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Adding "report" directory creation to tandemmapper.py

Open lucblassel opened this issue 4 years ago • 0 comments

When running tandemmapper.py on its own without running tandemquast.py the execution will crash with the following error:

Traceback (most recent call last):
  File "./tandemmapper.py", line 80, in <module>
    main()
  File "/usr/local/Caskroom/miniconda/base/envs/tandemNew/lib/python3.6/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/usr/local/Caskroom/miniconda/base/envs/tandemNew/lib/python3.6/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/usr/local/Caskroom/miniconda/base/envs/tandemNew/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/usr/local/Caskroom/miniconda/base/envs/tandemNew/lib/python3.6/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "./tandemmapper.py", line 72, in main
    make_alignments.do(assemblies, reads_fname, reads_real_coords, out_dir, threads, no_reuse, no_nucl_alignment)
  File "/Users/lucblassel/gitPulls/TandemTools/scripts/make_alignments.py", line 208, in do
    make_plotly_noise(assemblies, all_data, out_dir)
  File "/Users/lucblassel/gitPulls/TandemTools/scripts/reporting.py", line 130, in make_plotly_noise
    with open(bed_fname, "w") as f:
FileNotFoundError: [Errno 2] No such file or directory: '/Users/lucblassel/gitPulls/TandemTools/tandemRes/report/kmers_dist_diff.bed'

This is because bed_fname is <out_dir>/report/kmers_dist_diff.bed in scripts/reporting.py

However, the <out_dir>/report subdirectory is never created in tandemmapper.py but it is created in tandemquast.py

This PR aims to fix this problem by adding the creation of the <out_dir>/report subdirectory if it does not already exist.

lucblassel avatar Feb 23 '21 13:02 lucblassel