33efa29f7bf07da99da316e6228ad86957bf760b
max
  Wed Mar 29 12:11:54 2017 -0700
adding bedJoinTabOffset tool, for new track type by Kate, no redmine

diff --git src/utils/bedJoinTabOffset src/utils/bedJoinTabOffset
new file mode 100755
index 0000000..548717a
--- /dev/null
+++ src/utils/bedJoinTabOffset
@@ -0,0 +1,110 @@
+#!/usr/bin/env python2.7
+
+import logging, sys, optparse, string
+from collections import defaultdict
+import os
+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] inTabFile inBedFile outBedFile - given a bed file and tab file where each have a column with matching values: first get the value of column0, the offset and line length from inTabFile. Then go over the bed file, use the name field and append its offset and length to the bed file as two separate fields. Write the new bed file to outBed.")
+
+    parser.add_option("-d", "--debug", dest="debug", action="store_true", help="show debug messages")
+    parser.add_option("-t", "--tabKeyField", dest="tabKeyField", action="store", type="int", \
+        help="the index of the key field in the tab file that matches the key field in the bed file. default %default", default=0)
+    parser.add_option("-b", "--bedKeyField", dest="bedKeyField", action="store", type="int", \
+        help="the index of the key field in the bed file that matches the key field in the tab file. default %default", default=3)
+    #parser.add_option("", "--headers", dest="headers", action="store", help="comma-separated list of headers for outFile")
+    #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)
+    else:
+        logging.basicConfig(level=logging.INFO)
+    return args, options
+
+def iterLineOffsets(ifh):
+    """ parse a text file and yield tuples of (line, startOffset, endOffset).
+    endOffset does include the newline
+    """
+    line = True
+    start = 0
+    while line!='':
+       line = ifh.readline()
+       end = ifh.tell()
+       if line!="":
+           yield line, start, end
+       start = ifh.tell()
+
+def tabOffsets(fnames, keyCol):
+    " iterate over all lines in tab filenames and return dict with value -> (offset, lineLen) "
+    idxFnames = {}
+    ret = {}
+    for i, fname in enumerate(fnames):
+        print ("Reading %s, %0.f %%"  % (fname, float(100*i)/len(fnames)))
+        offset = 0
+        for line, start, end in iterLineOffsets(open(fname, "rb")):
+            if keyCol==0:
+                # most common case: saves a bit of time by not building a huge list
+                key, restLine = string.split(line, "\t", 1)
+            else:
+                key = line.rstrip("\n").split("\t")[keyCol]
+
+            if key in idxFnames:
+                print("Warning: duplicate key %s, found in files %s and %s" % \
+                    (key, fname, idxFnames[key]))
+                continue
+            idxFnames[key] = fname
+
+            ret[key] = (start, len(line))
+
+    return ret
+
+def bedJoinTabOffset(inTab, inBed, outBed, options):
+    " cat and index all files in inDir "
+
+    #if isdir(inTab):
+    #print ("Getting files in directory %s" % inDir)
+    #fnames = os.listdir(inDir)
+    #print ("Found %d files" % len(fnames))
+
+    keyToOffLen = tabOffsets([inTab], options.tabKeyField)
+    allKeys = set(keyToOffLen)
+
+    bedOfh = open(outBed, "wb")
+
+    keyIdx = options.bedKeyField
+    for line in open(inBed):
+        if line=="\n":
+            continue
+        fields = line.rstrip("\n").split("\t")
+        key = fields[keyIdx]
+        offLen = keyToOffLen.get(key)
+        if offLen == None:
+           logging.error("bed key '%s' is not in the tab-sep file" % key)
+           assert(False)
+        offset, lineLen = offLen
+        newLine = "%s\t%s\t%s\n" % (line.rstrip("\n"), offset, lineLen)
+        bedOfh.write(newLine)
+        allKeys.remove(key)
+
+    bedOfh.close()
+    logging.info("Wrote %s" % outBed)
+
+    if len(allKeys)!=0:
+        logging.warn("The following keys in the tab file were not referenced in the bed file: %s" % ", ".join(allKeys))
+
+# ----------- main --------------
+def main():
+    args, options = parseArgs()
+    inTab, inBed, outBed = args
+    bedJoinTabOffset(inTab, inBed, outBed, options)
+
+main()