BED12LeftRightExtender.py

#!/usr/bin/python3
#BED12LeftRightExtender.py
#This script takes Annotation bed12 as input, extend col2 and col3 borders, considering the splicing
#This is similar to bedtools slop, but considering the splicing, so only the first and last exon length may change.
#Version: Yu H. Sun, 2018-10-02
#Version: Yu H. Sun, 2020-04-30, finalized
                                                                          
import sys

def Extender():
    fi=open(sys.argv[1],'r')
    Left=int(sys.argv[2])
    Right=int(sys.argv[3])
    fo=open(sys.argv[4],'w')
    
    for line in fi:
        Coor=line.strip()
        CoorList=Coor.split()
        Start=int(CoorList[1])
        End=int(CoorList[2])
        Strand=CoorList[5]
        ORFStart=int(CoorList[6])
        ORFEnd=int(CoorList[7])
        ExonNum=int(CoorList[9])
        ExonLenBlock=CoorList[10]
        ExonStartBlock=CoorList[11]

        if ExonLenBlock[-1:] == ",":
            ExonLenBlock_clean=ExonLenBlock[:-1]
        else:
            ExonLenBlock_clean=ExonLenBlock

        if ExonStartBlock[-1:] == ",":
            ExonStartBlock_clean=ExonStartBlock[:-1]
        else:
            ExonStartBlock_clean=ExonStartBlock    

        if ExonNum == 1:
            NewExonBlock=int(ExonLenBlock_clean)+Left+Right
            if Strand == "+":
                fo.write(CoorList[0]+"\t"+str(Start-Left)+"\t"+str(End+Right)+"\t"+CoorList[3]+"\t"+CoorList[4]+"\t"+Strand+"\t"+CoorList[6]+"\t"+CoorList[7]+"\t"+CoorList[8]+"\t"+str(ExonNum)+"\t"+str(NewExonBlock)+"\t"+ExonStartBlock+"\n")
            elif Strand == "-":
                fo.write(CoorList[0]+"\t"+str(Start-Right)+"\t"+str(End+Left)+"\t"+CoorList[3]+"\t"+CoorList[4]+"\t"+Strand+"\t"+CoorList[6]+"\t"+CoorList[7]+"\t"+CoorList[8]+"\t"+str(ExonNum)+"\t"+str(NewExonBlock)+"\t"+ExonStartBlock+"\n")
        else:
            ExonLenBlock_clean_list=ExonLenBlock_clean.split(",")
            ExonStartBlock_clean_list=ExonStartBlock_clean.split(",")
            if Strand == "+":
                #Mutate start and end exons
                ExonLenBlock_clean_list[0]=int(ExonLenBlock_clean_list[0])+Left
                ExonLenBlock_clean_list[-1]=int(ExonLenBlock_clean_list[-1])+Right
                for i in range(len(ExonStartBlock_clean_list)):
                    if i!=0:
                        ExonStartBlock_clean_list[i]=int(ExonStartBlock_clean_list[i])+Left
                fo.write(CoorList[0]+"\t"+str(Start-Left)+"\t"+str(End+Right)+"\t"+CoorList[3]+"\t"+CoorList[4]+"\t"+Strand+"\t"+CoorList[6]+"\t"+CoorList[7]+"\t"+CoorList[8]+"\t"+str(ExonNum)+"\t"+",".join(map(str,ExonLenBlock_clean_list))+"\t"+",".join(map(str,ExonStartBlock_clean_list))+"\n")                
            else:
                ExonLenBlock_clean_list[0]=int(ExonLenBlock_clean_list[0])+Right
                ExonLenBlock_clean_list[-1]=int(ExonLenBlock_clean_list[-1])+Left
                for i in range(len(ExonStartBlock_clean_list)):
                    if i!=0:
                        ExonStartBlock_clean_list[i]=int(ExonStartBlock_clean_list[i])+Right
                fo.write(CoorList[0]+"\t"+str(Start-Right)+"\t"+str(End+Left)+"\t"+CoorList[3]+"\t"+CoorList[4]+"\t"+Strand+"\t"+CoorList[6]+"\t"+CoorList[7]+"\t"+CoorList[8]+"\t"+str(ExonNum)+"\t"+",".join(map(str,ExonLenBlock_clean_list))+"\t"+",".join(map(str,ExonStartBlock_clean_list))+"\n")

if len(sys.argv) != 5:
    print("*******************************************************************************************************")
    print("*                            Welcome to use BED12LeftRightExtender.py!                                *")
    print("*This script takes Annotation bed12 as input, extend col2 and col3 borders, considering the splicing  *")
    print("*This is similar to bedtools slop, but considering the splicing                                       *")
    print("*[Usage]: [BED12LeftRightExtender.py] [Gene.bed12] [LeftExtension] [RightExtension] [Output.ext.bed12]*")
    print("*******************************************************************************************************")
else:
    Extender()