iranges: base structures and functions not unlike memoryviews

The module reflects the content of the R/Bioconductor package IRanges. It defines Python-level classes for the R/S4 classes, and gives otherwise access to R-level commands the usual rpy2:robjects way.

The variable iranges_env in the module is an rpy2.robjects.REnvironment for the modules namespace. Accessing explicitly a module’s object is then straightforward.

The class inheritance diagram presents the parent-child relationships between the elements.

Inheritance diagram of bioc.iranges

A module to model the IRanges library in Bioconductor

Copyright 2009 - Laurent Gautier

class bioc.iranges.AnnotatedList
class bioc.iranges.AtomicList
class bioc.iranges.CharacterList
class bioc.iranges.ComplexList
class bioc.iranges.CompressedAtomicList
class bioc.iranges.DataFrame
class bioc.iranges.IRanges
class bioc.iranges.IRangesList
class bioc.iranges.IntegerList
class bioc.iranges.IntervalTree
class bioc.iranges.LogicalList
class bioc.iranges.MaskCollection
get_width()
classmethod new(mask_width)
class bioc.iranges.NormalIRanges
max
Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.
min
Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.
class bioc.iranges.NumericList
class bioc.iranges.RangedData
end
Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.
get_names()
names
start
Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.
width
Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.
class bioc.iranges.Ranges
as_DataFrame()
as_integer()
as_matrix()
end
Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.
isdisjoint()
isempty()
isnormal()
mid()
start
Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.
whichfirst_notnormal()
width
Python representation of an R function such as the character ‘.’ is replaced with ‘_’ whenever present in the R argument name.
class bioc.iranges.RangesDataList
class bioc.iranges.RangesList
class bioc.iranges.RawList
class bioc.iranges.Rle
class bioc.iranges.RleViews
class bioc.iranges.Sequence
Abstract class
class bioc.iranges.SimpleAtomicList
class bioc.iranges.SimpleList
class bioc.iranges.Views
get_subject()
Get the ‘subject’
subject
Get the ‘subject’
class bioc.iranges.XDataFrameList
class bioc.iranges.XRanges
bioc.iranges.iranges_conversion(robj)

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