2777956c1202283ecc5bf8b773b9ab82bab5d849
max
  Thu Feb 23 12:01:05 2023 +0100
adding genark support to chromToUcsc, refs #30454

diff --git src/utils/chromToUcsc/chromToUcsc src/utils/chromToUcsc/chromToUcsc
index 090c802..65c93dc 100755
--- src/utils/chromToUcsc/chromToUcsc
+++ src/utils/chromToUcsc/chromToUcsc
@@ -187,31 +187,42 @@
                     handledUnmappedChrom(chrom, skipUnknown, skipWarned,
                                          "line %d: chrom name %s is not in chromAlias table" % (lineNo, repr(chrom)))
                     continue
             if isSam:
                 mateChrom = row[6]
                 if mateChrom not in ("=", "*"):
                     row[6] = toUcsc[mateChrom]
 
             row[fieldIdx] = ucscChrom
 
         line = sep.join(row)
         ofh.write(line)
         ofh.write("\n")
 
 def download(db):
+    " download chromAlias file from UCSC "
+    # Genark assemblies are in a different directory of the download server
+    if "_" in db:
+        p1 = db[0:3]
+        p2 = db[4:7]
+        p3 = db[7:10]
+        p4 = db[10:13]
+        url = "https://hgdownload.soe.ucsc.edu/hubs/%s/%s/%s/%s/%s/%s.chromAlias.txt" % (p1, p2, p3, p4, db, db)
+        asd
+    else:
         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))
     print("You can now convert a file with 'chromToUcsc -a %s -i infile.bed -o outfile.bed'" % outFname)
     exit(0)
 
 def main():