58f787640ea77f16c8f6d4481693a83ec9ef647b
vsmalladi
  Tue May 8 10:29:52 2012 -0700
First step in python lib reogranization. Redmine #7029.
diff --git python/lib/ucscGb/ucscUtils.py python/lib/ucscGb/ucscUtils.py
deleted file mode 100644
index 8399505..0000000
--- python/lib/ucscGb/ucscUtils.py
+++ /dev/null
@@ -1,152 +0,0 @@
-#!/hive/groups/encode/dcc/bin/python
-import sys, string, os, re, argparse, subprocess, math
-
-def isGbdbFile(file, table, database):
-    errors = []
-    if os.path.isfile("/gbdb/%s/bbi/%s" % (database, file)):
-        return 1
-    else:
-        cmd = "hgsql %s -e \"select fileName from (%s)\"" % (database, table)
-        p = subprocess.Popen(cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, close_fds=True)
-        cmdoutput = p.stdout.read()
-        if os.path.isfile(cmdoutput.split("\n")[1]):
-            return 1
-        else:
-            return 0
-            
-def makeFileSizes(inlist, path=None):
-    checklist = list()
-
-    for i in inlist:
-    	if path:
-            checklist.append("%s/%s" % (path, i))    
-        else:
-            checklist.append(i)
-    filesizes = 0
-    for i in checklist:
-        realpath = os.path.realpath(i)
-        filesizes = filesizes + int(os.path.getsize(realpath))
-
-    filesizes = math.ceil(float(filesizes) / (1024**2))
-
-    return int(filesizes)
-    
-def printIter(set, path=None):
-    output = []
-    for i in sorted(set):
-        if path:
-            output.append("%s/%s" % (path, i))
-        else:
-            output.append("%s" % (i))
-    return output
-
-def zeros(m,n):
-    cross = list()
-    for i in range(m):
-        cross.append(list())
-        for j in range(n):
-            cross[i].append(0)
-    return cross
-
-def mergeList(list1,list2):
-    """ Takes in two lists, returns a single list merged into a consensus list using a modified Needleman-Wunsch
-        alignment. The comment lines with two comments are there to signalify a change to Smith-Waterman, remove the 
-        double commented lines to convert.
-        Single comment lines are for debugging, remove when this routine matures.
-    """
-
-    m,n = len(list1),len(list2)
-    score = zeros(m+1,n+1)
-    pointer = zeros(m+1,n+1)
-    penalty = -1
-    max_i = 0
-    max_j = 0
-    maxScore = 0
-     
-    #print "len_i = %s, len_j = %s" % (m,n)
-    for i in range(1,m+1):
-        for j in range(1,n+1):
-            scoreUp = score[i-1][j]+penalty
-            scoreDown = score[i][j-1]+penalty
-            scoreDiagonal = score[i-1][j-1]-5
-            if list1[i-1] == list2[j-1]:
-                scoreDiagonal = scoreDiagonal + 10
-            score[i][j] = max(0,scoreUp,scoreDown,scoreDiagonal)
-            if score[i][j] == 0:
-                pointer[i][j] = 0
-            if score[i][j] == scoreUp:
-                pointer[i][j] = 1
-            if score[i][j] == scoreDown:
-                pointer[i][j] = 2
-            if score[i][j] == scoreDiagonal:
-                pointer[i][j] = 3
-            ##if score[i][j] >= maxScore:
-            ##    max_i = i
-            ##    max_j = j
-            ##    maxScore = score[i][j]
-
-    #for k in pointer:
-    #    line = ""
-    #    for l in k:
-    #        line = line + "%s " % l
-    #    print line
-
-    align1,align2 = list(),list()
-    ##after_i,after_j = max_i,max_j
-    #print "max_i = %s, max_j = %s" % (max_i, max_j)
-    while pointer[i][j] != 0:
-        if pointer[i][j] == 3:
-            align1.append(str(list1[i-1]))
-            align2.append(str(list2[j-1]))
-            i = i-1
-            j = j-1
-        elif pointer[i][j] == 2:
-            align1.append('-')
-            align2.append(str(list2[j-1]))
-            j = j-1
-        elif pointer[i][j] == 1:
-            align1.append(str(list1[i-1]))
-            align2.append('-')
-            i = i-1
-
-    before_i,before_j = i,j
-    align1.reverse()
-    align2.reverse()
-    consensus = list()
-
-    #for i in range(len(align1)):
-    #    print "%s = %s" % (align1[i], align2[i])
-
-    for i in range(len(align1)):
-        if align1[i] == align2[i]:
-            consensus.append(align1[i])
-        elif align1[i] == "-":
-            consensus.append(align2[i])
-        elif align2[i] == "-":
-            consensus.append(align1[i])
-        elif align1[i] != align2[i]:
-            consensus.append(align1[i])
-            consensus.append(align2[i])
-    before = list()
-    if before_i != 0:
-        before.extend(list1[0:before_i])
-    if before_j != 0:
-        before.extend(list2[0:before_j])
-    ##if after_i < len(list1):
-    ##    consensus.extend(list1[after_i:])
-    ##if after_j < len(list2):
-    ##    consensus.extend(list2[after_j:])
-    before.extend(consensus)
-    setcon = list()
-    p = re.compile('^#')
-    p2 = re.compile('^\s*$')
-    for i in before:
-        if p.match(i) or p2.match(i):
-            setcon.append(i)
-            continue
-        if i in setcon:
-            continue
-        else:
-            setcon.append(i)
-    
-    return setcon
