#!/usr/bin/python3 import sys import pyBigWig import requests import re import argparse from argparse import RawTextHelpFormatter import itertools def parse_arguments(defaults): parser = argparse.ArgumentParser(description='Convert chromosome names for bigwig files between ensembl, gencode and UCSC naming schemes\n' + "Per default it writes to the same location as original file, however with a modified filename:\n" + "eg. test.bw --> test.[toFormat]_chroms.bw\n" + "Change this with the -o option!\n\n" + "Mapping tables are taken from https://github.com/dpryan79/ChromosomeMappings\n\n" + "Provided mapping options need to exactly match an existing file\n" + "[GENOME]_[FROM_FORMAT]2[TO_FORMAT].txt in this repo!", usage='$ convertChroms BIGWIG', formatter_class=RawTextHelpFormatter) parser.add_argument('bw_in_filename', metavar='BIGWIG', help='bigwig file that will be converted') parser.add_argument('--genome', '-g', action='store', dest='genome', help='Genome version of original bigwig \n' + '(GRCm37|GRCm38|GRCh37|GRCh38|BDGP6|dm3|GRCz10|GRCz11|\n' + 'JGI_4.2|MEDAKA1|R64-1-1|WBcel235|Zv9|galGal4|rn5|rn6)\n' + '(default: %(default)s)', default=defaults["genome"]) parser.add_argument('--fromFormat', '-f', action='store', dest='from_format', help='Chr naming format of original bigwig (ensembl|gencode|UCSC) (default: %(default)s)', default=defaults["fromFormat"]) parser.add_argument('--toFormat', '-t', action='store', dest='to_format', help='Chr naming format of converted bigwig (ensembl|gencode|UCSC) (default: %(default)s)', default=defaults["toFormat"]) parser.add_argument('--outFileName', '-o', action='store', dest='bw_out_filename', help='Chr naming format of converted bigwig (ensembl|gencode|UCSC) (default: %(default)s)', default=defaults["bw_out_filename"]) parser.add_argument('--baseURL', '-u', action='store', dest='base_url', help='base url where the mapping tables can be found (default: %(default)s)\n' + 'Local files can be given with \'file://[BASE_DIR]/\'', default=defaults["base_url"]) parser.add_argument('--verbose', '-v', action='store_true', dest='verbose', help='Be more verbose where possible (default: %(default)s)', default=defaults["verbose"]) return parser def get_chromosome_mapping(genome="GRCm38", from_format="ensembl", to_format="UCSC", verbose=True, base_url='https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/'): """ creates a dict with chromosome name mappings according to provided conversion formats default base URL access a github repo with conversion files, but you can also give eg. a path to local directory """ mapping_file = genome + '_' + from_format + '2' + to_format + '.txt' if re.match('^file:[/]+.*', base_url): base_url = re.sub("file:[/]*(/.*)", "\\1", base_url) if verbose: print("load mapping table (" + mapping_file + ') from ' + base_url) tab = None if re.match('^https?://.*', base_url): try: r = requests.get(base_url + '/' + mapping_file) r.raise_for_status() except requests.exceptions.RequestException as e: print("\n", e, "\n\nPlease provide correct name (GENOME, FROM_FORMAT, TO_FORMAT) for a mapping table!\n") sys.exit(1) tab = r.text elif re.match('^[/]+.*', base_url): try: tab = open(base_url + '/' + mapping_file).read() except IOError as e: print("\n", e, "\n\nPlease provide a correct name (GENOME, FROM_FORMAT, TO_FORMAT) for a mapping table!\n") sys.exit(1) else: print("\nPlease provide a correct BASE_URL for a mapping table!\n") sys.exit(1) mapping_table = {} for ent in tab.split("\n"): if len(ent) == 0: continue pair = ent.split("\t") if (len(pair[1]) <= 0): # if (verbose): # print("skip chrom \'" + pair[0] + "\' - cannot be mapped to "+to_format) continue mapping_table[pair[0]] = pair[1] return mapping_table def convert_bigwig(mapping_table, bw_in_filename, bw_out_filename, verbose=False): """ convert chromosome names of a bigwig file according to given mapping_table it checks which chromosome names that can correctly mapped, all other chromosomes are skipped """ bw = pyBigWig.open(bw_in_filename) curr_chroms = bw.chroms() final_mapping_table = {} new_chroms = {} for c in curr_chroms: if c not in mapping_table: if (verbose): print("skip original chrom \'" + c + "\' - cannot be found in mapping table! Right GENOME & FROM_FORMAT?") continue final_mapping_table[c] = mapping_table[c] new_chroms[mapping_table[c]] = curr_chroms[c] if (len(new_chroms) <= 0): print("No chromosomes found for mapping! Wrong 'FROM_FORMAT'?") sys.exit(1) bw_out = pyBigWig.open(bw_out_filename, "w") bw_out.addHeader(list(new_chroms.items())) for c in final_mapping_table: c_int = bw.intervals(c) c_map = final_mapping_table[c] if verbose: print("convert chromosome: ", c, " --> ", c_map) bw_out.addEntries(list(itertools.repeat(c_map, len(c_int))), [x[0] for x in c_int], ends=[x[1] for x in c_int], values=[x[2] for x in c_int]) bw_out.close() bw.close() if (verbose): print("\nbigwig conversion finished!\n") def main(args=None): defaults = { 'genome': 'GRCm38', 'fromFormat': 'ensembl', 'toFormat': 'UCSC', 'verbose': False, 'bw_out_filename': None, 'base_url': 'https://raw.githubusercontent.com/dpryan79/ChromosomeMappings/master/' } args = parse_arguments(defaults).parse_args(args) bw_out_filename = args.bw_out_filename if args.bw_out_filename is None: bw_out_filename = re.sub(r"(.[^\.]+)$", ".%s\\1" % (args.to_format + "_chroms"), args.bw_in_filename) print("\noutput_file: " + bw_out_filename) mapping_table = get_chromosome_mapping(genome=args.genome, from_format=args.from_format, to_format=args.to_format, verbose=args.verbose, base_url=args.base_url) convert_bigwig(mapping_table, args.bw_in_filename, bw_out_filename, args.verbose) if __name__ == "__main__": args = None if len(sys.argv) == 1: args = ["--help"] main(args)