Invalid '==' comparison, cannot compare expressions of type 'call' and 'str'

[iris-garden]

Note

The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.

(Nov 30, 2023 at 21:54) mgarcia said:

Hello,

I am attempting to run the following block of code as part of a WES variant QC script, but I continue to generate the following error. What is the correct way to probe whether the genotypes listed under ds.GT are equal to a particular string if not with the ‘==’ operator?

Thank you in advance.

'GRNC_cond2': lambda ds: ((ds.GT == './0') | (ds.GT == './1') | (ds.GT == '0/.') | (ds.GT == '1/.'))

  File "/gpfs/fs1/home/mg1646/.conda/envs/variantqc_hailenv/lib/python3.8/site-packages/hail/expr/expressions/base_expression.py", line 781, in __eq__
    return self._compare_op("==", other)
  File "/gpfs/fs1/home/mg1646/.conda/envs/variantqc_hailenv/lib/python3.8/site-packages/hail/expr/expressions/base_expression.py", line 587, in _compare_op
    raise TypeError(f"Invalid '{op}' comparison, cannot compare expressions "
TypeError: Invalid '==' comparison, cannot compare expressions of type 'call' and 'str'

Code here:

# dict of lambdas for filter expressions
    genotype_exprs = {
        # DP: Genotypes below reading depth
        'GDP' : lambda ds: ds.DP < args.depth_threshold,
        # GDP: heterozygous genotypes outside of allelic balance
        'GAB' : lambda ds: (
            ds.GT.is_het() & (
                (ds.AD[0]/ds.DP > max(1 - args.allelic_balance, args.allelic_balance))
                | (ds.AD[0]/ds.DP < min(1 - args.allelic_balance, args.allelic_balance))
            )
        ),
        # GGQ: Genotypes below quality threshold
        'GGQ': lambda ds: ds.GQ < args.genotype_quality,
        # GNP: Male het chrX nonpar variants
        'GNP': lambda ds: ds.GT.is_het() & ds.locus.in_x_nonpar() & (ds.sa.GENDER == "Male"),
        # GRNC: Genotypes with RNC == 1
        'GRNC_cond1': lambda ds: ds.RNC[0] == "11",
        'GRNC_cond2': lambda ds: ((ds.GT == './0') | (ds.GT == './1') | (ds.GT == '0/.') | (ds.GT == '1/.'))
    }

[iris-garden]

Note

The following post was exported from discuss.hail.is, a forum for asking questions about Hail which has since been deprecated.

(Dec 05, 2023 at 18:21) anh151 said:

Try using hl.Call to compare to the ds.GT field.
I.e
ds.GT == hl.Call([0, 1])

https://hail.is/docs/0.2/genetics/hail.genetics.Call.html#call