BedContainer Module

Module Description

The BedContainer Module is composed by 2 Classes.

• BedContainer
• BedContainer6

BedContainer is the parent class of BedContainer6, and so all methods and attributes presented in BedContainer will be also present in BedContainer6. It was necessary overwriting some of them, so the way of working of some methods can vary from one class to the other. But will share the same key features.

The internal structure of a BedContainer object is a Dictionary of Lists, each of one corresponding to one chromosome. For some methods is possible to parallelize activities by running them for each chromosome individually.

Different BedContainer classes accommodate different BedEntry objects:

• BedContainer -> BedEntry
• BedContainer6 -> BedEntry6

Classes Description and Methods Sum-up Table

• BedContainer Methods Sum-up Table
  • BedContainer Methods
  • BedContainer6 Methods
• BedContainer Classes
  • BedContainer Class (BedEntry 3 Col)
    • Build-in Functions
  • BedContainer Class (6 Col)
    • Build-in Functions

from bedContainer.BedContainer import BedContainer
from bedContainer.BedContainer6 import BedContainer6
from bedContainer.BedContainer12 import BedContainer12


if __name__ == '__main__':
    """
    Create Instance of BedContainer
    """
    container1 = BedContainer6(addExtras=True)  # With extraFields
    container2 = BedContainer6(addExtras=False) # WithOUT extraFields

    """
    Read From BED files
    """
    container1.readFromBedFile("file1.bed")
    container2.readFromBedFile("file2.bed")

    """
    Sorting BedEntry objects
    """
    container1.sort()
    container1.sort()

    """
    Add new Entry
    """
    #Input as List:
    container1.addFrom_List(["A", 1, 2, "NAME", ".", "+",["A", "B", "C"]])

    #Input already a BedEntry object
    bedEntryObj = BedEntry6("chr1", 20, 50, 'GeneName',0, "+", ["A", "B" , "C","D"])
    container1.addFrom_BedEntryObj(bedEntryObj)

    """
    Remove a entry from BedContainer
    """
    container1.removeEntryBed(container1[0])

    """
    Merge 2 BedContainer
    """
    containerMerge = BedContainer6.merge(container2, container1)

    """

    It's also possible to iterate over the BedContainer
    """
    for elem in containerMerge:
        #Do something
        pass

    """
    Write in File BedContainer
    """
    containerMerge.writeToBedFile("FinalOutput.bed")