a5b8dc9064dc31482e96b5a1f4e4ce6a2cd8523a
max
  Mon Nov 16 05:08:43 2020 -0800
allowing wiggle files in chromToUcsc, no redmine, came up when trying to process a lemur single cell dataset

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index 7b55228..636ed54 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -3,79 +3,82 @@
 from sys import stdin, stdout, stderr, exit, modules
 from os.path import basename
 
 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 BytesIO # 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.
+    parser = optparse.OptionParser("""usage: %prog [options] filename - change NCBI or Ensembl chromosome names to UCSC names in tabular or wiggle files, using a chromAlias table.
 
     Requires a <genome>.chromAlias.tsv file which can be downloaded like this:
         %prog --get hg19              # download the file hg19.chromAlias.tsv into current directory
 
     If you do not want to use the --get option to retrieve the mapping tables, you can also download the alias mapping
     files yourself, e.g. for mm10 with 'wget https://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromAlias.txt.gz'
 
     Then the script can be run like this:
         %prog -i in.bed -o out.bed -a hg19.chromAlias.tsv
         %prog -i in.bed -o out.bed -a https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromAlias.txt.gz
     Or in pipes, like this:
         cat test.bed | %prog -a mm10.chromAlias.tsv > test.ucsc.bed
 
     """)
 
     parser.add_option("", "--get", dest="downloadDb", action="store", help="download a chrom alias table from UCSC for the genomeDb into the current directory and exit")
-    parser.add_option("-a", "--chromAlias", dest="aliasFname", action="store", help="a UCSC chromAlias file in tab-sep format. or a URL to one")
+    parser.add_option("-a", "--chromAlias", dest="aliasFname", action="store", help="a UCSC chromAlias file in tab-sep format or the http/https URL to one")
     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("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
     parser.add_option("-k", "--field", dest="fieldNo", action="store", type="int", \
             help="index of field to convert, default is %default (1-based), for most formats, e.g. BED. For genePred, the chromosome is field 2, for PSL it is 10 or 14.", default=1)
 
     (options, args) = parser.parse_args()
 
     if options.downloadDb 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 line.startswith("fixedStep") or line.startswith("variableStep"):
+            row = line.split()
+            yield lineNo, " ", row # *step lines are always space-separated
+        else:
             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)
             row = line.rstrip("\n\t").split(sep)
             lineNo += 1
             yield lineNo, sep, row
 
 def parseAlias(fname):
     " parse tsv file with at least two columns, orig chrom name and new chrom name "
     toUcsc = {}
     if fname.startswith("http://") or fname.startswith("https://"):
         ifh = urlopen(fname)
         if fname.endswith(".gz"):
             data = gzip.GzipFile(fileobj=ifh).read().decode()
             ifh = data.splitlines()
     elif fname.endswith(".gz"):
         ifh = gzip.open(fname)
     else:
@@ -83,43 +86,59 @@
 
     for line in ifh:
         if line.startswith("alias"):
             continue
         row = line.rstrip("\n").split("\t")
         toUcsc[row[0]] = row[1]
     return toUcsc
 
 def chromToUcsc(aliasFname, fieldIdx, ifh, ofh):
     " convert column number fieldIdx to UCSC-style chrom names "
     toUcsc = parseAlias(aliasFname)
 
     ucscChroms = set(toUcsc.values())
 
     for lineNo, sep, row in splitLines(ifh):
+        if len(row)<=2:
+            pass # fixedStep or variableStep lines are just passed through
+        elif row[0]=="fixedStep" or row[0]=="variableStep":
+            # fixedStep chrom=NC_033660.1 start=15778865 step=1
+            key, chrom = row[1].split("=")
+            assert(key=="chrom") # we assume that the first field has the chrom, that saves a lot of time
+            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
+            row[1] = "chrom="+ucscChrom
+
+        else:
             # just pass through any UCSC chrom names
             chrom = row[fieldIdx]
             if row[0].startswith("#") or chrom in ucscChroms:
                 ucscChrom = chrom
             else:
                 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
 
             row[fieldIdx] = ucscChrom
-        ofh.write(sep.join(row))
+
+        line = sep.join(row)
+        ofh.write(line)
         ofh.write("\n")
 
 def download(db):
     url = "http://hgdownload.soe.ucsc.edu/goldenPath/%s/database/chromAlias.txt.gz" % db
     gzData = urlopen(url).read()
 
     if 'cStringIO' in modules:
         data = StringIO(gzData)
     else:
         data = BytesIO(gzData)
     
     data = gzip.GzipFile(fileobj=data).read().decode()
     outFname = db+".chromAlias.tsv"
     open(outFname, "w").write(data)
     print("Wrote %s to %s" % (url, outFname))