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):
# 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):
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)
"""Take PWM gff hits, and make aligned PWM hits. This was done b/c Rithun needs hits for the controls."""
import cm_scan3, pickle, os
gff_file = '../Doc/fasta/human1ku-corrected.fasta.MA0001random.gff'
alignment_file = '../Doc/pickle/alignment.pickle'
with open(alignment_file) as f:
alignment = pickle.load(f)
species = ('human', 'chimp', 'mouse', 'rat', 'dog')
pval = '-9'
print 'ControlType\tPWM\tPWMhit\tSpecies\tSeq'
for gff_file in os.listdir('../Doc/fasta/'):
pwm_type = ''
if 'shuffle' in gff_file and pval in gff_file:
pwm_type = 'shuffle'
elif 'random' in gff_file and pval in gff_file:
pwm_type = 'random'
if pwm_type:
with open('../Doc/fasta/' + gff_file) as f:
motif_hits = cm_scan3.buildMotifs(f, alignment)
for idx, hit in enumerate(motif_hits):
for org, seq in zip(species, hit):
pwm = gff_file.split(pwm_type)[0]
print pwm_type + '\t' + pwm + '\t' + str(idx+1) + '\t' + org + '\t' + seq
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)