clintval/sample-sheet

CellRanger indexes are not recognized

Closed this issue · 7 comments

golharam commented

Is it possible to bypass index validation?

    sample_sheet = SampleSheet(args.samplesheet)
  File "/home/ec2-user/cellranger-docker/env/lib/python3.6/site-packages/sample_sheet/__init__.py", line 418, in __init__
    self._parse(self.path)
  File "/home/ec2-user/cellranger-docker/env/lib/python3.6/site-packages/sample_sheet/__init__.py", line 524, in _parse
    self.add_sample(Sample(dict(zip(sample_header, line))))
  File "/home/ec2-user/cellranger-docker/env/lib/python3.6/site-packages/sample_sheet/__init__.py", line 296, in __init__
    raise ValueError(f'Not a valid index: {value}')
ValueError: Not a valid index: SI-GA-F8
clintval commented

Looks reasonable to me! We could update what is considered a valid index to include the union of characters Illumina and 10x allow here:

sample-sheet/sample_sheet/__init__.py

Line 275 in 8da5c6b

_valid_index_value_pattern = re.compile(r'^[ACGTN]*$')

I probably won't have time to get to in the next few days FYI but it's now on my radar.

golharam commented
clintval commented

Thank you for the patch, and the unit test! I just published sample_sheet==0.10.0 with this feature. Please pip install! Bioconda will find the change automatically in the next few days.

clintval commented

I'm migrating to an official public API freeze in 1.0.0. The API may change slightly, but function should remain the same.

Any feature requests, critiques of the API, and criticisms welcome before I commit. Thanks!

golharam commented

I just pushed a final change as I missed an index set in the first PR. I wonder if an option to bypass index checking would be good for a future release.

clintval commented

Thanks for the idea! Noted!

clintval commented

Just published 0.11.0 to PyPi, Bioconda should follow after some period of lag.