def main(args):
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 = [1, 2, 3, 4, 5, 6]
pvals = [-9, -10]
len1 = 0
len2 = 0
f1 = ""
f2 = ""
offset = 0
for j in pvals:
#if j == -9: offset = 60
#else: offset = 0
print "Doing pval " + str(j)
pwms = []
pwmsShuffled = []
for i in range(111):
if i+1 < 10:
pwms.append("MA000" + str(i+1) + "(p " + str(j) + ").gff")
pwmsShuffled.append("MA000" + str(i+1) + "random(p " + str(j) + ").gff")
elif i+1 < 100:
pwms.append("MA00" + str(i+1) + "(p " + str(j) + ").gff")
pwmsShuffled.append("MA00" + str(i+1) + "random(p " + str(j) + ").gff")
else:
pwms.append("MA0" + str(i+1) + "(p " + str(j) + ").gff")
pwmsShuffled.append("MA0" + str(i+1) + "random(p " + str(j) + ").gff")
for i in range(len(pwms)-offset):
f1 = open("../doc/fasta/" + pwms[i+offset], "r")
f2 = open("../doc/fasta/" + pwmsShuffled[i+offset], "r")
m1 = cm_scan3.buildMotifs(f1, alignment)
m2 = cm_scan3.buildMotifs(f2, alignment)
len1 = len(m1)
len2 = len(m2)
f1.close()
f2.close()
try:
print len1, len2
if len1 != 0 and len2 != 0:
print pwms[i+offset]
cm_scan3NA.mainRunner(pwms[i+offset], m1, min([len1, len2]), "LL all PWM pval " + str(j) + "/")
print pwmsShuffled[i+offset]
cm_scan3NA.mainRunner(pwmsShuffled[i+offset], m2, min([len1, len2]), "LL all PWMRandom pval " + str(j) + "/")
else: print "NO HITS"
except KeyError:
print "\t\tkey problem", pwms[i+offset]
sys.exit(0)
def main(args):
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, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25]
pvals = [-9, -10]
len1 = 0
f1 = ""
for j in pvals:
print "Doing pval " + str(j)
pwms = []
for i in range(111):
if i+1 < 10:
pwms.append("MA000" + str(i+1))
elif i+1 < 100:
pwms.append("MA00" + str(i+1))
else:
pwms.append("MA0" + str(i+1))
for s in skip:
for i in range(len(pwms)):
f1 = open("../doc/fasta/" + pwms[i] + "(p " + str(j) + ").gff", "r")
m1 = cm_scan3.buildMotifs(f1, alignment)
len1 = findLength(pwms[i] + ".pwm")
f1.close()
print len(m1)
if len1 > s+1:
try:
if len(m1) != 0:
print pwms[i]
cm_scan3NA.mainRunner(pwms[i] + "(p " + str(j) + ").gff", m1, len(m1), "LL all PWM pval " + str(j) + " NA " + str(s) + "/", s)
else: print "NO HITS"
except KeyError:
print "\t\tkey problem", pwms[i]
makeGraphs.make("LL all PWM pval " + str(j) + " NA " + str(s) + "/", j, s)
cm_scanTester2.mainRunner(s, j)
sys.exit(0)