def alignfast(names, seqs):
    """
    Performs MUSCLE alignments on cluster and returns output as string
    """
    matfile = op.join(datadir, "blosum80.mat")
    cmd = "poa -read_fasta - -pir stdout {0} -tolower -silent -hb -fuse_all".format(matfile)
    p = Popen(cmd, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
    s = ""
    for i, j in zip(names, seqs):
        s += "\n".join((i, j)) + "\n"
    return p.communicate(s)[0]
def alignfast ( names , seqs ) : matfile = op . join ( datadir , "blosum80.mat" ) cmd = "poa -read_fasta - -pir stdout {0} -tolower -silent -hb -fuse_all" . format ( matfile ) p = Popen ( cmd , shell = True , stdin = PIPE , stdout = PIPE , stderr = STDOUT , close_fds = True ) s = "" for i , j in zip ( names , seqs ) : s += "\n" . join ( ( i , j ) ) + "\n" return p . communicate ( s ) [ 0 ]
Performs MUSCLE alignments on cluster and returns output as string