9d1979a4f98e25cc266d29e1139dd515d11d3e61 max Wed Nov 13 05:30:48 2019 -0800 removing a feature (data stored in script itself) entirely as it was confusing, refs #24432 diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc index 0a2d2fa..c57e42f 100755 --- src/utils/chromToUcsc/chromToUcsc +++ src/utils/chromToUcsc/chromToUcsc @@ -1,153 +1,134 @@ #!/usr/bin/env python import logging, optparse, gzip from sys import stdin, stdout, stderr, exit try: from urllib.request import urlopen # py2 except ImportError: from urllib2 import urlopen # py3 try: from cStringIO import StringIO # py2 except ImportError: from io import StringIO # py3 # ==== functions ===== def parseArgs(): " setup logging, parse command line arguments and options. -h shows auto-generated help page " parser = optparse.OptionParser("""usage: %prog [options] filename - change NCBI or Ensembl chromosome names to UCSC names using the chromAlias table of the genome browser. Examples: - %prog -i test.bed -o test.ucsc.bed -g hg19 - %prog -g mm10 --get - %prog -i test2.bed -o test2.ucsc.bed -a mm10.chromAlias.tsv + %prog -g hg19 --get + %prog -i test2.bed -o test2.ucsc.bed -a hg19.chromAlias.tsv -g hg19 cat test.bed | %prog -a mm10.chromAlias.tsv > test.ucsc.bed """) - parser.add_option("-g", "--genomeDb", dest="db", action="store", help="a UCSC assembly ID, like hg19, hg38 or similar. Not required if -a is used. ") - parser.add_option("-a", "--chromAlias", dest="aliasFname", action="store", help="a UCSC chromAlias table in tab-sep format. The alias tables for hg19 or hg38 are hardcoded in the script, they do not require a chromAlias table..") + parser.add_option("", "--get", dest="doDownload", action="store_true", help="download a chrom alias table from UCSC for --genomeDb into the current directory and exit") + parser.add_option("-a", "--chromAlias", dest="aliasFname", action="store", help="a UCSC chromAlias table in tab-sep format. The alias tables for hg19 or hg38 are hardcoded in the script, they do not require a chromAlias table. Use the -g option for those.") + parser.add_option("-g", "--genomeDb", dest="db", action="store", help="a UCSC assembly ID, like hg19. Not required. Activates assembly-specific warning messages, only for hg19 right now.") parser.add_option("-i", "--in", dest="inFname", action="store", help="input filename, default: /dev/stdin") parser.add_option("-o", "--out", dest="outFname", action="store", help="output filename, default: /dev/stdout") - parser.add_option("", "--get", dest="doDownload", action="store_true", help="download a chrom alias table from UCSC for --genomeDb into the current directory and exit") parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages") #parser.add_option("", "--test", dest="test", action="store_true", help="do something") (options, args) = parser.parse_args() if options.db is None and options.aliasFname is None: parser.print_help() exit(1) if options.debug: logging.basicConfig(level=logging.DEBUG) else: logging.basicConfig(level=logging.INFO) return args, options # ----------- main -------------- def splitLines(ifh): " yield (chromName, restOfLine) for all lines of ifh " sep = -1 #if (sys.version_info > (3, 0)): lineNo = 0 for line in ifh: if sep==-1: if "\t" in line: sep = "\t" else: sep = None # = split on any whitespace, consec. whitespc counts as one chrom, rest = line.split(sep, 1) lineNo += 1 yield lineNo, sep, chrom, rest def parseAlias(fname): " parse tsv file with at least two columns, orig chrom name and new chrom name " toUcsc = {} for line in open(fname): if line.startswith("alias"): continue row = line.rstrip("\n").split("\t") toUcsc[row[0]] = row[1] return toUcsc -def chromFixer(db, aliasFname, ifh, ofh): +def chromToUcsc(db, aliasFname, ifh, ofh): " convert the first column to UCSC-style chrom names " - if aliasFname is None: - toUcsc = aliasData[db] - else: toUcsc = parseAlias(aliasFname) ucscChroms = set(toUcsc.values()) mtSkipCount = 0 for lineNo, sep, chrom, rest in splitLines(ifh): # just pass through any UCSC chrom names if chrom in ucscChroms: ucscChrom = chrom else: if db=="hg19" and (chrom=="MT" or chrom=="M"): mtSkipCount += 1 continue ucscChrom = toUcsc.get(chrom) if ucscChrom is None: logging.error("line %d: chrom name %s is not in chromAlias table" % (lineNo, repr(chrom))) exit(1) continue ofh.write(ucscChrom) ofh.write(sep) ofh.write(rest) if mtSkipCount!=0: - stderr.write("%d features were skipped because they were located on the M or MT chromosome. hg19 includes an older version of the mitochondrial genome and these features cannot be mapped\n" % mtSkipCount) - -def patchScript(fnameStr, outFname): - " read alias tables from fnameStr, put into this script and write patched script to outFname " - aliasData = {} - for fname in fnameStr.split(","): - db = fname.split(".")[0] - print("Reading alias table for %s: %s" % (db, fname)) - aliasData[db] = parseAlias(fname) - - myFname = __file__ - oldScript = open(myFname).read() - assert("#ALIASDATA#" in oldScript) - newScript = oldScript.replace("#ALIASDATA#", "aliasData = "+repr(aliasData)) - open(outFname, "w").write(newScript) - print("Patched script written to "+outFname) - exit(0) + stderr.write("%d features were skipped because they were located on the M or MT chromosome. hg19 includes an older version of the mitochondrial genome and these features cannot be mapped yet.\n" % mtSkipCount) def download(db): url = "http://hgdownload.soe.ucsc.edu/goldenPath/%s/database/chromAlias.txt.gz" % db gzData = urlopen(url).read() data = gzip.GzipFile(fileobj=StringIO.StringIO(gzData)).read() outFname = db+".chromAlias.tsv" open(outFname, "w").write(data) print("Wrote %s" % outFname) exit(0) def main(): args, options = parseArgs() db = options.db aliasFname = options.aliasFname inFname = options.inFname outFname = options.outFname - if db=="build": - patchScript(aliasFname, outFname) + if aliasFname is None: + logging.error("You need to provide an alias table with the -a option") + exit(1) + if options.doDownload: download(db) if inFname is None: ifh = stdin else: ifh = open(inFname) if outFname is None: ofh = stdout else: ofh = open(outFname, "w") - chromFixer(db, aliasFname, ifh, ofh) + chromToUcsc(db, aliasFname, ifh, ofh) -#ALIASDATA# main()