def find_presence(gene,filelist,algene):
fpri = []
rpri = []
for x in filelist:
if(gene in x):
fpri,rpri = utils.read_trad_primer(x)
fon = []
for i in range(0,len(fpri)):
if(utils.if_amplified(fpri[i],rpri[i],algene[gene])):
fon.append([fpri[i],rpri[i]])
return fon
def main():
#read list
list_gene = {}
for line in open(sys.argv[1],'r'):
spl = line.strip().split('\t')
if(list_gene.has_key(spl[2])):
temp = list_gene[spl[2]]
temp.append(spl[1])
list_gene[spl[2]] = temp
else:
temp = [spl[1]]
list_gene[spl[2]] = temp
#read fasta
fafile = sys.argv[2]
faseq = utils.read_fasta_usda(fafile)
#read primers -> primer
mypath = sys.argv[3]
onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]
primer = {}
for file in onlyfiles:
if (file[:1] == "."):
continue
fullpath = mypath+file
fpri,rpri = utils.read_trad_primer(fullpath)
locus = file.split('.')[0]
if(primer.has_key(locus)):
temp = primer[locus]
temp.append([fpri,rpri])
primer[locus] = temp
else:
primer[locus] = [fpri,rpri]
# print list_gene
for item in list_gene.items():
if(len(item[1]) >1):
genename = item[0]
g1 = item[1][0]
g2 = item[1][1]
if( primer.has_key(g1) and primer.has_key(g2)):
find_least_primer_two_gene(g1,g2,faseq,primer,genename)
#else:
# print g1,g2
else:
genename = item[0]
g1 = item[1][0]
if(primer.has_key(g1)):
find_lease_primer_one_gene(g1,faseq,primer,genename)
def main():
oligotm = sys.argv[1]
ntthal = sys.argv[2]
minTm = 55
maxTm = 100
maxHair = 24
#read primer
file = sys.argv[3]
fpri,rpri = utils.read_trad_primer(file)
#print fpri
#print rpri
for f in fpri:
check_mt(f,oligotm, minTm, maxTm)
check_hair(f,ntthal,maxHair)
for r in rpri:
check_mt(r,oligotm, minTm, maxTm)
check_hair(r,ntthal,maxHair)
def main():
min = 200
max = 370
#parameters that used
mis = 0
#read primer
fpri, rpri = utils.read_trad_primer(sys.argv[1])
lfile = sys.argv[2]
num = 0
seq = utils.read_fasta(sys.argv[2])
for item in seq.items():
se = item[1]
for f in fpri:
for i in range(0, len(se)-len(f)):
str1 = se[i:len(f)+i]
#print str1, f
#print mismatch(str1,f,mis)
if mismatch(str1,f,mis):
#print "match"
num += 1
output = ">F:"+lfile+"_"+str(num)+"\n"+f+'\n'
#print output
#print ">F:",f, i
for r in rpri:
rp = r
for j in range(0, len(se)-len(rp)):
str2 = se[j:len(rp)+j]
if mismatch(str2,rp,mis):
#print "match"
frp = reverse_complement.get_rc(rp)
#print ">R:",frp,j+len(rp), j+len(rp)-i
flen = j+len(rp)-i
#print flen
if(flen >min and flen<max):
output = output + ">R:"+lfile+"_"+str(num)+"\n"+frp+'\n'
print output
