Updated normalization

arnavm · Aug 5, 2020 · d5f66e0 · d5f66e0
1 parent b0ee976
commit d5f66e0
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Showing 7 changed files with 40 additions and 4 deletions.
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -11,6 +11,9 @@ Welcome to blockify's documentation!
    pages/commands/normalize
    pages/commands/downsample
    pages/api/segmentation
+   pages/api/annotation
+   pages/api/normalization
+   pages/api/downsampling
 
 
 

diff --git a/docs/source/pages/api/annotation.rst b/docs/source/pages/api/annotation.rst
@@ -0,0 +1,5 @@
+API: annotation (peak calling)
+==========================
+
+.. automodule:: blockify.annotation
+    :members:
diff --git a/docs/source/pages/api/downsampling.rst b/docs/source/pages/api/downsampling.rst
@@ -0,0 +1,5 @@
+API: downsampling
+==========================
+
+.. automodule:: blockify.downsampling
+    :members:
diff --git a/docs/source/pages/api/normalization.rst b/docs/source/pages/api/normalization.rst
@@ -0,0 +1,5 @@
+API: normalization
+==========================
+
+.. automodule:: blockify.normalization
+    :members:
diff --git a/docs/source/pages/api/segmentation.rst b/docs/source/pages/api/segmentation.rst
@@ -1,4 +1,4 @@
-API: Segmentation
+API: segmentation
 ==========================
 
 .. automodule:: blockify.segmentation

diff --git a/lib/blockify/normalization.py b/lib/blockify/normalization.py
@@ -12,6 +12,7 @@
 
 
 def validateNormalizationArguments(input_file, regions_bed, libraryFactor, lengthFactor):
+    """Validates parameters passed via the command line."""
     # Check that the input file is sorted
     assert utilities.isSortedBEDObject(input_file), "input file must be sorted"
     # Check that regions is also sorted
@@ -24,6 +25,24 @@ def validateNormalizationArguments(input_file, regions_bed, libraryFactor, lengt
 
 
 def normalize(input_file, regions_bed, libraryFactor, lengthFactor):
+    """Primary segmentation method
+
+    Parameters
+    ----------
+    input_file: BedTool object
+        BedTool object (instantiated from pybedtools) for input data
+    regions_bed: BedTool object
+        BedTool object (instantiated from pybedtools) for regions over which we are normalizing input_file
+    libraryFactor: float
+        Scalar to normalize by input_file's library size.
+    lengthFactor: float or None
+        Scalar to normalize by each block's length. If None, no length normalization is performed.
+    Returns
+    -------
+    bedgraph: BedTool
+        A BedTool object in bedGraph format, using the intervals supplied in regions_bed
+    """
+
     # input_file and regions_bed are BedTool objects
     # Calculate library scaling constant, which is the total number
     # Validate normalization arguments
@@ -55,9 +74,8 @@ def normalize(input_file, regions_bed, libraryFactor, lengthFactor):
         )
 
 
-# Normalize the rate of events in a file over a set of regions
-# Thin wrapper for normalize()
 def normalize_from_command_line(args):
+    """Wrapper function for the command line function ``blockify normalize``"""
     input_file = BedTool(args.input)
     # If regions has been supplied, use it;
     if args.regions:

diff --git a/lib/blockify/segmentation.py b/lib/blockify/segmentation.py
@@ -82,7 +82,7 @@ def segment(input_file, method, p0=None, prior=None):
     method: str
         String specifying whether to use OP or PELT for the segmentation
     p0: float, optional
-        Float used to parameterize the prior on the total number of blocks; must be in the interval [0, 1]
+        Float used to parameterize the prior on the total number of blocks; must be in the interval [0, 1]. Default: 0.05
     prior: float, optional
         Explicit value for the total number of priors (specifying this is not recommended)