seq1
ACTGTGTGTGTACAGTGCA
seq2
ACTGTGTGTGTACGT
seq3
ACAACACGTGTGTTTTTTT

file1 = open(sys.argv[1], "r")

counter = 0
for line in file1:
    counter = counter + 1
    line = line.strip("n")
    if counter%2 != 0:
        print(">"+line)
    else:
        print(line)

file1.close()

counter = 0
for line in file1:
    counter = counter + 1
    if counter%2 != 0:
        print(">", end="")
    print(line.strip("n"))

with open('file1.txt') as f:
    for i,v in enumerate(f,1):
        if i%2!=0:
            print(v) # add '>' like ('>'+v)

seq1

seq2

seq3