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morrislab / phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.
GNU General Public License v3.0
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Assestion Error with the parser #127

Open PCApple opened 4 years ago

PCApple commented 4 years ago

Hello, Right now I am running into a problem while trying to parse my cnv and vcf data. I am currently able to parse the vcf data without the cnv data(using regions=all), but when I try to use the --cnvs I keep getting this error: Traceback (most recent call last): File "create_phylowgs_inputs.py", line 1420, in main() File "create_phylowgs_inputs.py", line 1388, in main grouper.exclude_variants_in_multiple_abnormal_or_unlisted_regions() File "create_phylowgs_inputs.py", line 989, in exclude_variants_in_multiple_abnormal_or_unlisted_regions self._filter_variants_outside_regions(self._multisamp_cnv.load_cnvs(), 'all_variants', 'within_cn_regions') File "create_phylowgs_inputs.py", line 856, in load_cnvs abnormal_cnvs = self.load_single_abnormal_state_cnvs() File "create_phylowgs_inputs.py", line 811, in load_single_abnormal_state_cnvs states_for_all_samples = self._get_abnormal_state_for_all_samples(chrom, cnv) File "create_phylowgs_inputs.py", line 773, in _get_abnormal_state_for_all_samples assert len(retained_sampidxs) == len(set(retained_sampidxs)) AssertionError

The error is accompanied by this comment in the code: Sanity check: we should have no duplicate samples. While a given sample may report any number of records for a region, above we discarded normal regions, and ensured that only one abnormal state exists in all samples. Thus, we should have no more than one record per sample for this region.

I check through the cnv data, and as far as I could tell, there were no duplicates, and I am only working with one sample. I'm not really proficient with the biology side of this, but as least from the cs side I was seeing that in _get_abnormal_state_for_all_samples() function, the retained_smapidx was picking up 2 entries sometimes instead of 1. Do you know why this may be happening? Thanks in advance.

Ignatiocalvin commented 3 years ago

Hi,

I'd also like to know if there were any solutions for this.

Thank you.