def main(args):
# Create the tree structure
supertree = Tree([])
root = TreeNode("r")
rodent = TreeNode("")
primate = TreeNode("")
highermammal = TreeNode("")
mouse = TreeNode("3")
rat = TreeNode("4")
human = TreeNode("1")
chimp = TreeNode("2")
dog = TreeNode("5")
root.children = [ rodent, highermammal ]
rodent.children = [ mouse, rat ]
highermammal.children = [ dog, primate ]
primate.children = [ human, chimp ]
supertree.r = root
supertree.node = [ root, highermammal, rodent, mouse,
rat, primate, human, chimp ]
a = ["A", "C", "T", "G"]
#first I need to make all the trees
trees = dict()
for n1 in a:
for n2 in a:
for n3 in a:
for n4 in a:
for n5 in a:
trees[n1+n2+n3+n4+n5] = color(supertree, [n1, n2, n3, n4, n5])
a_file = open("../doc/pickle/alignment.pickle", "r")
# Load the 5-way alignment
alignment = pickle.load(a_file)
# Close relevant files
a_file.close()
skip = [0]#, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12]
pvals = [-9]
len1 = 0
f1 = ""
for j in pvals:
print "Doing pval " + str(j)
for s in skip:
f1 = open("../doc/fasta/MA0112(p " + str(j) + ").gff", "r")
m1 = cm_scan3.buildMotifs(f1, alignment)
len1 = findLength("MA0112.pwm")
f1.close()
print len(m1)
if len1 > s+1:
if len(m1) != 0:
scanNonAdj2.mainRunner("MA0112(p " + str(j) + ").gff", m1, len(m1), "LL all PWM pval " + \
str(j) + " NA " + str(s) + "/", s, trees)
else: print "NO HITS"
#makeGraphs.make("LL all PWM pval " + str(j) + " NA " + str(s) + "/", j, s)
#randomScanNonAdj2.mainRunner(s, j, trees)
sys.exit(0)
def main(args):
# Create the tree structure
supertree = Tree([])
root = TreeNode("r")
rodent = TreeNode("")
primate = TreeNode("")
highermammal = TreeNode("")
mouse = TreeNode("3")
rat = TreeNode("4")
human = TreeNode("1")
chimp = TreeNode("2")
dog = TreeNode("5")
root.children = [ rodent, highermammal ]
rodent.children = [ mouse, rat ]
highermammal.children = [ dog, primate ]
primate.children = [ human, chimp ]
supertree.r = root
supertree.node = [ root, highermammal, rodent, mouse,
rat, primate, human, chimp ]
a = ["A", "C", "T", "G"]
#first I need to make all the trees
trees = dict()
for n1 in a:
for n2 in a:
for n3 in a:
for n4 in a:
for n5 in a:
trees[n1+n2+n3+n4+n5] = color(supertree, [n1, n2, n3, n4, n5])
a_file = open("../../Doc/pickle/alignment.pickle", "r")
# Load the 5-way alignment
alignment = pickle.load(a_file)
# Close relevant files
a_file.close()
pwmFile = open("../../Doc/Vertebrate PWM/PWMlist.txt", "r")
pwms = pickle.load(pwmFile)
pwmFile.close()
skip = range(1)
pvals = [-9]
len1 = 0
f1 = ""
for j in pvals:
print "Doing pval " + str(j)
for s in skip:
for i in range(len(pwms)):
#f1 = open("../doc/fasta/" + pwms[i] + "random(p " + str(j) + ").gff", "r")
f1 = open("../../Doc/fasta/sortedhuman1ku-corrected.fasta." + pwms[i] + "cc.gff", "r")
m1 = cm_scan3.buildMotifs(f1, alignment)
len1 = findLength(pwms[i] + "cc.pwm")
f1.close()
print len(m1)
if len1 > s+1:
if len(m1) != 0:
print pwms[i]
scanNonAdj2.mainRunner("sortedhuman1ku-corrected.fasta." + pwms[i] + "cc.gff", m1, len(m1), \
"../../Results/Controls/Comp Permuted PWMs/Raw Data/Gap " + \
str(s) + "/", s, trees)
#scanNonAdj2.mainRunner(pwms[i] + "(p " + str(j) + ").gff", m1, len(m1), "LL all PWM pval " + \
# str(j) + " NA " + str(s) + "/", s, trees)
#else: print "NO HITS"
#randomScanNonAdj2.mainRunner(s, j, trees)
sys.exit(0)
