Diff of /openomics/genomics.py [000000] .. [548210]

Switch to side-by-side view

--- 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__