>Potrs164783
AGGAAGTGTGAGATTGAAAAAACATTACTATTGAGGAATTTTTGACCAGATCAGAATTGAACCAACATGATGAAGGGGAT
TGTTTGCCATCAGAATATGGCATGAAATTTCTCCCCTAGATCGGTTCAAGCTCCTGTAGGTTTGGAGTCCTTAGTGAGAA
CTTTCTTAAGAGAATCTAATCTGGTCTGTTCCTCGTCATAAGTTAAAGAAAAACTTGAAACAAATAACAAGCATGCATAA
>Potrs164784
TTACCCTCTACCAGCACCAATGCCTATGATCTTACAAAAATCCTTAATAAAAAGAAATCCAAAACCATTGTTACCATTCC
GGAATTACATTCTGAGATAAAAACCCTCAAATCTGAATTACAATCCCTTAAACAAGCCCAACAAAAAGACTCTGCCATAC

>conc
AGGAAGTGTGAGATTGAAAAAACATTACTATTGAGGAATTTTTGACCAGA
TCAGAATTGAACCAACATGATGAAGGGGATTGTTTGCCATCAGAATATGG
CATGAAATTTCTCCCCTAGATCGGTTCAAGCTCCTGTAGGTTTGGAGTCC
TTAGTGAGAACTTTCTTAAGAGAATCTAATCTGGTCTGTTCCTCGTCATA
AGTTAAAGAAAAACTTGAAACAAATAACAAGCATGCATAAACCATATGGC
ATTTTGCATCCATTTGTGCATTTCATTTAGTTTACTTGCATTCATTCAGG

final = list()

with open("test.fa", 'r') as fh_in:
    for line in fh_in:
        line = line.strip()
        if not line.startswith(">"):
            final.append(line)

final2 = "".join(final)

with open("testconcat.fa", 'w') as fh_out:
    fh_out.write(">con")
    fh_out.write("n")
    fh_out.write(final2)