search

bcgsc / mavis

Merging, Annotation, Validation, and Illustration of Structural variants
http://mavis.bcgsc.ca
GNU General Public License v3.0
72 stars 13 forks source link

TypeError: object of type 'float' has no len() #254

Closed calchoo closed 2 years ago

calchoo commented 2 years ago

Error in loading converted output in v3

                      loading: /projects/trans_scratch/validations/workspace/cchoo/test_mavis/gd-P02862_gn-P02865_rd-P02864/mavis_v2.2.9/2601/converted_outputs/chimerascan4.tab
Traceback (most recent call last):
  File "/projects/trans_scratch/validations/workspace/cchoo/mavis/mavis_v3/venv/bin/mavis", line 33, in <module>
    sys.exit(load_entry_point('mavis', 'console_scripts', 'mavis')())
  File "/projects/trans_scratch/validations/workspace/cchoo/mavis/mavis_v3/src/mavis/main.py", line 292, in main
    raise err
  File "/projects/trans_scratch/validations/workspace/cchoo/mavis/mavis_v3/src/mavis/main.py", line 226, in main
    library=args.library,
  File "/projects/trans_scratch/validations/workspace/cchoo/mavis/mavis_v3/src/mavis/cluster/main.py", line 115, in main
    expand_svtype=True,
  File "/projects/trans_scratch/validations/workspace/cchoo/mavis/mavis_v3/src/mavis/util.py", line 227, in read_inputs
    finput, required_columns=[COLUMNS.protocol, *required_columns], **kwargs
  File "/projects/trans_scratch/validations/workspace/cchoo/mavis/mavis_v3/src/mavis/util.py", line 559, in read_bpp_from_input_file
    bpp, distance=lambda x, y: Interval(y - x)
  File "/projects/trans_scratch/validations/workspace/cchoo/mavis/mavis_v3/src/mavis/breakpoint.py", line 386, in classify
    if pair.net_size(distance).start > 0:
  File "/projects/trans_scratch/validations/workspace/cchoo/mavis/mavis_v3/src/mavis/breakpoint.py", line 414, in net_size
    size = Interval(len(self.untemplated_seq))
TypeError: object of type 'float' has no len()

It seems like np.nan isn't getting checked for properly, so we just need to convert them to None