def write_phy(data, sidx, pnames):
    """ 
    write the phylip output file from the tmparr[seqarray] 
    """

    ## grab seq data from tmparr
    start = time.time()
    tmparrs = os.path.join(data.dirs.outfiles, "tmp-{}.h5".format(data.name)) 
    with h5py.File(tmparrs, 'r') as io5:
        seqarr = io5["seqarr"]

        ## trim to size b/c it was made longer than actual
        end = np.where(np.all(seqarr[:] == "", axis=0))[0]
        if np.any(end):
            end = end.min()
        else:
            end = seqarr.shape[1] 

        ## write to phylip 
        with open(data.outfiles.phy, 'w') as out:
            ## write header
            out.write("{} {}\n".format(seqarr.shape[0], end))

            ## write data rows
            for idx, name in enumerate(pnames):
                out.write("{}{}\n".format(name, "".join(seqarr[idx, :end])))
    LOGGER.debug("finished writing phy in: %s", time.time() - start)
def write_phy(data, sidx, pnames):
    """ 
    write the phylip output file from the tmparr[seqarray] 
    """

    ## grab seq data from tmparr
    start = time.time()
    tmparrs = os.path.join(data.dirs.outfiles, "tmp-{}.h5".format(data.name)) 
    with h5py.File(tmparrs, 'r') as io5:
        seqarr = io5["seqarr"]

        ## trim to size b/c it was made longer than actual
        end = np.where(np.all(seqarr[:] == "", axis=0))[0]
        if np.any(end):
            end = end.min()
        else:
            end = seqarr.shape[1] 

        ## write to phylip 
        with open(data.outfiles.phy, 'w') as out:
            ## write header
            out.write("{} {}\n".format(seqarr.shape[0], end))

            ## write data rows
            for idx, name in enumerate(pnames):
                out.write("{}{}\n".format(name, "".join(seqarr[idx, :end])))
    LOGGER.debug("finished writing phy in: %s", time.time() - start)
def write_phy ( data , sidx , pnames ) : ## grab seq data from tmparr start = time . time ( ) tmparrs = os . path . join ( data . dirs . outfiles , "tmp-{}.h5" . format ( data . name ) ) with h5py . File ( tmparrs , 'r' ) as io5 : seqarr = io5 [ "seqarr" ] ## trim to size b/c it was made longer than actual end = np . where ( np . all ( seqarr [ : ] == "" , axis = 0 ) ) [ 0 ] if np . any ( end ) : end = end . min ( ) else : end = seqarr . shape [ 1 ] ## write to phylip  with open ( data . outfiles . phy , 'w' ) as out : ## write header out . write ( "{} {}\n" . format ( seqarr . shape [ 0 ] , end ) ) ## write data rows for idx , name in enumerate ( pnames ) : out . write ( "{}{}\n" . format ( name , "" . join ( seqarr [ idx , : end ] ) ) ) LOGGER . debug ( "finished writing phy in: %s" , time . time ( ) - start )
write the phylip output file from the tmparr[seqarray]
write the phylip output file from the tmparr [ seqarray ]