bowtie --version returns strings like this:
    bowtie version 0.12.7
    32-bit
    Built on Franklin.local
    Tue Sep  7 14:25:02 PDT 2010

def _bowtie_major_version(stdout):
    """
    bowtie --version returns strings like this:
    bowtie version 0.12.7
    32-bit
    Built on Franklin.local
    Tue Sep  7 14:25:02 PDT 2010
    """
    version_line = stdout.split("\n")[0]
    version_string = version_line.strip().split()[2]
    major_version = int(version_string.split(".")[0])
    # bowtie version 1 has a leading character of 0 or 1
    if major_version == 0 or major_version == 1:
        major_version = 1
    return major_version