ExpandBedFile.py

from benbiohelpers.TkWrappers.TkinterDialog import TkinterDialog
import os


# This function takes a bed file and expands its coordinates to encompass extra bases on each side.
# Returns the file path to the expanded bed file.
def expandBedFile(baseBedFilePath: str, expansionRadius = 50):

    # Generate paths to the files needed to expand the binding motif.
    expandedBedFilePath = f"{baseBedFilePath.rsplit('.',1)[0]}_{expansionRadius}bp_expanded.bed"

    # Expand the bed coordinates.
    print("Expanding nucleosome coordinates...")
    with open(baseBedFilePath,'r') as baseBedFile:
        with open(expandedBedFilePath, 'w') as expandedBedFile:

            # Write the expanded positions to the new file, one line at a time.
            for line in baseBedFile:
                choppedUpLine = line.strip().split('\t')
                choppedUpLine[1] = str(int(choppedUpLine[1]) - expansionRadius)
                choppedUpLine[2] = str(int(choppedUpLine[2]) + expansionRadius)

                # Write the results to the expansion file as long as it is not before the start of the chromosome.
                if int(choppedUpLine[1]) > -1: expandedBedFile.write('\t'.join(choppedUpLine) + '\n')
                else: print("Nucleosome at chromosome", choppedUpLine[0], "with expanded start pos", choppedUpLine[1],
                            "extends into invalid positions.  Skipping.")                                      

    return expandedBedFilePath

def main():

    #Create the Tkinter UI
    with TkinterDialog(workingDirectory=os.path.dirname(__file__)) as dialog:
        dialog.createFileSelector("Bed File:", 0, ("Bed Files",".bed"))
        dialog.createTextField("Expansion Radius:", 1, 0, defaultText="50")

    expandBedFile(dialog.selections.getIndividualFilePaths()[0],
                  int(dialog.selections.getTextEntries()[0]))

if __name__ == "__main__": main()