def main():
#read list
li = read_list(sys.argv[1])
#read fasta
algene = utils.read_fasta_usda(sys.argv[2])
#find overlap
for it in li:
find_overlap(it,algene)
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)