pepkit/ngstk

Next-generation sequencing toolkit

ngstk

Next-generation sequencing toolkit

ngstk's Issues

Handle errors if file not existing/empty

ngstk.inspect.peek_read_lengths_and_paired_counts_from_bam throws a IndexError if the bam file does not exist or is empty and that stops a looper run command.

os not imported in inspection.py

[2019-05-10 09:39:52,873] ERROR in caravel: Unhandled Exception: name 'os' is not defined
Traceback (most recent call last):
  File "/apps/software/standard/core/anaconda/5.2.0-py3.6/lib/python3.6/site-packages/flask/app.py", line 1813, in full_dispatch_request
    rv = self.dispatch_request()
  File "/apps/software/standard/core/anaconda/5.2.0-py3.6/lib/python3.6/site-packages/flask/app.py", line 1799, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/caravel/caravel.py", line 89, in decorated
    return func(*args, **kwargs)
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/caravel/caravel.py", line 371, in action
    run_looper(prj=globs.p, args=args, act=globs.act, log_path=globs.log_path, logging_lvl=globs.logging_lvl)
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/caravel/helpers.py", line 376, in decorated
    func(*args, **kwargs)
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/caravel/helpers.py", line 402, in run_looper
    run(args, None, rerun=(act == "rerun"))
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/looper/looper.py", line 399, in __call__
    curr_pl_fails = conductor.add_sample(sample, rerun=rerun)
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/looper/conductor.py", line 195, in add_sample
    self.pl_iface, pipeline_name=self.pl_key)
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/looper/sample.py", line 158, in set_pipeline_attributes
    self.input_file_size = get_file_size(self.all_inputs)
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/ngstk/inspection.py", line 28, in get_file_size
    return float(sum([get_file_size(x) for x in filename]))
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/ngstk/inspection.py", line 28, in <listcomp>
    return float(sum([get_file_size(x) for x in filename]))
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/ngstk/inspection.py", line 31, in get_file_size
    for f in filename.split(" ") if f is not ''])
  File "/home/mjs5kd/.local/lib/python3.6/site-packages/ngstk/inspection.py", line 31, in <listcomp>
    for f in filename.split(" ") if f is not ''])
NameError: name 'os' is not defined