + gene_index: + usecols: + gene_level: + sample_level: + transform_fn: + dropna: + npartitions: + cohort_name: + """ + super().__init__(data=data, transpose=transpose, gene_index=gene_index, + usecols=usecols, gene_level=gene_level, + sample_level=sample_level, transform_fn=transform_fn, + dropna=dropna, npartitions=npartitions, cohort_name=cohort_name) + + @classmethod + def name(cls): + return cls.__name__ + + +class SomaticMutation(Expression, Annotatable): + def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index", + transform_fn=None, dropna=False, npartitions=None, cohort_name=None): + """ + Args: + data: + transpose: + gene_index: + usecols: + gene_level: + sample_level: + transform_fn: + dropna: + npartitions: + cohort_name: + """ + super().__init__(data=data, transpose=transpose, gene_index=gene_index, usecols=usecols, + gene_level=gene_level, sample_level=sample_level, + transform_fn=transform_fn, dropna=dropna, npartitions=npartitions, + cohort_name=cohort_name) + + @classmethod + def name(cls): + return cls.__name__ + + +class DNAMethylation(Expression, Annotatable): + def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index", + transform_fn=None, dropna=False, npartitions=None, cohort_name=None): + """ + Args: + data: + transpose: + gene_index: + usecols: + gene_level: + sample_level: + transform_fn: + dropna: + npartitions: + cohort_name: + """ + super().__init__(data=data, transpose=transpose, gene_index=gene_index, usecols=usecols, + gene_level=gene_level, sample_level=sample_level, + transform_fn=transform_fn, dropna=dropna, npartitions=npartitions, + cohort_name=cohort_name) + + @classmethod + def name(cls): + return cls.__name__ + + +class CopyNumberVariation(Expression, Annotatable): + def __init__(self, data, transpose, gene_index, usecols=None, gene_level=None, sample_level="sample_index", + transform_fn=None, dropna=False, npartitions=None, cohort_name=None): + """ + Args: + data: + transpose: + gene_index: + usecols: + gene_level: + sample_level: + transform_fn: + dropna: + npartitions: + cohort_name: + """ + super().__init__(data=data, transpose=transpose, gene_index=gene_index, + usecols=usecols, gene_level=gene_level, sample_level=sample_level, + transform_fn=transform_fn, dropna=dropna, npartitions=npartitions, + cohort_name=cohort_name) + + @classmethod + def name(cls): + return cls.__name__