Get matrix, barcodes and features from H5 file

Question

[jonathanpa12]

Hello everyone

I'm trying to extract the matrix, barcodes and features from a H5 file following the python code of https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices:

import collections
import scipy.sparse as sp_sparse
import tables

CountMatrix = collections.namedtuple('CountMatrix', ['feature_ref', 'barcodes', 'matrix'])

def get_matrix_from_h5(filename):
    with tables.open_file(filename, 'r') as f:
        mat_group = f.get_node(f.root, 'matrix')
        barcodes = f.get_node(mat_group, 'barcodes').read()
        data = getattr(mat_group, 'data').read()
        indices = getattr(mat_group, 'indices').read()
        indptr = getattr(mat_group, 'indptr').read()
        shape = getattr(mat_group, 'shape').read()
        matrix = sp_sparse.csc_matrix((data, indices, indptr), shape=shape)

        feature_ref = {}
        feature_group = f.get_node(mat_group, 'features')
        feature_ids = getattr(feature_group, 'id').read()
        feature_names = getattr(feature_group, 'name').read()
        feature_types = getattr(feature_group, 'feature_type').read()
        feature_ref['id'] = feature_ids
        feature_ref['name'] = feature_names
        feature_ref['feature_type'] = feature_types
        tag_keys = getattr(feature_group, '_all_tag_keys').read()
        for key in tag_keys:
            feature_ref[key] = getattr(feature_group, key).read()

        return CountMatrix( matrix)

filtered_matrix_h5 = "GSM4785601_P6_2.filtered_feature_bc_matrix.h5"
filtered_feature_bc_matrix = get_matrix_from_h5(filtered_matrix_h5)

but I'm getting this error. Can someone help me please?

Traceback (most recent call last):
  File "/home/jonathan/extracth5.py", line 32, in <module>
    filtered_feature_bc_matrix = get_matrix_from_h5(filtered_matrix_h5)
  File "/home/jonathan/extracth5.py", line 27, in get_matrix_from_h5
    feature_ref[key] = getattr(feature_group, key).read()
TypeError: getattr(): attribute name must be string

Thank you in advance

[Nitin Narwade]

I am not entirely sure about this but can you try str(key) on line number 27 in your code feature_ref[key] = getattr(feature_group, key).read().

NOTE: I am suggesting this purely based on error reported in your error log.

[jonathanpa12]

I tried it, but I didn't work.