Python get_divergence_trajectories_local_filenameの例

コード例 #1

def get_divergence_trajectory_local(pname,
                                    fragment,
                                    block_length=150,
                                    VERBOSE=0):
    '''Get local divergence trajectory'''
    from hivwholeseq.patients.filenames import get_divergence_trajectories_local_filename
    fn = get_divergence_trajectories_local_filename(pname, fragment)
    npz = np.load(fn)
    return (npz['dg'], npz['ind'], npz['block_length'], npz['L'])

コード例 #2

ファイル: store_divergence_diversity_local.py プロジェクト: iosonofabio/hivwholeseq

            if use_sliding:
                (x, dg, ds) = get_divergence_diversity_sliding(aft, block_length,
                                                               VERBOSE=VERBOSE)
            else:
                (x, dg, ds) = get_divergence_diversity_blocks(aft, block_length,
                                                              VERBOSE=VERBOSE)

            # FIXME: avoid this var to get different conv and aft indices
            times = patient.times[ind]
            dgs[(pname, fragment)] = (patient.times[ind], dg)
            dss[(pname, fragment)] = (patient.times[ind], ds)

            if save_to_file:
                from hivwholeseq.patients.filenames import \
                        get_divergence_trajectories_local_filename, \
                        get_diversity_trajectories_local_filename

                # savez does not support masked arrays
                dg_save = np.array(dg).copy()
                dg_save[dg.mask] = -1
                ds_save = np.array(ds).copy()
                ds_save[ds.mask] = -1
                L = aft.shape[2]

                fn_out = get_divergence_trajectories_local_filename(pname, fragment)
                np.savez(fn_out, ind=ind, dg=dg_save, L=L, block_length=[block_length])
                fn_out = get_diversity_trajectories_local_filename(pname, fragment)
                np.savez(fn_out, ind=ind, ds=ds_save, L=L, block_length=[block_length])
                if VERBOSE >= 1:
                    print 'saved to file'

コード例 #3

ファイル: get_divergence_diversity_local.py プロジェクト: iosonofabio/hivwholeseq

def get_divergence_trajectory_local(pname, fragment, block_length=150, VERBOSE=0):
    '''Get local divergence trajectory'''
    from hivwholeseq.patients.filenames import get_divergence_trajectories_local_filename
    fn = get_divergence_trajectories_local_filename(pname, fragment)
    npz = np.load(fn)
    return (npz['dg'], npz['ind'], npz['block_length'], npz['L'])

コード例 #4

            dgs[(pname, fragment)] = (patient.times[ind], dg)
            dss[(pname, fragment)] = (patient.times[ind], ds)

            if save_to_file:
                from hivwholeseq.patients.filenames import \
                        get_divergence_trajectories_local_filename, \
                        get_diversity_trajectories_local_filename

                # savez does not support masked arrays
                dg_save = np.array(dg).copy()
                dg_save[dg.mask] = -1
                ds_save = np.array(ds).copy()
                ds_save[ds.mask] = -1
                L = aft.shape[2]

                fn_out = get_divergence_trajectories_local_filename(
                    pname, fragment)
                np.savez(fn_out,
                         ind=ind,
                         dg=dg_save,
                         L=L,
                         block_length=[block_length])
                fn_out = get_diversity_trajectories_local_filename(
                    pname, fragment)
                np.savez(fn_out,
                         ind=ind,
                         ds=ds_save,
                         L=L,
                         block_length=[block_length])
                if VERBOSE >= 1:
                    print 'saved to file'