4e1f462b2f1a3e877ee4041550b0fd276bcaa4a2
max
  Tue Nov 5 16:24:55 2019 +0100
renaming chromFixer to chromToUcsc, refs #24407

diff --git src/utils/chromFixer/chromFixer src/utils/chromFixer/chromFixer
deleted file mode 100755
index 657647a..0000000
--- src/utils/chromFixer/chromFixer
+++ /dev/null
@@ -1,151 +0,0 @@
-#!/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
-        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("-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):
-    " 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__
-    newScript = open(myFname).read().replace("#ALIASDATA#", "aliasData = "+repr(aliasData))
-    open(outFname, "w").write(newScript)
-    print("Patched script written to "+outFname)
-    exit(0)
-
-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 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)
-
-#ALIASDATA#
-main()