bbcflib::bFlatMajor Namespace Reference

Namespaces
namespace	bedtools
namespace	figure
namespace	numeric
namespace	stream
Classes
class	bFlatMajorGroup
Functions
def	run
Variables
list	__all__ = ['bFlatMajorGroup']
string	_here = 'bbcflib.bFlatMajor.'
list	_module_list = ['stream','numeric','figure']

---

Detailed Description

This packages provides algorithms working on :func:`FeatureStream <bbcflib.btrack.FeatureStream>`.
It is divided into three major groups depending on the algorithm's return type:

* :mod:`bbcflib.bFlatMajor.stream` returns :func:`FeatureStream <bbcflib.btrack.FeatureStream>` objects,
* :mod:`bbcflib.bFlatMajor.numeric` returns numeric arrays or matrices,
* :mod:`bbcflib.bFlatMajor.figure` returns figure files (pdf, png, etc.).

Algorithms can be used via a direct import::

    from bbcflib.bFlatMajor import stream
    for chrom in track1.chrmeta.keys():
        catstream = stream.concatenate([track1.read(chrom),track2.read(chrom)])

or via the global :func:`run <bbcflib.bFlatMajor.run>` function. The latter will take file names as input parameters, while a direct call requires :func:`FeatureStream <bbcflib.btrack.FeatureStream>` to be created beforehands.

Most functions in :mod:`bFlatMajor <bbcflib.bFlatMajor>` take one or more lists of :func:`FeatureStream <bbcflib.btrack.FeatureStream>` as parameters, plus additional algorithm-specific parameters.

---

Function Documentation

def bbcflib::bFlatMajor::run

(

kwargs

)

Wrapper function to execute any operation contained in this package, directly from
file inputs. Arguments are:

:param operation: (str) the name of the function to be called.
:param output: (str) a filename or a directory to write the results into.
:param assembly: (str) a genome assembly identifier if needed.
:param chromosome: (str) a chromosome name if operation must be restricted to a single chromsome.
:param ...: additional parameters passed to `operation`.

Example::

    run(operation="mean_score_by_feature",
        output="score_output.bed", chromosome="chr1",
        trackScores="density_file.sql", trackFeatures="genes.sql")