Created
April 24, 2016 20:03
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| import sys | |
| from warnings import warn | |
| import os | |
| __author__ = "Parashar Dhapola" | |
| __email__ = "" | |
| __desc__ = """ | |
| This script converts whole gene coordinates into TSS coordinates. | |
| Ideally this script should work on any table downloaded form UCSC | |
| table browser but has been only testedin "SGD track". | |
| """ | |
| def optParse(): | |
| """Returns filehandles if input parameters are correct. Else return 'False'""" | |
| try: | |
| input_bed = sys.argv[1] | |
| out_bed = sys.argv[2] | |
| except IndexError: | |
| print "USAGE:\npython %s <input_bed_file> <output_bed_file>" % __file__ | |
| return False | |
| try: | |
| fhi = open(input_bed) | |
| except IOError: | |
| print "Input bed file doesn't exist" | |
| return False | |
| try: | |
| fho = open(out_bed, 'w') | |
| except: | |
| print "Couldn't create output file. Check permission" | |
| return False | |
| return fhi, fho | |
| if __name__ == "__main__": | |
| opt_ret = optParse() | |
| if opt_ret is False: | |
| sys.exit() | |
| fhi, fho = opt_ret | |
| out_bed_data = {} | |
| for n,l in enumerate(fhi): | |
| c = l.rstrip('\n').split('\t') | |
| if c[3] not in out_bed_data: | |
| if c[5] == "+": | |
| tss = int(c[1]) | |
| elif c[5] == "-": | |
| tss = int(c[2])-1 # Because end coordinate is excluded in BED format | |
| else: | |
| raise ValueError("Unrecognized symbol for strand found in line %d. Exiting!" % n) | |
| out_bed_data[c[3]] = "\t".join(map(str, [c[0], tss, tss+1, c[3]])) | |
| else: | |
| warn("Ignoring duplicate gene name %s" % c[3]) | |
| fhi.close() | |
| fho.write("\n".join(out_bed_data.values())) | |
| fho.close() | |
| print "Output written to file %s" % sys.argv[2] | |
| print "Please run following command on bash shell to sort or use BedTools (use Excel if on Windows :( ))" | |
| print "sort -k1,1 -k2n,2 %s > %s" % (sys.argv[2], sys.argv[2].split('.')[0]+"_sorted.bed") | |
| print "Job completed!!" |
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