9e42bf8546abb0abc46036b726c8a25515db80a0
max
  Thu Feb 28 05:08:28 2019 -0800
adding tool for sorting of a trackDb (e.g. trackHub) file. no redmine

diff --git src/utils/trackDbRename src/utils/trackDbRename
deleted file mode 100755
index 7a283bb..0000000
--- src/utils/trackDbRename
+++ /dev/null
@@ -1,92 +0,0 @@
-#!/usr/bin/env python
-
-import logging, sys, optparse, string
-from collections import defaultdict
-from os.path import join, basename, dirname, isfile
-
-# ==== functions =====
-    
-def parseArgs():
-    " setup logging, parse command line arguments and options. -h shows auto-generated help page "
-    parser = optparse.OptionParser("""usage: %prog [options] inFile tagName replaceFile outFile - mass-rename trackDb tags given a file with oldVal<tab>newVal
-            
-    Examples:
-        %prog trackDb.orig.txt track replace.tsv trackDb.txt
-        %prog trackDb.orig.txt shortLabel replace.tsv trackDb.txt
-    """)
-
-    parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
-    parser.add_option("", "--newMeta", dest="newMeta", action="store", help="keep the old name as metadata tag with this name")
-    parser.add_option("", "--suffList", dest="suffList", action="store", help="comma-sep list of suffixes. These are ignored when comparing values. Many tracks need suffixes for the various track types, e.g. peaks and coverage. A typical value could be 'pk,cov'")
-    #parser.add_option("-f", "--file", dest="file", action="store", help="run on file") 
-    #parser.add_option("", "--test", dest="test", action="store_true", help="do something") 
-    (options, args) = parser.parse_args()
-
-    if args==[]:
-        parser.print_help()
-        exit(1)
-
-    if options.debug:
-        logging.basicConfig(level=logging.DEBUG)
-        logging.getLogger().setLevel(logging.DEBUG)
-    else:
-        logging.basicConfig(level=logging.INFO)
-        logging.getLogger().setLevel(logging.INFO)
-
-    return args, options
-
-def parseRepl(fname):
-    d = {}
-    for line in open(fname):
-        key, val = line.rstrip("\n").split("\t")
-        assert(key not in d) # error: duplicate keys in replace file
-        d[key] = val
-    return d
-
-# ----------- main --------------
-def main():
-    args, options = parseArgs()
-
-    inFn, onlyTag, replFn, outFn = args
-    newMeta = options.newMeta
-    suffList = options.suffList.split(",")
-
-    replDict = parseRepl(replFn)
-    
-
-    ofh = open(outFn, "w")
-    for line in open(inFn):
-        if line=="\n":
-            ofh.write(line)
-            continue
-
-        tag, val = string.split(line.strip(), " ",maxsplit=1)
-        if tag!=onlyTag:
-            ofh.write(line)
-            continue
-
-        origVal = val
-        for suf in suffList:
-            val = val.replace(suf, "")
-        val = val.strip()
-
-        if val not in replDict:
-            logging.info("value '%s' (original: '%s') was not replaced, line passed though" % (val, origVal))
-            ofh.write(line)
-            continue
-
-        spcCount = len(line) - len(line.lstrip(" "))
-        suffix = origVal.replace(val, "")
-        suffix = suffix.replace("Cov", "Cv")
-        suffix = suffix.replace("Junc", "Sp")
-        newLine = "%s%s %s%s" % (" "*spcCount, tag, replDict[val], suffix)
-        ofh.write(newLine+"\n")
-        if newMeta:
-            ofh.write("%smetadata %s=%s\n" % (" "*spcCount, newMeta, val.replace(" ", "_")))
-
-    ofh.close()
-    print("Wrote "+ofh.name)
-
-
-
-main()