Hi,
I am tyring to combine some scrna seq loom files into one to run rna velocity. Following is my code:
#####check ca and ra keys()
test=loompy.connect("/scratch/scrna_seq_dat_files/looms/test.loom")
test.ca.keys()
['QC.fraction.of.mtrna', 'QC.number.of.features', 'QC.number.of.reads', 'QC.number.of.umi', 'QC.sequence.saturation', 'batch', 'cell', 'cell_number', 'library_id', 'molecule_h5', 'observation_id', 'platform', 'platform_chemistry', 'platform_name', 'purification', 'qcc', 'sample_bc', 'sample_id', 'sample_id_rainier', 'sample_origin', 'sample_source_id', 'sample_type', 'seq_cycles', 'seq_instrument', 'seq_site', 'tissue_type']
test.ra.keys()
['accession_id', 'name', 'symbol']
files=["file1.loom","files2.loom","file3.loom",...."file23.loom"]
loompy.combine(files,"combined.loom",key="accession_id")
#ERROR
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /home/yfstkchy/miniconda3/envs/myenv/lib/python3.7/site-packages/loompy/loompy.py, line 471
Traceback (most recent call last):
File "", line 1, in
File "/home/yfstkchy/miniconda3/envs/myenv/lib/python3.7/site-packages/loompy/loompy.py", line 1353, in combine
ds.add_loom(f, key, batch_size=batch_size, convert_attrs=convert_attrs)
File "/home/yfstkchy/miniconda3/envs/myenv/lib/python3.7/site-packages/loompy/loompy.py", line 472, in add_loom
ca = {key: v[selection] for key, v in other.col_attrs.items()}
File "/home/yfstkchy/miniconda3/envs/myenv/lib/python3.7/site-packages/loompy/loompy.py", line 472, in
ca = {key: v[selection] for key, v in other.col_attrs.items()}
TypeError: only integer scalar arrays can be converted to a scalar index
any insight is greatly appreciated.
Hi,
I am tyring to combine some scrna seq loom files into one to run rna velocity. Following is my code:
#####check ca and ra keys()
files=["file1.loom","files2.loom","file3.loom",...."file23.loom"]
loompy.combine(files,"combined.loom",key="accession_id")
#ERROR
WARNING:root:╭── 'batch_scan_layers' is deprecated. Use 'scan' instead
WARNING:root:╰──> at /home/yfstkchy/miniconda3/envs/myenv/lib/python3.7/site-packages/loompy/loompy.py, line 471
Traceback (most recent call last):
File "", line 1, in
File "/home/yfstkchy/miniconda3/envs/myenv/lib/python3.7/site-packages/loompy/loompy.py", line 1353, in combine
ds.add_loom(f, key, batch_size=batch_size, convert_attrs=convert_attrs)
File "/home/yfstkchy/miniconda3/envs/myenv/lib/python3.7/site-packages/loompy/loompy.py", line 472, in add_loom
ca = {key: v[selection] for key, v in other.col_attrs.items()}
File "/home/yfstkchy/miniconda3/envs/myenv/lib/python3.7/site-packages/loompy/loompy.py", line 472, in
ca = {key: v[selection] for key, v in other.col_attrs.items()}
TypeError: only integer scalar arrays can be converted to a scalar index
any insight is greatly appreciated.