Source code for iCallSV.checkBlackList

"""
checkBlackList
~~~~~~~~~~~~~~

:Description: This module will read the Black List file and tell if and event is blacklisted or not

"""
'''
Created on Nov 20, 2015
@author: Ronak H Shah
::Inputs::
BlackListFile: List of Position that have Black List Structural Variants (Tab-delimited Format without header:chr1    start1    end1	chr2    start2    end2).
chr1: Chromosome location for 1st breakpoint
start1: Start location of the 1st breakpoint
chr2: Chromosome location for 2nd breakpoint
start2: Start Location of the second breakpoint
extention: How much should the intervals be extended in positive and negative directions
'''
import os


# Read the hotspot file and make a dictionary of it
[docs]def ReadBlackListFile(BlackListFile): """ Read the ``blacklist region file`` :param str BlackListFile: str of file to be read. :return: A list containing black listed regions. :rtype: list. """ blacklist = [] if os.path.isfile(BlackListFile): with open(BlackListFile, 'r') as filecontent: for line in filecontent: #(chrom1, start1, chrom2, start2) = line.rstrip().split("\t") blacklist.append(line) return(blacklist)
# Read the hotspot dictionary and tell if the event occurs in blacklist or not
[docs]def CheckIfItIsBlacklisted(chr1, start1, chr2, start2, blacklist, extention): """ Check if coordinate are present in the ``blacklist region file`` :param str chr1: str of the breakpoint in first chromosome :param int start1: int of the start location of the breakpoint in first chromosome :param str chr2: str of the breakpoint in second chromosome :param int start2: int of the start location of the breakpoint in second chromosome :param list blacklist: A list containing black listed regions :param int extension: an value for search in positive and negative direction of the start1 and start2 location :return: A boolean tag indicating True or False :rtype: bool """ blacklistTag = None chr1 = str(chr1) chr2 = str(chr2) start1 = int(start1) start2 = int(start2) if chr1 == chr2: start = start1 end = start2 for entries in blacklist: (bchr1, bstart1, bchr2, bstart2) = entries.rstrip().split("\t") bstart1 = int(bstart1) bstart2 = int(bstart2) if(bchr1 == bchr2): if(chr1 == bchr1): if(((start <= int(bstart1 - extention)) and (start >= int(bstart1 + extention))) and ((end <= int(bstart2 - extention)) and (end <= int(bstart2 + extention)))): blacklistTag = True else: blacklistTag = False if(((end <= int(bstart1 - extention)) and (end >= int(bstart1 + extention))) and ((start <= int(bstart2 - extention)) and (start <= int(bstart2 + extention)))): blacklistTag = True else: blacklistTag = False else: continue else: continue else: for entries in blacklist: (bchr1, bstart1, bchr2, bstart2) = entries.rstrip().split("\t") bstart1 = int(bstart1) bstart2 = int(bstart2) if(((chr1 == bchr1) and (chr2 == bchr2)) or ((chr1 == bchr2) and (chr2 == bchr1))): if(((start1 <= int(bstart1 - extention)) and (start1 >= int(bstart1 + extention))) and ((start2 <= int(bstart2 - extention)) and (start2 <= int(bstart2 + extention)))): blacklistTag = True else: blacklistTag = False if(((start2 <= int(bstart1 - extention)) and (start2 >= int(bstart1 + extention))) and ((start1 <= int(bstart2 - extention)) and (start1 <= int(bstart2 + extention)))): blacklistTag = True else: blacklistTag = False else: continue return(blacklistTag)